commands - zygaena/coral

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/******************************************************************************
               __               ____                __
              / /   ___  ____ _/ __/_____________ _/ /__
             / /   / _ \/ __ `/ /_/ ___/ ___/ __ `/ / _ \
            / /___/  __/ /_/ / __(__  ) /__/ /_/ / /  __/
           /_____/\___/\__,_/_/ /____/\___/\__,_/_/\___/

   (C)opyright 2025, Leafscale, LLC -  https://www.leafscale.com

   Project: Zygaena
  Filename: build.reef
   Authors: Chris Tusa <chris.tusa@leafscale.com>
   License: <see LICENSE file included with this source code>
Description: Build command - compile packages from ports

******************************************************************************/

module commands.build

import sys.args
import sys.process
import io.file
import io.dir
import io.path
import io.console
import core.str
import core.port
import core.config
import core.database
import core.resolver
import util.version as ver
import types
import util.color
import util.prompt
import util.checksum
import util.archive
import util.mtree
import util.http as uhttp
import exitcodes as ec
import core.result as res

export
    fn execute(opts: types.GlobalOptions): int
end export

// Build context
type BuildContext = struct
    port: types.Port
    work_dir: string
    pkg_dir: string
    src_dir: string
    cfg: config.Config
    noclean: bool
    force_clean: bool
    log_file: string
    logging: bool
    quiet: bool
end BuildContext

// Load a port from path or find it by name
fn load_or_find_port(port_path: string): types.PortResult
    // Check if it's a valid port directory (must contain package.toml)
    // This prevents confusion with binary files or other directories with same name
    if dir.dir_exists(port_path)
        let toml_path = path.join_path(port_path, "package.toml")
        if file.fileExists(toml_path)
            color.print_action("Loading port from: " + port_path)
            return port.load(port_path)
        end if
    end if

    // Not a valid port directory, search by name
    color.print_action("Finding port: " + port_path)
    return port.find(port_path)
end load_or_find_port

fn execute(opts: types.GlobalOptions): int
    // Parse arguments
    let argc = args.count()

    // Port argument should be after the command
    if argc <= opts.cmd_index + 1
        print_usage()
        return ec.EXIT_USAGE()
    end if

    // Parse flags
    mut noclean = false
    mut force_clean = false
    mut quiet_flag = false
    mut verbose_flag = false
    mut install_flag = false
    mut port_path = ""

    mut i = opts.cmd_index + 1
    while i < argc
        let arg = args.get(i)
        // Skip global flags with values
        if arg == "--root" or arg == "--prefix"
            i = i + 2
            continue
        elif arg == "--no-chroot-scripts"
            i = i + 1  // valueless flag: skip only itself
            continue
        end if
        if arg == "--noclean" or arg == "-n"
            noclean = true
        elif arg == "--clean" or arg == "-c"
            force_clean = true
        elif arg == "--quiet" or arg == "-q"
            quiet_flag = true
        elif arg == "--verbose" or arg == "-v"
            verbose_flag = true
        elif arg == "--install"
            install_flag = true
        elif arg == "--no-install"
            install_flag = false
        elif not str.starts_with(arg, "-")
            if str.length(port_path) == 0
                port_path = arg
            end if
        end if
        i = i + 1
    end while

    if str.length(port_path) == 0
        print_usage()
        return ec.EXIT_USAGE()
    end if

    // Handle "." for current directory
    if port_path == "."
        port_path = res.unwrap_or(dir.current_dir(), "")
    end if

    // Load configuration
    let cfg = config.load()
    uhttp.enable_proxy(config.get_use_proxy(cfg))

    // Try to find the port by name if path doesn't exist
    let result = load_or_find_port(port_path)

    if not result.success
        color.print_error(result.error)
        return ec.EXIT_PKG_NOT_FOUND()
    end if

    let p = result.port
    color.print_success("Loaded port: " + p.info.name + " " + p.info.version)

    // Dry-run: show build plan without executing
    if opts.dry_run
        color.print_info("Dry run — would build: " + p.info.name + " " + p.info.version)
        let dry_resolve = resolver.resolve_build_deps(p.info.name)
        if dry_resolve.success and dry_resolve.count > 1
            color.print_info("Dependencies to build first:")
            mut di = 0
            while di < dry_resolve.count - 1
                let dep_port = port.find(dry_resolve.packages[di])
                if dep_port.success
                    color.print_info("  " + dry_resolve.packages[di] + " " + dep_port.port.info.version)
                else
                    color.print_info("  " + dry_resolve.packages[di])
                end if
                di = di + 1
            end while
        end if
        color.print_info("Dry run — no changes made")
        return ec.EXIT_SUCCESS()
    end if

    // Resolve, build, and install missing dependencies before building
    if not resolve_and_build_deps(p, opts, cfg)
        // Check if the failure was due to circular dependencies
        let check_result = resolver.resolve_build_deps(p.info.name)
        if not check_result.success and str.starts_with(check_result.error, "Circular")
            color.print_error("Cannot build " + p.info.name + " — circular dependency")
            return ec.EXIT_DEPS_CIRCULAR()
        end if
        color.print_error("Cannot build " + p.info.name + " — missing dependencies")
        return ec.EXIT_DEPS_UNMET()
    end if

    // Determine quiet mode: CLI flag overrides config, verbose overrides quiet
    mut quiet_mode = config.get_quiet(cfg)
    if quiet_flag
        quiet_mode = true
    end if
    if verbose_flag
        quiet_mode = false
    end if

    // Create build context
    let ctx = create_context(p, cfg, noclean, force_clean, quiet_mode)

    // Step 1: Setup directories
    if not setup_directories(ctx)
        color.print_error("Failed to create build directories")
        return ec.EXIT_ERROR()
    end if

    // Initialize logging after directories are created
    init_log(ctx)
    if ctx.logging and str.length(ctx.log_file) > 0
        log_info(ctx, "Log file: " + ctx.log_file)
    end if

    // Step 2: Download sources
    if not download_sources(ctx)
        log_error(ctx, "Failed to download sources")
        print_log_location(ctx)
        cleanup_build(ctx)
        return ec.EXIT_DOWNLOAD_FAILED()
    end if

    // Step 3: Verify checksums
    if not verify_checksums(ctx)
        log_error(ctx, "Checksum verification failed")
        print_log_location(ctx)
        cleanup_build(ctx)
        return ec.EXIT_CHECKSUM_FAILED()
    end if

    // Step 4: Extract sources
    if not extract_sources(ctx)
        log_error(ctx, "Failed to extract sources")
        print_log_location(ctx)
        cleanup_build(ctx)
        return ec.EXIT_EXTRACT_FAILED()
    end if

    // Step 5: Apply patches
    if not apply_patches(ctx)
        log_error(ctx, "Failed to apply patches")
        print_log_location(ctx)
        cleanup_build(ctx)
        return ec.EXIT_PATCH_FAILED()
    end if

    // Step 6: Run build script
    if not run_build(ctx)
        log_error(ctx, "Build failed")
        print_log_location(ctx)
        cleanup_build(ctx)
        return ec.EXIT_BUILD_FAILED()
    end if

    // Step 7: Compress man pages (if enabled)
    if config.get_compress_man(ctx.cfg)
        compress_man_pages(ctx)
    end if

    // Step 8: Create package
    if not create_package(ctx)
        log_error(ctx, "Failed to create package")
        print_log_location(ctx)
        cleanup_build(ctx)
        return ec.EXIT_PACKAGE_FAILED()
    end if

    // Success!
    let pkg_name = p.info.name + "-" + p.info.version + "-" + int_to_str(p.info.release) + ".pkg.tar.xz"
    let pkg_path = path.join_path(config.get_packages_dir(cfg), pkg_name)
    log_success(ctx, "Package created: " + pkg_path)

    // Cleanup work directory on success
    cleanup_build(ctx)

    // Step 9: Install the built package (only with --install)
    if install_flag
        color.print_action("Installing " + p.info.name + "...")
        let self_exe = args.get(0)
        let install_cmd = self_exe + " install -y -f \"" + pkg_path + "\""
        let install_pid = process.process_spawn_shell(install_cmd)
        if install_pid < 0
            color.print_error("Failed to launch installer for " + p.info.name)
            return ec.EXIT_INSTALL_FAILED()
        end if
        let install_exit = process.process_wait(install_pid)
        if install_exit != 0
            color.print_error("Failed to install " + p.info.name)
            return ec.EXIT_INSTALL_FAILED()
        end if
    else
        color.print_success("Package ready (use --install to install, or: coral install \"" + pkg_path + "\")")
    end if

    return ec.EXIT_SUCCESS()
end execute

proc print_usage()
    println("Usage: coral build [options] <port-path>")
    println("")
    println("Build a package from a port directory.")
    println("")
    println("Arguments:")
    println("  <port-path>    Path to port directory (use . for current)")
    println("")
    println("Options:")
    println("  --install      Install the package after building")
    println("  --no-install   Build only, do not install (default)")
    println("  -n, --noclean  Don't clean work/pkg directories after build")
    println("  -c, --clean    Force cleanup even if disabled in config")
    println("  -q, --quiet    Hide subprocess output (still logged to file)")
    println("  -v, --verbose  Show all output (overrides quiet)")
    println("")
    println("Examples:")
    println("  coral build /usr/zports/base/vim")
    println("  coral build --install base/vim")
    println("  coral build --noclean .")
    println("  coral build --quiet vim")
end print_usage

// Resolve all build dependencies recursively, build from source, and install each.
// Returns true if all dependencies are satisfied (either already installed or built+installed).
fn resolve_and_build_deps(p: types.Port, opts: types.GlobalOptions, cfg: config.Config): bool
    // Resolve the full dependency tree (runtime + build deps, recursive)
    let resolve_result = resolver.resolve_build_deps(p.info.name)

    if not resolve_result.success
        color.print_error("Dependency resolution failed: " + resolve_result.error)
        return false
    end if

    // The result includes the target package as the last element — strip it
    mut dep_count = resolve_result.count
    if dep_count > 0
        let last = resolve_result.packages[dep_count - 1]
        if str.equals(last, p.info.name)
            dep_count = dep_count - 1
        end if
    end if

    // No deps to build
    if dep_count == 0
        return true
    end if

    // Look up version info for each dep to display in the build plan
    mut dep_versions: [string] = new [string](256)
    mut i = 0
    while i < dep_count
        let dep_port_result = port.find(resolve_result.packages[i])
        if dep_port_result.success
            dep_versions[i] = dep_port_result.port.info.version
        else
            dep_versions[i] = ""
        end if
        i = i + 1
    end while

    // Show build plan and ask for confirmation
    if not prompt.confirm_build_plan(resolve_result.packages, dep_versions, dep_count, p.info.name, opts)
        color.print_info("Build cancelled")
        return false
    end if

    // Build and install each dependency in topological order
    i = 0
    while i < dep_count
        let dep_name = resolve_result.packages[i]
        println("")
        color.print_action("[" + int_to_str(i + 1) + "/" + int_to_str(dep_count) + "] Building dependency: " + dep_name)

        // Build the dependency from source
        if not build_single_port(dep_name, cfg, opts)
            color.print_error("Failed to build dependency: " + dep_name)
            return false
        end if

        // Install the built package
        let dep_port_result = port.find(dep_name)
        if not dep_port_result.success
            color.print_error("Cannot find port after build: " + dep_name)
            return false
        end if

        let dp = dep_port_result.port
        let pkg_filename = dp.info.name + "-" + dp.info.version + "-" + int_to_str(dp.info.release) + ".pkg.tar.xz"
        let pkg_path = path.join_path(config.get_packages_dir(cfg), pkg_filename)

        if not file.fileExists(pkg_path)
            color.print_error("Built package not found: " + pkg_path)
            return false
        end if

        color.print_action("Installing " + dep_name + "...")
        let self_exe = args.get(0)
        let install_cmd = self_exe + " install -y \"" + pkg_path + "\""
        let pid = process.process_spawn_shell(install_cmd)
        if pid < 0
            color.print_error("Failed to launch installer for " + dep_name)
            return false
        end if
        let exit_code = process.process_wait(pid)
        if exit_code != 0
            color.print_error("Failed to install " + dep_name)
            return false
        end if

        color.print_success("Dependency ready: " + dep_name)
        i = i + 1
    end while

    println("")
    color.print_success("All " + int_to_str(dep_count) + " dependencies built and installed")
    return true
end resolve_and_build_deps

// Build a single port from source. Used for dependency builds.
// Returns true if build succeeds and package archive is created.
fn build_single_port(name: string, cfg: config.Config, opts: types.GlobalOptions): bool
    let port_result = port.find(name)
    if not port_result.success
        color.print_error("Port not found: " + name)
        return false
    end if

    let p = port_result.port

    // Determine quiet mode
    mut quiet_mode = config.get_quiet(cfg)
    if opts.verbose
        quiet_mode = false
    end if
    if opts.quiet
        quiet_mode = true
    end if

    let ctx = create_context(p, cfg, false, false, quiet_mode)

    // Run the full build pipeline
    if not setup_directories(ctx)
        color.print_error("Failed to create build directories for " + name)
        return false
    end if

    init_log(ctx)

    if not download_sources(ctx)
        log_error(ctx, "Failed to download sources for " + name)
        print_log_location(ctx)
        cleanup_build(ctx)
        return false
    end if

    if not verify_checksums(ctx)
        log_error(ctx, "Checksum verification failed for " + name)
        print_log_location(ctx)
        cleanup_build(ctx)
        return false
    end if

    if not extract_sources(ctx)
        log_error(ctx, "Failed to extract sources for " + name)
        print_log_location(ctx)
        cleanup_build(ctx)
        return false
    end if

    if not apply_patches(ctx)
        log_error(ctx, "Failed to apply patches for " + name)
        print_log_location(ctx)
        cleanup_build(ctx)
        return false
    end if

    if not run_build(ctx)
        log_error(ctx, "Build failed for " + name)
        print_log_location(ctx)
        cleanup_build(ctx)
        return false
    end if

    // Compress man pages (if enabled)
    if config.get_compress_man(cfg)
        compress_man_pages(ctx)
    end if

    if not create_package(ctx)
        log_error(ctx, "Failed to create package for " + name)
        print_log_location(ctx)
        cleanup_build(ctx)
        return false
    end if

    let pkg_filename = p.info.name + "-" + p.info.version + "-" + int_to_str(p.info.release) + ".pkg.tar.xz"
    let pkg_path = path.join_path(config.get_packages_dir(cfg), pkg_filename)
    log_success(ctx, "Package created: " + pkg_path)

    cleanup_build(ctx)
    return true
end build_single_port

fn create_context(p: types.Port, cfg: config.Config, noclean: bool, force_clean: bool, quiet: bool): BuildContext
    // New directory structure:
    //   /usr/zports/pkgs/build/<pkgname>/src/   - extracted sources, compilation
    //   /usr/zports/pkgs/build/<pkgname>/stage/ - DESTDIR for make install
    let build_base = config.get_build_dir(cfg)
    let pkg_build_dir = path.join_path(build_base, p.info.name)
    let work_dir = path.join_path(pkg_build_dir, "src")
    let pkg_dir = path.join_path(pkg_build_dir, "stage")

    // Generate log file path with timestamp (in package build root, not src/)
    let logging_enabled = config.get_logging(cfg)
    mut log_path = ""
    if logging_enabled
        log_path = path.join_path(pkg_build_dir, "coral-build-" + p.info.name + "-" + get_timestamp() + ".log")
    end if

    return BuildContext{
        port: p,
        work_dir: work_dir,
        pkg_dir: pkg_dir,
        src_dir: "",
        cfg: cfg,
        noclean: noclean,
        force_clean: force_clean,
        log_file: log_path,
        logging: logging_enabled,
        quiet: quiet
    }
end create_context

// Get current timestamp for log filename
fn get_timestamp(): string
    // Use date command to get timestamp
    let tmp_file = "/tmp/coral_ts_" + int_to_str(process.getpid()) + ".txt"
    let cmd = "date '+%Y%m%d-%H%M%S' > \"" + tmp_file + "\""
    let pid = process.process_spawn_shell(cmd)
    if pid > 0
        process.process_wait(pid)
    end if

    let ts = res.unwrap_or(file.readFile(tmp_file), "")

    // Cleanup
    let rm_cmd = "rm -f \"" + tmp_file + "\""
    let rm_pid = process.process_spawn_shell(rm_cmd)
    if rm_pid > 0
        process.process_wait(rm_pid)
    end if

    return str.trim(ts, '\n')
end get_timestamp

// Initialize log file with header
proc init_log(ctx: BuildContext)
    if not ctx.logging
        return
    end if

    mut header = "=== Coral Build Log ===\n"
    header = header + "Package: " + ctx.port.info.name + "\n"
    header = header + "Version: " + ctx.port.info.version + "\n"
    header = header + "Work Dir: " + ctx.work_dir + "\n"
    header = header + "Log File: " + ctx.log_file + "\n"
    header = header + "========================\n\n"

    file.writeFile(ctx.log_file, header)
end init_log

// Log a message to file and optionally to screen
proc log_msg(ctx: BuildContext, msg: string, show_screen: bool)
    // Always write to log file if logging enabled
    if ctx.logging and str.length(ctx.log_file) > 0
        file.appendFile(ctx.log_file, msg + "\n")
    end if

    // Show on screen unless quiet mode suppresses it
    if show_screen
        println(msg)
    end if
end log_msg

// Log info message (always show on screen)
proc log_info(ctx: BuildContext, msg: string)
    if ctx.logging and str.length(ctx.log_file) > 0
        file.appendFile(ctx.log_file, "[INFO] " + msg + "\n")
    end if
    color.print_info(msg)
end log_info

// Log success message (always show on screen)
proc log_success(ctx: BuildContext, msg: string)
    if ctx.logging and str.length(ctx.log_file) > 0
        file.appendFile(ctx.log_file, "[OK] " + msg + "\n")
    end if
    color.print_success(msg)
end log_success

// Log error message (always show on screen)
proc log_error(ctx: BuildContext, msg: string)
    if ctx.logging and str.length(ctx.log_file) > 0
        file.appendFile(ctx.log_file, "[ERROR] " + msg + "\n")
    end if
    color.print_error(msg)
end log_error

// Log action message (always show on screen)
proc log_action(ctx: BuildContext, msg: string)
    if ctx.logging and str.length(ctx.log_file) > 0
        file.appendFile(ctx.log_file, "[ACTION] " + msg + "\n")
    end if
    color.print_action(msg)
end log_action

// Log warning message (always show on screen)
proc log_warning(ctx: BuildContext, msg: string)
    if ctx.logging and str.length(ctx.log_file) > 0
        file.appendFile(ctx.log_file, "[WARN] " + msg + "\n")
    end if
    color.print_warning(msg)
end log_warning

// Print log file location (for debugging failed builds)
proc print_log_location(ctx: BuildContext)
    if ctx.logging and str.length(ctx.log_file) > 0
        color.print_info("Build log: " + ctx.log_file)
    end if
end print_log_location

// Run a shell command with output captured to log
// Returns exit code
fn run_logged_cmd(ctx: BuildContext, cmd: string): int
    if ctx.logging and str.length(ctx.log_file) > 0
        file.appendFile(ctx.log_file, "[CMD] " + cmd + "\n")
    end if

    // Build command that logs output to file
    // Redirects all output to log file to avoid tee pipeline issues
    // (tee caused SIGPIPE on long builds and masked exit codes)
    mut full_cmd = cmd
    if ctx.logging and str.length(ctx.log_file) > 0
        // Both quiet and normal mode: log to file only
        // Real-time terminal output is sacrificed for build reliability
        full_cmd = "(" + cmd + ") >> \"" + ctx.log_file + "\" 2>&1"
    else
        if ctx.quiet
            // No logging, quiet mode: suppress output
            full_cmd = "(" + cmd + ") >/dev/null 2>&1"
        end if
        // No logging, not quiet: just run normally
    end if

    // Flush stdout before spawning subprocess to ensure proper output ordering
    console.flushOutput()

    let pid = process.process_spawn_shell(full_cmd)
    if pid < 0
        return -1
    end if

    return process.process_wait(pid)
end run_logged_cmd

fn setup_directories(ctx: BuildContext): bool
    color.print_info("Setting up build directories...")

    // Create work directory
    if dir.dir_exists(ctx.work_dir)
        // Clean existing work dir
        let cmd = "rm -rf \"" + ctx.work_dir + "\""
        let pid = process.process_spawn_shell(cmd)
        if pid > 0
            process.process_wait(pid)
        end if
    end if

    if not res.is_ok(dir.create_dir_all(ctx.work_dir))
        return false
    end if

    // Create pkg directory (for DESTDIR)
    if dir.dir_exists(ctx.pkg_dir)
        let cmd = "rm -rf \"" + ctx.pkg_dir + "\""
        let pid = process.process_spawn_shell(cmd)
        if pid > 0
            process.process_wait(pid)
        end if
    end if

    if not res.is_ok(dir.create_dir_all(ctx.pkg_dir))
        return false
    end if

    // Ensure sources directory exists
    let sources_dir = config.get_sources_dir(ctx.cfg)
    if not dir.dir_exists(sources_dir)
        if not res.is_ok(dir.create_dir_all(sources_dir))
            return false
        end if
    end if

    // Ensure packages directory exists
    let packages_dir = config.get_packages_dir(ctx.cfg)
    if not dir.dir_exists(packages_dir)
        if not res.is_ok(dir.create_dir_all(packages_dir))
            return false
        end if
    end if

    return true
end setup_directories

fn download_sources(ctx: BuildContext): bool
    if ctx.port.sources.count == 0
        color.print_info("No sources to download")
        return true
    end if

    color.print_info("Downloading sources...")

    let sources_dir = config.get_sources_dir(ctx.cfg)

    mut i = 0
    while i < ctx.port.sources.count
        let src = ctx.port.sources.sources[i]
        let filename = src.file
        let dest = path.join_path(sources_dir, filename)

        // Check if already cached with valid checksum
        if file.fileExists(dest)
            if verify_single_checksum(dest, src.checksum)
                color.print_info("Using cached: " + filename)
                i = i + 1
                continue
            else
                // Cached file has wrong checksum, re-download
                color.print_warning("Cached file checksum mismatch, re-downloading: " + filename)
            end if
        end if

        // Try each mirror URL in order
        mut download_success = false
        mut url_idx = 0
        while url_idx < src.url_count
            let url = src.urls[url_idx]

            if url_idx > 0
                color.print_info("Trying mirror: " + url)
            end if

            // Check if this is a local file (no http:// or https:// prefix)
            if is_local_source(url)
                // Local file - copy from port directory to sources cache
                if copy_local_source(url, dest, ctx.port.port_dir)
                    if verify_single_checksum(dest, src.checksum)
                        download_success = true
                        break
                    else
                        color.print_warning("Checksum mismatch for local file, trying next...")
                        let rm_cmd = "rm -f \"" + dest + "\""
                        let rm_pid = process.process_spawn_shell(rm_cmd)
                        if rm_pid > 0
                            process.process_wait(rm_pid)
                        end if
                    end if
                end if
            else
                // Remote URL - download via HTTP
                if uhttp.download(url, dest)
                    // Verify checksum after download
                    if verify_single_checksum(dest, src.checksum)
                        download_success = true
                        break
                    else
                        color.print_warning("Checksum mismatch from mirror, trying next...")
                        // Delete bad file
                        let rm_cmd = "rm -f \"" + dest + "\""
                        let rm_pid = process.process_spawn_shell(rm_cmd)
                        if rm_pid > 0
                            process.process_wait(rm_pid)
                        end if
                    end if
                end if
            end if

            url_idx = url_idx + 1
        end while

        if not download_success
            color.print_error("Failed to download: " + filename + " (all sources failed)")
            return false
        end if

        i = i + 1
    end while

    return true
end download_sources

// Check if a URL is a local file path (not http:// or https://)
fn is_local_source(url: string): bool
    if str.starts_with(url, "http://")
        return false
    end if
    if str.starts_with(url, "https://")
        return false
    end if
    return true
end is_local_source

// Copy a local source file from port directory to sources cache
fn copy_local_source(source_path: string, dest: string, port_dir: string): bool
    // Resolve the source path
    mut full_path = source_path

    // If it's a relative path, resolve relative to port directory
    if not str.starts_with(source_path, "/")
        full_path = path.join_path(port_dir, source_path)
    end if

    // Check if file exists
    if not file.fileExists(full_path)
        color.print_error("Local source file not found: " + full_path)
        return false
    end if

    color.print_info("Copying local source: " + source_path)

    // Copy the file
    let cmd = "cp \"" + full_path + "\" \"" + dest + "\""
    let pid = process.process_spawn_shell(cmd)
    if pid < 0
        return false
    end if

    let exit_code = process.process_wait(pid)
    if exit_code != 0
        color.print_error("Failed to copy local source: " + source_path)
        return false
    end if

    color.print_success("Copied: " + source_path)
    return true
end copy_local_source

// Verify a single file's checksum
fn verify_single_checksum(file_path: string, expected: string): bool
    // Handle special checksum values
    if str.equals(expected, "SKIP") or str.equals(expected, "BOOTSTRAP") or str.equals(expected, "skip")
        return true
    end if

    if str.length(expected) == 0
        return true
    end if

    return checksum.verify_checksum_with_algo(file_path, expected)
end verify_single_checksum

fn verify_checksums(ctx: BuildContext): bool
    if ctx.port.sources.count == 0
        return true
    end if

    color.print_info("Verifying checksums...")

    let sources_dir = config.get_sources_dir(ctx.cfg)

    mut i = 0
    while i < ctx.port.sources.count
        let src = ctx.port.sources.sources[i]
        let filename = src.file
        let file_path = path.join_path(sources_dir, filename)
        let expected = src.checksum

        // Handle special checksum values
        if str.equals(expected, "SKIP") or str.equals(expected, "BOOTSTRAP") or str.equals(expected, "skip")
            color.print_warning("Checksum verification skipped: " + filename)
        elif str.length(expected) > 0
            if not checksum.verify_checksum_with_algo(file_path, expected)
                color.print_error("Checksum mismatch: " + filename)
                return false
            end if
            color.print_success("Checksum verified: " + filename)
        else
            color.print_warning("No checksum for: " + filename)
        end if

        i = i + 1
    end while

    return true
end verify_checksums

fn extract_sources(ctx: BuildContext): bool
    if ctx.port.sources.count == 0
        return true
    end if

    color.print_info("Extracting sources...")

    let sources_dir = config.get_sources_dir(ctx.cfg)

    mut i = 0
    while i < ctx.port.sources.count
        let src = ctx.port.sources.sources[i]
        let filename = src.file
        let archive_path = path.join_path(sources_dir, filename)

        // Check extract flag
        if not src.extract
            // Copy file to work_dir instead of extracting (for patches, etc.)
            let dest_path = path.join_path(ctx.work_dir, filename)
            let cp_cmd = "cp \"" + archive_path + "\" \"" + dest_path + "\""
            let cp_pid = process.process_spawn_shell(cp_cmd)
            if cp_pid > 0
                let exit_code = process.process_wait(cp_pid)
                if exit_code != 0
                    color.print_error("Failed to copy: " + filename)
                    return false
                end if
            end if
            color.print_info("Copied (no extract): " + filename)
            i = i + 1
            continue
        end if

        if not archive.extract(archive_path, ctx.work_dir)
            color.print_error("Failed to extract: " + filename)
            return false
        end if

        color.print_success("Extracted: " + filename)
        i = i + 1
    end while

    return true
end extract_sources

fn apply_patches(ctx: BuildContext): bool
    if ctx.port.patches.count == 0
        return true
    end if

    log_info(ctx, "Applying patches...")

    let strip = ctx.port.patches.strip

    // Find the source directory (first subdirectory in work_dir)
    let find_srcdir = "cd \"" + ctx.work_dir + "\" && ls -d */ 2>/dev/null | head -1 | tr -d '/'"

    mut i = 0
    while i < ctx.port.patches.count
        let patch_file = ctx.port.patches.files[i]
        let patch_path = path.join_path(ctx.port.port_dir, patch_file)

        if not file.fileExists(patch_path)
            log_error(ctx, "Patch file not found: " + patch_file)
            return false
        end if

        // Apply patch from within the source directory
        let cmd = "cd \"" + ctx.work_dir + "/$(" + find_srcdir + ")\" && patch -p" + int_to_str(strip) + " < \"" + patch_path + "\""
        let exit_code = run_logged_cmd(ctx, cmd)
        if exit_code != 0
            log_error(ctx, "Failed to apply patch: " + patch_file)
            return false
        end if

        log_success(ctx, "Applied patch: " + patch_file)
        i = i + 1
    end while

    return true
end apply_patches

fn run_build(ctx: BuildContext): bool
    log_action(ctx, "Building " + ctx.port.info.name + "...")

    // Look for build.sh in port directory
    let build_script = path.join_path(ctx.port.port_dir, "build.sh")

    if not file.fileExists(build_script)
        log_error(ctx, "No build.sh found in port directory")
        return false
    end if

    // Set up environment
    let destdir = ctx.pkg_dir
    let cflags = config.get_cflags(ctx.cfg)
    let cxxflags = config.get_cxxflags(ctx.cfg)
    let jobs = config.get_jobs(ctx.cfg)

    mut jobs_str = ""
    if jobs > 0
        jobs_str = int_to_str(jobs)
    else
        // Auto-detect: use getconf (portable across illumos/Linux, unlike nproc)
        jobs_str = "$(getconf NPROCESSORS_ONLN 2>/dev/null || getconf _NPROCESSORS_ONLN 2>/dev/null || echo 1)"
    end if

    // Find the extracted source directory (first directory in work_dir)
    // Typically the tarball extracts to a subdirectory like "zlib-1.3.1"
    let find_srcdir_cmd = "cd \"" + ctx.work_dir + "\" && ls -d */ 2>/dev/null | head -1 | tr -d '/'"

    // Determine PREFIX: package.toml override → coral.conf → default (/usr)
    mut prefix = config.get_prefix(ctx.cfg)
    if str.length(ctx.port.prefix) > 0
        prefix = ctx.port.prefix
    end if

    // Determine SYSCONFDIR: package.toml override → coral.conf → default (/etc)
    mut sysconfdir = config.get_sysconfdir(ctx.cfg)
    if str.length(ctx.port.sysconfdir) > 0
        sysconfdir = ctx.port.sysconfdir
    end if

    // PKG_ROOT is the alternate root (empty means /)
    let pkg_root = config.get_root(ctx.cfg)

    // Build the command with all environment variables
    // Per Hammerhead porting guide: no uname wrappers, replace bundled config.guess/config.sub,
    // use system config.guess for BUILD_TRIPLE (returns x86_64-zygaena-hammerhead)
    mut cmd = "cd \"" + ctx.work_dir + "\" && "
    cmd = cmd + "export SRCDIR=\"" + ctx.work_dir + "/$(" + find_srcdir_cmd + ")\" && "
    cmd = cmd + "export PKGDIR=\"" + destdir + "\" && "
    cmd = cmd + "export DESTDIR=\"" + destdir + "\" && "
    cmd = cmd + "export PREFIX=\"" + prefix + "\" && "
    cmd = cmd + "export SYSCONFDIR=\"" + sysconfdir + "\" && "
    cmd = cmd + "export PKG_ROOT=\"" + pkg_root + "\" && "
    cmd = cmd + "export JOBS=\"" + jobs_str + "\" && "
    cmd = cmd + "export CFLAGS=\"" + cflags + "\" && "
    cmd = cmd + "export CXXFLAGS=\"" + cxxflags + "\" && "
    cmd = cmd + "export LDFLAGS=\"-R" + prefix + "/lib\" && "
    cmd = cmd + "export PKG_CONFIG_PATH=\"" + prefix + "/lib/pkgconfig\" && "
    cmd = cmd + "export MAKEFLAGS=\"-j" + jobs_str + "\" && "
    cmd = cmd + "export PKG_NAME=\"" + ctx.port.info.name + "\" && "
    cmd = cmd + "export PKG_VERSION=\"" + ctx.port.info.version + "\" && "
    cmd = cmd + "export BUILD_TRIPLE=\"$(/usr/share/autoconf/build-aux/config.guess 2>/dev/null || echo x86_64-zygaena-hammerhead)\" && "
    cmd = cmd + "export PATH=\"/usr/gnu/bin:$PATH\" && "
    cmd = cmd + "export MAKE=gmake && "
    cmd = cmd + "export TAR=gtar && "
    cmd = cmd + "for _f in config.guess config.sub; do find \"$SRCDIR\" -name \"$_f\" -exec cp /usr/share/autoconf/build-aux/\"$_f\" {} \\; 2>/dev/null; done; "
    cmd = cmd + "zsh \"" + build_script + "\""

    log_info(ctx, "Running build script...")

    let exit_code = run_logged_cmd(ctx, cmd)
    if exit_code != 0
        log_error(ctx, "Build script failed with exit code: " + int_to_str(exit_code))
        return false
    end if

    log_success(ctx, "Build completed successfully")
    return true
end run_build

// Compress uncompressed man pages in the staging directory
proc compress_man_pages(ctx: BuildContext)
    // Find uncompressed man pages and gzip them
    // Uses -exec {} + (batch mode) to avoid shell escaping issues with \;
    // Uses -type f to skip symlinks (avoids creating dangling refs)
    let script = "find '" + ctx.pkg_dir + "' -type f -path '*/man/man*/*' ! -name '*.gz' ! -name '*.bz2' ! -name '*.xz' -exec gzip -9 {} +"

    let pid = process.process_spawn_shell(script)
    if pid > 0
        let exit_code = process.process_wait(pid)
        if exit_code == 0
            log_info(ctx, "Compressed man pages")
        end if
    end if
end compress_man_pages

fn create_package(ctx: BuildContext): bool
    color.print_action("Creating package...")

    // Validate that staging directory has content (not just metadata files)
    if not validate_staging_dir(ctx.pkg_dir)
        color.print_error("Staging directory is empty - build produced no files")
        color.print_error("Check that build.sh installs files to $DESTDIR or $PKGDIR")
        return false
    end if

    // Generate .PKGINFO
    if not generate_pkginfo(ctx)
        return false
    end if

    // Generate .MANIFEST (mtree file inventory)
    if not generate_manifest_file(ctx)
        return false
    end if

    // Create the package archive
    let pkg_name = ctx.port.info.name + "-" + ctx.port.info.version + "-" + int_to_str(ctx.port.info.release) + ".pkg.tar.xz"
    let pkg_path = path.join_path(config.get_packages_dir(ctx.cfg), pkg_name)

    if not archive.create_package(ctx.pkg_dir, pkg_path)
        color.print_error("Failed to create package archive")
        return false
    end if

    return true
end create_package

// Validate that staging directory has actual content (not empty)
fn validate_staging_dir(pkg_dir: string): bool
    // Count files in staging directory, excluding metadata files
    // A valid package should have at least one real file
    let cmd = "find \"" + pkg_dir + "\" -type f ! -name '.PKGINFO' ! -name '.MANIFEST' ! -name '.FOOTPRINT' | head -1"
    let tmp_file = "/tmp/coral_validate_" + int_to_str(process.getpid()) + ".txt"
    let full_cmd = cmd + " > \"" + tmp_file + "\""

    let pid = process.process_spawn_shell(full_cmd)
    if pid < 0
        return false
    end if

    process.process_wait(pid)

    // Read result
    let content = res.unwrap_or(file.readFile(tmp_file), "")

    // Clean up
    let rm_cmd = "rm -f \"" + tmp_file + "\""
    let rm_pid = process.process_spawn_shell(rm_cmd)
    if rm_pid > 0
        process.process_wait(rm_pid)
    end if

    // If content is empty, staging dir has no real files
    if str.length(content) == 0
        return false
    end if

    // Trim newlines and check again
    let trimmed = str.trim(content, '\n')
    if str.length(trimmed) == 0
        return false
    end if

    return true
end validate_staging_dir

fn generate_pkginfo(ctx: BuildContext): bool
    let pkginfo_path = path.join_path(ctx.pkg_dir, ".PKGINFO")

    mut content = "[package]\n"
    content = content + "name = \"" + ctx.port.info.name + "\"\n"
    content = content + "version = \"" + ctx.port.info.version + "\"\n"
    content = content + "release = " + int_to_str(ctx.port.info.release) + "\n"
    content = content + "description = \"" + ctx.port.info.description + "\"\n"
    content = content + "url = \"" + ctx.port.info.url + "\"\n"
    content = content + "license = \"" + ctx.port.info.license + "\"\n"
    content = content + "maintainer = \"" + ctx.port.info.maintainer + "\"\n"
    content = content + "arch = \"" + ctx.port.info.arch + "\"\n"

    // Emit [dependencies] section if there are any
    let has_runtime = ctx.port.deps.runtime_count > 0
    let has_build = ctx.port.deps.build_count > 0

    if has_runtime or has_build
        content = content + "\n[dependencies]\n"

        if has_runtime
            content = content + "runtime = ["
            mut i = 0
            while i < ctx.port.deps.runtime_count
                if i > 0
                    content = content + ", "
                end if
                content = content + "\"" + ctx.port.deps.runtime[i] + "\""
                i = i + 1
            end while
            content = content + "]\n"
        end if

        if has_build
            content = content + "build = ["
            mut i = 0
            while i < ctx.port.deps.build_count
                if i > 0
                    content = content + ", "
                end if
                content = content + "\"" + ctx.port.deps.build[i] + "\""
                i = i + 1
            end while
            content = content + "]\n"
        end if
    end if

    return res.is_ok(file.writeFile(pkginfo_path, content))
end generate_pkginfo

fn generate_manifest_file(ctx: BuildContext): bool
    let manifest_path = path.join_path(ctx.pkg_dir, ".MANIFEST")

    // Generate mtree manifest using native fs operations
    // BUG-033 (GC candidate overflow) fixed in Reef 0.5.6
    // uid/gid resolution now uses zero-allocation stat.uid_name()/gid_name()
    let content = mtree.generate_manifest(ctx.pkg_dir)
    if str.length(content) == 0
        return false
    end if

    return res.is_ok(file.writeFile(manifest_path, content))
end generate_manifest_file

proc cleanup_build(ctx: BuildContext)
    // Check if cleanup is disabled by --noclean flag
    if ctx.noclean
        color.print_info("Skipping cleanup (--noclean specified)")
        return
    end if

    // Determine cleanup behavior from config and flags
    mut clean_work = config.get_clean_work(ctx.cfg)
    mut clean_pkg = config.get_clean_pkg(ctx.cfg)

    // --clean flag forces cleanup
    if ctx.force_clean
        clean_work = true
        clean_pkg = true
    end if

    // Clean work directory
    if clean_work and dir.dir_exists(ctx.work_dir)
        color.print_info("Cleaning work directory: " + ctx.work_dir)
        let cmd = "rm -rf \"" + ctx.work_dir + "\""
        let pid = process.process_spawn_shell(cmd)
        if pid > 0
            let exit_code = process.process_wait(pid)
            if exit_code == 0
                color.print_success("Cleaned work directory")
            else
                color.print_warning("Failed to clean work directory")
            end if
        end if
    end if

    // Clean pkg directory (DESTDIR staging)
    if clean_pkg and dir.dir_exists(ctx.pkg_dir)
        color.print_info("Cleaning pkg directory: " + ctx.pkg_dir)
        let cmd = "rm -rf \"" + ctx.pkg_dir + "\""
        let pid = process.process_spawn_shell(cmd)
        if pid > 0
            let exit_code = process.process_wait(pid)
            if exit_code == 0
                color.print_success("Cleaned pkg directory")
            else
                color.print_warning("Failed to clean pkg directory")
            end if
        end if
    end if
end cleanup_build

// Helper: extract filename from URL
fn extract_filename(url: string): string
    let last_slash = str.last_index_of_char(url, '/')
    if last_slash < 0
        return url
    end if

    let filename = str.substring(url, last_slash + 1, str.length(url) - last_slash - 1)

    // Remove query string if present
    let query_pos = str.index_of_char(filename, '?')
    if query_pos > 0
        return str.substring(filename, 0, query_pos)
    end if

    return filename
end extract_filename

// Helper: convert int to string
fn int_to_str(n: int): string
    if n == 0
        return "0"
    end if

    mut negative = false
    mut value = n
    if n < 0
        negative = true
        value = 0 - n
    end if

    mut result = ""
    while value > 0
        let digit = value % 10
        result = str.concat(str.substring("0123456789", digit, 1), result)
        value = value / 10
    end while

    if negative
        result = str.concat("-", result)
    end if

    return result
end int_to_str

end module
/******************************************************************************
               __               ____                __
              / /   ___  ____ _/ __/_____________ _/ /__
             / /   / _ \/ __ `/ /_/ ___/ ___/ __ `/ / _ \
            / /___/  __/ /_/ / __(__  ) /__/ /_/ / /  __/
           /_____/\___/\__,_/_/ /____/\___/\__,_/_/\___/

   (C)opyright 2025, Leafscale, LLC -  https://www.leafscale.com

   Project: Zygaena
  Filename: clean.reef
   Authors: Chris Tusa <chris.tusa@leafscale.com>
   License: <see LICENSE file included with this source code>
Description: Clean command - remove build artifacts and caches

******************************************************************************/

module commands.clean

import sys.args
import sys.process
import io.file
import io.dir
import io.path
import core.str
import core.config
import types
import util.color
import exitcodes as ec
import core.result as res

export
    fn execute(): int
end export

fn execute(): int
    let argc = args.count()

    if argc < 3
        print_usage()
        return ec.EXIT_USAGE()
    end if

    let subcommand = args.get(2)

    // Load config
    let cfg = config.load()

    if subcommand == "status"
        return show_status(cfg)
    elif subcommand == "sources"
        return clean_sources(cfg)
    elif subcommand == "packages"
        return clean_packages(cfg)
    elif subcommand == "build"
        return clean_build(cfg)
    elif subcommand == "all"
        return clean_all(cfg)
    else
        color.print_error("Unknown subcommand: " + subcommand)
        print_usage()
        return ec.EXIT_USAGE()
    end if
end execute

fn show_status(cfg: config.Config): int
    color.print_action("Build artifact status:")
    println("")

    // Built packages
    let packages_dir = config.get_packages_dir(cfg)
    let pkg_count = count_files(packages_dir, ".pkg.tar.xz")
    mut pkg_protected = ""
    if config.get_keep_packages(cfg)
        pkg_protected = " [protected]"
    end if
    println("  Packages (" + packages_dir + "):" + pkg_protected)
    println("    " + int_to_str(pkg_count) + " built package(s)")

    // Source tarballs
    let sources_dir = config.get_sources_dir(cfg)
    let src_count = count_files(sources_dir, "")
    mut src_protected = ""
    if config.get_keep_sources(cfg)
        src_protected = " [protected]"
    end if
    println("  Sources (" + sources_dir + "):" + src_protected)
    println("    " + int_to_str(src_count) + " source archive(s)")

    // Build workspace
    let build_dir = config.get_build_dir(cfg)
    let build_count = count_subdirs(build_dir)
    println("  Build (" + build_dir + "):")
    println("    " + int_to_str(build_count) + " build workspace(s)")

    return ec.EXIT_SUCCESS()
end show_status

fn clean_sources(cfg: config.Config): int
    // Respect keep_sources config unless --force is passed
    if config.get_keep_sources(cfg) and not args.has_flag("force")
        color.print_warning("Source cache is configured to be preserved (keep_sources = true)")
        color.print_info("Use --force to override")
        return ec.EXIT_SUCCESS()
    end if

    let sources_dir = config.get_sources_dir(cfg)
    color.print_action("Cleaning source archives...")
    println("  Location: " + sources_dir)

    if not dir.dir_exists(sources_dir)
        color.print_info("No sources directory to clean")
        return ec.EXIT_SUCCESS()
    end if

    let cmd = "rm -rf \"" + sources_dir + "\"/*"
    let pid = process.process_spawn_shell(cmd)
    if pid > 0
        process.process_wait(pid)
    end if

    color.print_success("Source archives cleaned")
    return ec.EXIT_SUCCESS()
end clean_sources

fn clean_packages(cfg: config.Config): int
    // Respect keep_packages config unless --force is passed
    if config.get_keep_packages(cfg) and not args.has_flag("force")
        color.print_warning("Package cache is configured to be preserved (keep_packages = true)")
        color.print_info("Use --force to override")
        return ec.EXIT_SUCCESS()
    end if

    let packages_dir = config.get_packages_dir(cfg)
    color.print_action("Cleaning built packages...")
    println("  Location: " + packages_dir)

    if not dir.dir_exists(packages_dir)
        color.print_info("No packages directory to clean")
        return ec.EXIT_SUCCESS()
    end if

    let cmd = "rm -rf \"" + packages_dir + "\"/*"
    let pid = process.process_spawn_shell(cmd)
    if pid > 0
        process.process_wait(pid)
    end if

    color.print_success("Built packages cleaned")
    return ec.EXIT_SUCCESS()
end clean_packages

fn clean_build(cfg: config.Config): int
    let build_dir = config.get_build_dir(cfg)
    color.print_action("Cleaning build workspaces...")
    println("  Location: " + build_dir)

    if not dir.dir_exists(build_dir)
        color.print_info("No build directory to clean")
        return ec.EXIT_SUCCESS()
    end if

    let cmd = "rm -rf \"" + build_dir + "\"/*"
    let pid = process.process_spawn_shell(cmd)
    if pid > 0
        process.process_wait(pid)
    end if

    color.print_success("Build workspaces cleaned")
    return ec.EXIT_SUCCESS()
end clean_build

fn clean_all(cfg: config.Config): int
    color.print_action("Cleaning all build artifacts...")
    println("")

    clean_sources(cfg)
    clean_packages(cfg)
    clean_build(cfg)

    println("")
    color.print_success("All build artifacts cleaned")
    return ec.EXIT_SUCCESS()
end clean_all

fn count_files(dir_path: string, extension: string): int
    if not dir.dir_exists(dir_path)
        return 0
    end if

    let entries = res.unwrap_or(dir.list_dir(dir_path), new [string](0))
    let count = entries.length()

    if str.length(extension) == 0
        return count
    end if

    mut matched = 0
    mut i = 0
    while i < count
        if str.ends_with(entries[i], extension)
            matched = matched + 1
        end if
        i = i + 1
    end while

    return matched
end count_files

fn count_subdirs(dir_path: string): int
    if not dir.dir_exists(dir_path)
        return 0
    end if

    let entries = res.unwrap_or(dir.list_dir(dir_path), new [string](0))
    let count = entries.length()

    // Count only directories (packages being built)
    mut dirs = 0
    mut i = 0
    while i < count
        let entry = entries[i]
        if str.length(entry) > 0 and entry[0] != '.'
            let full_path = path.join_path(dir_path, entry)
            if dir.dir_exists(full_path)
                dirs = dirs + 1
            end if
        end if
        i = i + 1
    end while

    return dirs
end count_subdirs

proc print_usage()
    println("Usage: coral clean <target>")
    println("")
    println("Remove build artifacts and cached files.")
    println("")
    println("Targets:")
    println("  status    Show what can be cleaned")
    println("  sources   Remove downloaded source archives")
    println("  packages  Remove built binary packages")
    println("  build     Remove build workspaces")
    println("  all       Remove all of the above")
    println("")
    println("Locations:")
    println("  sources:  /usr/zports/pkgs/sources/")
    println("  packages: /usr/zports/pkgs/packages/")
    println("  build:    /usr/zports/pkgs/build/")
    println("")
    println("Options:")
    println("  --force   Override keep_packages/keep_sources config protection")
    println("")
    println("Note: This does NOT affect installed packages or the package database.")
    println("      Use 'coral remove' to uninstall packages.")
    println("")
    println("Examples:")
    println("  coral clean status")
    println("  coral clean build")
    println("  coral clean all")
end print_usage

// Helper: convert int to string
fn int_to_str(n: int): string
    if n == 0
        return "0"
    end if

    mut negative = false
    mut value = n
    if n < 0
        negative = true
        value = 0 - n
    end if

    mut result = ""
    while value > 0
        let digit = value % 10
        result = str.concat(str.substring("0123456789", digit, 1), result)
        value = value / 10
    end while

    if negative
        result = str.concat("-", result)
    end if

    return result
end int_to_str

end module
/******************************************************************************
               __               ____                __
              / /   ___  ____ _/ __/_____________ _/ /__
             / /   / _ \/ __ `/ /_/ ___/ ___/ __ `/ / _ \
            / /___/  __/ /_/ / __(__  ) /__/ /_/ / /  __/
           /_____/\___/\__,_/_/ /____/\___/\__,_/_/\___/

   (C)opyright 2025, Leafscale, LLC -  https://www.leafscale.com

   Project: Zygaena
  Filename: db.reef
   Authors: Chris Tusa <chris.tusa@leafscale.com>
   License: <see LICENSE file included with this source code>
Description: Database command - manage package database indexes

******************************************************************************/

module commands.db

import sys.args
import io.file
import io.dir
import core.str
import core.config
import core.pkgdb
import core.portindex
import types
import util.color
import exitcodes as ec

export
    fn execute(opts: types.GlobalOptions): int
end export

fn execute(opts: types.GlobalOptions): int
    let argc = args.count()

    // Subcommand should be at cmd_index + 1
    if argc <= opts.cmd_index + 1
        print_usage()
        return ec.EXIT_USAGE()
    end if

    // Load configuration and apply command-line overrides
    let base_cfg = config.load()
    let cfg = config.apply_overrides(base_cfg, opts.root, opts.prefix, opts.no_chroot)
    let root_path = config.get_root(cfg)

    // Show root if set (verbose mode)
    if opts.verbose and str.length(root_path) > 0
        color.print_info("Using root: " + root_path)
    end if

    let subcommand = args.get(opts.cmd_index + 1)

    if subcommand == "init"
        return db_init(root_path)
    elif subcommand == "rebuild"
        return db_rebuild(root_path)
    elif subcommand == "status"
        return db_status(root_path)
    elif subcommand == "dump"
        return db_dump(root_path)
    else
        color.print_error("Unknown subcommand: " + subcommand)
        print_usage()
        return ec.EXIT_USAGE()
    end if
end execute

fn db_init(root_path: string): int
    if str.length(root_path) > 0
        color.print_action("Initializing package database in " + root_path + "...")
    else
        color.print_action("Initializing package database...")
    end if
    println("")

    // Check if database already exists (use rooted version if root is set)
    let exists = check_indexes_exist(root_path)
    if exists
        color.print_warning("Database indexes already exist")
        color.print_info("Use 'coral db rebuild' to regenerate indexes")
        return ec.EXIT_SUCCESS()
    end if

    // Initialize the database directory (use rooted version if root is set)
    if not init_pkgdb(root_path)
        color.print_error("Failed to create database directory")
        return ec.EXIT_DB_ERROR()
    end if

    // Build initial indexes (use rooted version if root is set)
    if not rebuild_pkgdb(root_path)
        color.print_error("Failed to build initial indexes")
        return ec.EXIT_DB_ERROR()
    end if

    // Build ports index
    portindex.rebuild_port_index()

    let stats = get_pkgdb_stats(root_path)
    let port_count = portindex.get_port_count()
    color.print_success("Database initialized successfully")
    println("  Packages indexed: " + int_to_str(stats.package_count))
    println("  Files indexed: " + int_to_str(stats.file_count))
    println("  Ports indexed: " + int_to_str(port_count))

    return ec.EXIT_SUCCESS()
end db_init

fn db_rebuild(root_path: string): int
    if str.length(root_path) > 0
        color.print_action("Rebuilding package database indexes in " + root_path + "...")
    else
        color.print_action("Rebuilding package database indexes...")
    end if
    println("")

    // Check if db directory exists (use rooted version if root is set)
    if not init_pkgdb(root_path)
        color.print_error("Failed to access database directory")
        color.print_info("Run 'coral db init' first")
        return ec.EXIT_DB_ERROR()
    end if

    // Rebuild indexes from source of truth (use rooted version if root is set)
    if not rebuild_pkgdb(root_path)
        color.print_error("Failed to rebuild indexes")
        return ec.EXIT_DB_ERROR()
    end if

    // Rebuild ports index
    portindex.rebuild_port_index()

    let stats = get_pkgdb_stats(root_path)
    let port_count = portindex.get_port_count()
    color.print_success("Database indexes rebuilt successfully")
    println("  Packages indexed: " + int_to_str(stats.package_count))
    println("  Files indexed: " + int_to_str(stats.file_count))
    println("  Ports indexed: " + int_to_str(port_count))

    return ec.EXIT_SUCCESS()
end db_rebuild

fn db_dump(root_path: string): int
    color.print_action("Dumping files index contents...")
    println("")

    mut paths: [string] = new [string](256)
    mut owners: [string] = new [string](256)
    let count = pkgdb.dump_files_index_rooted(root_path, paths, owners, 256)

    if count == 0
        color.print_warning("No files in index or index not loaded")
        return ec.EXIT_DB_ERROR()
    end if

    println("Files in index: " + int_to_str(count))
    println("")

    mut i = 0
    while i < count
        println("  [" + int_to_str(i) + "] '" + paths[i] + "' -> '" + owners[i] + "'")
        i = i + 1
    end while

    return ec.EXIT_SUCCESS()
end db_dump

fn db_status(root_path: string): int
    if str.length(root_path) > 0
        color.print_action("Package database status for " + root_path + ":")
    else
        color.print_action("Package database status:")
    end if
    println("")

    let stats = get_pkgdb_stats(root_path)

    if not check_indexes_exist(root_path)
        color.print_warning("Database indexes not found")
        color.print_info("Run 'coral db init' to create indexes")
        println("")
        if str.length(root_path) > 0
            println("  Source of truth: " + root_path + "/var/lib/coral/installed/")
        else
            println("  Source of truth: /var/lib/coral/installed/")
        end if
        println("  Packages installed: " + int_to_str(stats.package_count))
        return ec.EXIT_DB_INDEX_STALE()
    end if

    if str.length(root_path) > 0
        println("  Index location: " + root_path + types.get_index_dir())
    else
        println("  Index location: " + types.get_index_dir())
    end if
    println("  Packages indexed: " + int_to_str(stats.package_count))
    println("  Files indexed: " + int_to_str(stats.file_count))

    if stats.packages_db_size > 0
        println("  packages.db size: " + format_size(stats.packages_db_size))
    end if
    if stats.files_db_size > 0
        println("  files.db size: " + format_size(stats.files_db_size))
    end if

    // Ports index status
    if portindex.port_index_exists()
        let port_count = portindex.get_port_count()
        println("  Ports indexed: " + int_to_str(port_count))
    else
        println("  Ports index: not built")
    end if

    return ec.EXIT_SUCCESS()
end db_status

// Helper functions for rooted pkgdb operations
fn check_indexes_exist(root_path: string): bool
    if str.length(root_path) > 0
        return pkgdb.indexes_exist_rooted(root_path)
    end if
    return pkgdb.indexes_exist()
end check_indexes_exist

fn init_pkgdb(root_path: string): bool
    if str.length(root_path) > 0
        return pkgdb.init_db_rooted(root_path)
    end if
    return pkgdb.init_db()
end init_pkgdb

fn rebuild_pkgdb(root_path: string): bool
    if str.length(root_path) > 0
        return pkgdb.rebuild_indexes_rooted(root_path)
    end if
    return pkgdb.rebuild_indexes()
end rebuild_pkgdb

fn get_pkgdb_stats(root_path: string): pkgdb.IndexStats
    if str.length(root_path) > 0
        return pkgdb.get_index_stats_rooted(root_path)
    end if
    return pkgdb.get_index_stats()
end get_pkgdb_stats

fn format_size(bytes: int): string
    if bytes < 1024
        return int_to_str(bytes) + " B"
    elif bytes < 1024 * 1024
        return int_to_str(bytes / 1024) + " KB"
    elif bytes < 1024 * 1024 * 1024
        return int_to_str(bytes / (1024 * 1024)) + " MB"
    else
        return int_to_str(bytes / (1024 * 1024 * 1024)) + " GB"
    end if
end format_size

proc print_usage()
    println("Usage: coral db <command>")
    println("")
    println("Manage package database indexes.")
    println("")
    println("Commands:")
    println("  init      Initialize database (run once during system setup)")
    println("  rebuild   Rebuild indexes from installed packages")
    println("  status    Show database status and statistics")
    println("")
    println("The package database provides fast lookups for installed packages")
    println("and file ownership. The source of truth is always the installed/")
    println("directory; indexes can be safely rebuilt at any time.")
    println("")
    println("Examples:")
    println("  coral db init")
    println("  coral db rebuild")
    println("  coral db status")
end print_usage

// Helper: convert int to string
fn int_to_str(n: int): string
    if n == 0
        return "0"
    end if

    mut negative = false
    mut value = n
    if n < 0
        negative = true
        value = 0 - n
    end if

    mut result = ""
    while value > 0
        let digit = value % 10
        result = str.concat(str.substring("0123456789", digit, 1), result)
        value = value / 10
    end while

    if negative
        result = str.concat("-", result)
    end if

    return result
end int_to_str

end module
/******************************************************************************
               __               ____                __
              / /   ___  ____ _/ __/_____________ _/ /__
             / /   / _ \/ __ `/ /_/ ___/ ___/ __ `/ / _ \
            / /___/  __/ /_/ / __(__  ) /__/ /_/ / /  __/
           /_____/\___/\__,_/_/ /____/\___/\__,_/_/\___/

   (C)opyright 2025, Leafscale, LLC -  https://www.leafscale.com

   Project: Zygaena
  Filename: depends.reef
   Authors: Chris Tusa <chris.tusa@leafscale.com>
   License: <see LICENSE file included with this source code>
Description: Depends command - show package dependency tree

******************************************************************************/

module commands.depends

import sys.args
import core.str
import core.port
import core.portindex
import core.database
import core.resolver
import types
import util.color
import exitcodes as ec

export
    fn execute(): int
end export

fn execute(): int
    let argc = args.count()

    if argc < 3
        print_usage()
        return ec.EXIT_USAGE()
    end if

    let pkg_name = args.get(2)

    // Check for --reverse flag (show what depends on this package)
    if args.has_flag("reverse") or args.has_flag("r")
        show_reverse_deps(pkg_name)
        return ec.EXIT_SUCCESS()
    end if

    // Show forward dependencies
    show_deps(pkg_name)
    return ec.EXIT_SUCCESS()
end execute

proc show_deps(name: string)
    // Find the port
    let result = port.find(name)
    if not result.success
        color.print_error("Port not found: " + name)
        return
    end if

    let p = result.port

    color.print_action("Dependencies for " + name + ":")
    println("")

    // Show runtime dependencies
    if p.deps.runtime_count == 0
        color.print_info("No runtime dependencies")
    else
        color.print_info("Runtime dependencies:")
        show_dep_tree(name, 0)
    end if

    println("")

    // Show build dependencies
    if p.deps.build_count > 0
        color.print_info("Build dependencies:")
        mut i = 0
        while i < p.deps.build_count
            print("  ")
            let dep = p.deps.build[i]
            print(dep)
            if database.is_installed(dep)
                println(" [installed]")
            else
                println("")
            end if
            i = i + 1
        end while
    end if
end show_deps

proc show_dep_tree(name: string, depth: int)
    if depth > 10
        return
    end if

    let result = port.find(name)
    if not result.success
        return
    end if

    let p = result.port

    mut i = 0
    while i < p.deps.runtime_count
        let dep = p.deps.runtime[i]

        // Print with indentation
        print_indent(depth)
        print(dep)
        if database.is_installed(dep)
            println(" [installed]")
        else
            println("")
        end if

        // Recurse
        show_dep_tree(dep, depth + 1)

        i = i + 1
    end while
end show_dep_tree

proc show_reverse_deps(name: string)
    color.print_action("Packages that depend on " + name + ":")
    println("")

    mut found = 0

    // Try ports index first (fast path)
    if portindex.port_index_exists()
        mut results: [portindex.PortIndexEntry] = new [portindex.PortIndexEntry](512)
        let result_count = portindex.find_reverse_deps(name, results, 512)

        mut i = 0
        while i < result_count
            let entry = results[i]
            print("  ")
            print(entry.category)
            print("/")
            print(entry.name)
            if database.is_installed(entry.name)
                println(" [installed]")
            else
                println("")
            end if
            found = found + 1
            i = i + 1
        end while
    else
        // Fall back to filesystem scan
        mut cats: [string] = new [string](32)
        let cat_count = port.get_categories(cats, 32)

        mut i = 0
        while i < cat_count
            let category = cats[i]
            mut ports: [string] = new [string](256)
            let port_count = port.list_category(category, ports, 256)

            mut j = 0
            while j < port_count
                let port_name = ports[j]
                if depends_on(port_name, name)
                    print("  ")
                    print(category)
                    print("/")
                    print(port_name)
                    if database.is_installed(port_name)
                        println(" [installed]")
                    else
                        println("")
                    end if
                    found = found + 1
                end if
                j = j + 1
            end while

            i = i + 1
        end while
    end if

    if found == 0
        color.print_info("No packages depend on " + name)
    else
        println("")
        color.print_info("Total: " + int_to_str(found) + " package(s)")
    end if
end show_reverse_deps

fn depends_on(pkg_name: string, dep_name: string): bool
    let result = port.find(pkg_name)
    if not result.success
        return false
    end if

    let p = result.port

    // Check runtime deps
    mut i = 0
    while i < p.deps.runtime_count
        if p.deps.runtime[i] == dep_name
            return true
        end if
        i = i + 1
    end while

    // Check build deps
    i = 0
    while i < p.deps.build_count
        if p.deps.build[i] == dep_name
            return true
        end if
        i = i + 1
    end while

    return false
end depends_on

proc print_indent(depth: int)
    mut i = 0
    while i < depth
        print("  ")
        i = i + 1
    end while
    print("  ")  // Base indent
end print_indent

proc print_usage()
    println("Usage: coral depends <package> [options]")
    println("")
    println("Show dependency tree for a package.")
    println("")
    println("Arguments:")
    println("  <package>    Name of package to show dependencies for")
    println("")
    println("Options:")
    println("  -r, --reverse    Show packages that depend on this package")
    println("")
    println("Examples:")
    println("  coral depends vim")
    println("  coral depends vim --reverse")
end print_usage

// Helper: convert int to string
fn int_to_str(n: int): string
    if n == 0
        return "0"
    end if

    mut negative = false
    mut value = n
    if n < 0
        negative = true
        value = 0 - n
    end if

    mut result = ""
    while value > 0
        let digit = value % 10
        result = str.concat(str.substring("0123456789", digit, 1), result)
        value = value / 10
    end while

    if negative
        result = str.concat("-", result)
    end if

    return result
end int_to_str

end module
/******************************************************************************
               __               ____                __
              / /   ___  ____ _/ __/_____________ _/ /__
             / /   / _ \/ __ `/ /_/ ___/ ___/ __ `/ / _ \
            / /___/  __/ /_/ / __(__  ) /__/ /_/ / /  __/
           /_____/\___/\__,_/_/ /____/\___/\__,_/_/\___/

   (C)opyright 2025, Leafscale, LLC -  https://www.leafscale.com

   Project: Zygaena
  Filename: files.reef
   Authors: Chris Tusa <chris.tusa@leafscale.com>
   License: <see LICENSE file included with this source code>
Description: Files command - list files owned by a package

******************************************************************************/

module commands.files

import sys.args
import core.str
import core.config
import core.database
import types
import util.color
import exitcodes as ec

export
    fn execute(opts: types.GlobalOptions): int
end export

fn execute(opts: types.GlobalOptions): int
    let argc = args.count()

    // Package name should be at cmd_index + 1
    if argc <= opts.cmd_index + 1
        print_usage()
        return ec.EXIT_USAGE()
    end if

    // Load configuration and apply command-line overrides
    let base_cfg = config.load()
    let cfg = config.apply_overrides(base_cfg, opts.root, opts.prefix, opts.no_chroot)
    let root_path = config.get_root(cfg)

    // Show root if set (verbose mode)
    if opts.verbose and str.length(root_path) > 0
        color.print_info("Using root: " + root_path)
    end if

    let pkg_name = args.get(opts.cmd_index + 1)

    // Check if installed (use rooted version if root is set)
    if not check_installed(pkg_name, root_path)
        color.print_error(pkg_name + " is not installed")
        return ec.EXIT_PKG_NOT_FOUND()
    end if

    // Get files (use rooted version if root is set)
    mut files: [string] = new [string](4096)
    let file_count = get_files_list(pkg_name, files, 4096, root_path)

    if file_count == 0
        color.print_info("No files recorded for " + pkg_name)
        return ec.EXIT_SUCCESS()
    end if

    color.print_action("Files owned by " + pkg_name + ":")
    println("")

    mut i = 0
    while i < file_count
        println("/" + files[i])
        i = i + 1
    end while

    println("")
    color.print_info("Total: " + int_to_str(file_count) + " files")
    return ec.EXIT_SUCCESS()
end execute

// Helper functions for rooted operations
fn check_installed(name: string, root_path: string): bool
    if str.length(root_path) > 0
        return database.is_installed_rooted(name, root_path)
    end if
    return database.is_installed(name)
end check_installed

fn get_files_list(name: string, files: [string], max_count: int, root_path: string): int
    if str.length(root_path) > 0
        return database.get_files_rooted(name, files, max_count, root_path)
    end if
    return database.get_files(name, files, max_count)
end get_files_list

proc print_usage()
    println("Usage: coral files <package>")
    println("")
    println("List all files owned by an installed package.")
    println("")
    println("Arguments:")
    println("  <package>    Name of installed package")
    println("")
    println("Examples:")
    println("  coral files vim")
    println("  coral files hello")
end print_usage

// Helper: convert int to string
fn int_to_str(n: int): string
    if n == 0
        return "0"
    end if

    mut negative = false
    mut value = n
    if n < 0
        negative = true
        value = 0 - n
    end if

    mut result = ""
    while value > 0
        let digit = value % 10
        result = str.concat(str.substring("0123456789", digit, 1), result)
        value = value / 10
    end while

    if negative
        result = str.concat("-", result)
    end if

    return result
end int_to_str

end module
/******************************************************************************
               __               ____                __
              / /   ___  ____ _/ __/_____________ _/ /__
             / /   / _ \/ __ `/ /_/ ___/ ___/ __ `/ / _ \
            / /___/  __/ /_/ / __(__  ) /__/ /_/ / /  __/
           /_____/\___/\__,_/_/ /____/\___/\__,_/_/\___/

   (C)opyright 2025, Leafscale, LLC -  https://www.leafscale.com

   Project: Zygaena
  Filename: info.reef
   Authors: Chris Tusa <chris.tusa@leafscale.com>
   License: <see LICENSE file included with this source code>
Description: Info command - display package information

******************************************************************************/

module commands.info

import sys.args
import core.str
import core.config
import core.database
import core.port
import types
import util.color
import exitcodes as ec

export
    fn execute(opts: types.GlobalOptions): int
end export

fn execute(opts: types.GlobalOptions): int
    let argc = args.count()

    // Package name should be at cmd_index + 1
    if argc <= opts.cmd_index + 1
        print_usage()
        return ec.EXIT_USAGE()
    end if

    // Load configuration and apply command-line overrides
    let base_cfg = config.load()
    let cfg = config.apply_overrides(base_cfg, opts.root, opts.prefix, opts.no_chroot)
    let root_path = config.get_root(cfg)

    // Show root if set (verbose mode)
    if opts.verbose and str.length(root_path) > 0
        color.print_info("Using root: " + root_path)
    end if

    let pkg_name = args.get(opts.cmd_index + 1)

    // Check if installed (use rooted version if root is set)
    let is_installed = check_installed(pkg_name, root_path)

    // Find port
    let port_result = port.find(pkg_name)

    if not is_installed and not port_result.success
        color.print_error("Package not found: " + pkg_name)
        return ec.EXIT_PKG_NOT_FOUND()
    end if

    // Print package info
    if is_installed
        let installed_pkg = get_installed_pkg(pkg_name, root_path)
        print_installed_info(installed_pkg)

        if port_result.success
            let p = port_result.port
            // Check if upgrade available
            if str.compare(installed_pkg.info.version, p.info.version) < 0
                println("")
                color.print_info("Upgrade available: " + p.info.version)
            end if
        end if
    else
        // Not installed, show port info
        let p = port_result.port
        print_port_info(p)
    end if
    return ec.EXIT_SUCCESS()
end execute

// Helper functions for rooted operations
fn check_installed(name: string, root_path: string): bool
    if str.length(root_path) > 0
        return database.is_installed_rooted(name, root_path)
    end if
    return database.is_installed(name)
end check_installed

fn get_installed_pkg(name: string, root_path: string): types.InstalledPackage
    if str.length(root_path) > 0
        return database.get_installed_rooted(name, root_path)
    end if
    return database.get_installed(name)
end get_installed_pkg

proc print_usage()
    println("Usage: coral info <package>")
    println("")
    println("Display detailed information about a package.")
    println("")
    println("Arguments:")
    println("  <package>    Name of package to show info for")
    println("")
    println("Examples:")
    println("  coral info vim")
    println("  coral info hello")
end print_usage

proc print_installed_info(pkg: types.InstalledPackage)
    color.print_action("Package: " + pkg.info.name)
    println("")
    println("Status:       installed")
    println("Version:      " + pkg.info.version + "-" + int_to_str(pkg.info.release))
    println("Description:  " + pkg.info.description)
    println("URL:          " + pkg.info.url)
    println("License:      " + pkg.info.license)
    println("Maintainer:   " + pkg.info.maintainer)
    println("Architecture: " + pkg.info.arch)
    println("")
    println("Install date: " + pkg.install_date)
    println("Reason:       " + pkg.install_reason)
    println("Files:        " + int_to_str(pkg.files_count))
end print_installed_info

proc print_port_info(p: types.Port)
    color.print_action("Port: " + p.info.name)
    println("")
    println("Status:       not installed")
    println("Version:      " + p.info.version + "-" + int_to_str(p.info.release))
    println("Description:  " + p.info.description)
    println("URL:          " + p.info.url)
    println("License:      " + p.info.license)
    println("Maintainer:   " + p.info.maintainer)
    println("Architecture: " + p.info.arch)

    // Show dependencies if any
    if p.deps.runtime_count > 0
        println("")
        print("Depends on:   ")
        mut i = 0
        while i < p.deps.runtime_count
            if i > 0
                print(", ")
            end if
            print(p.deps.runtime[i])
            i = i + 1
        end while
        println("")
    end if

    if p.deps.build_count > 0
        println("")
        print("Build deps:   ")
        mut i = 0
        while i < p.deps.build_count
            if i > 0
                print(", ")
            end if
            print(p.deps.build[i])
            i = i + 1
        end while
        println("")
    end if
end print_port_info

// Helper: convert int to string
fn int_to_str(n: int): string
    if n == 0
        return "0"
    end if

    mut negative = false
    mut value = n
    if n < 0
        negative = true
        value = 0 - n
    end if

    mut result = ""
    while value > 0
        let digit = value % 10
        result = str.concat(str.substring("0123456789", digit, 1), result)
        value = value / 10
    end while

    if negative
        result = str.concat("-", result)
    end if

    return result
end int_to_str

end module
/******************************************************************************
               __               ____                __
              / /   ___  ____ _/ __/_____________ _/ /__
             / /   / _ \/ __ `/ /_/ ___/ ___/ __ `/ / _ \
            / /___/  __/ /_/ / __(__  ) /__/ /_/ / /  __/
           /_____/\___/\__,_/_/ /____/\___/\__,_/_/\___/

   (C)opyright 2025, Leafscale, LLC -  https://www.leafscale.com

   Project: Zygaena
  Filename: install.reef
   Authors: Chris Tusa <chris.tusa@leafscale.com>
   License: <see LICENSE file included with this source code>
Description: Install command - install packages from archives

******************************************************************************/

module commands.install

import sys.args
import sys.process
import io.file
import io.dir
import io.path
import core.str
import core.config
import core.database
import core.pkgdb
import core.package
import core.groups
import core.repository
import core.signing
import core.resolver
import core.port
import core.portindex
import util.checksum
import util.mtree
import util.http as uhttp
import util.prompt
import util.version as ver
import types
import util.color
import util.priv
import exitcodes as ec
import core.result as res

export
    fn execute(opts: types.GlobalOptions): int
end export

fn execute(opts: types.GlobalOptions): int
    let argc = args.count()

    // Package arguments start after the command
    if argc <= opts.cmd_index + 1
        print_usage()
        return ec.EXIT_USAGE()
    end if

    // Load configuration and apply command-line overrides
    let base_cfg = config.load()
    let cfg = config.apply_overrides(base_cfg, opts.root, opts.prefix, opts.no_chroot)
    uhttp.enable_proxy(config.get_use_proxy(cfg))

    // Auto-refresh port index if configured
    if config.get_auto_refresh(cfg)
        portindex.rebuild_port_index()
    end if

    // Show root/prefix if set (verbose mode)
    if opts.verbose
        let root = config.get_root(cfg)
        let prefix = config.get_prefix(cfg)
        if str.length(root) > 0
            color.print_info("Using root: " + root)
        end if
        if str.length(prefix) > 0
            color.print_info("Using prefix: " + prefix)
        end if
    end if

    // Collect all packages to install (expanding groups)
    mut packages: [string] = new [string](256)
    mut pkg_count = 0
    mut direct_files: [string] = new [string](16)
    mut direct_count = 0

    // Process each package argument (starting after the command)
    mut i = opts.cmd_index + 1
    while i < argc and pkg_count < 256
        let pkg_arg = args.get(i)

        // Skip flags and their values
        if pkg_arg == "--root" or pkg_arg == "--prefix"
            i = i + 2  // Skip flag and its value
            continue
        elif pkg_arg == "--no-chroot-scripts"
            i = i + 1  // valueless flag: skip only itself
            continue
        end if
        if str.starts_with(pkg_arg, "-")
            i = i + 1
            continue
        end if

        // Check if this is a direct file path to a .pkg.tar.xz
        if str.ends_with(pkg_arg, ".pkg.tar.xz") and file.fileExists(pkg_arg)
            direct_files[direct_count] = pkg_arg
            direct_count = direct_count + 1
            i = i + 1
            continue
        end if

        // Check if this is a group reference
        if groups.is_group(pkg_arg)
            // Expand group to member packages
            mut group_members: [string] = new [string](128)
            let member_count = groups.expand_group(pkg_arg, group_members, 128)

            if member_count == 0
                color.print_error("Group not found or empty: " + pkg_arg)
                i = i + 1
                continue
            end if

            color.print_info("Expanding group " + pkg_arg + " (" + int_to_str(member_count) + " packages)")

            // Add all group members to packages list
            mut j = 0
            while j < member_count and pkg_count < 256
                packages[pkg_count] = group_members[j]
                pkg_count = pkg_count + 1
                j = j + 1
            end while
        else
            // Regular package
            packages[pkg_count] = pkg_arg
            pkg_count = pkg_count + 1
        end if

        i = i + 1
    end while

    // Handle direct file installs — bypass resolver, install immediately
    if direct_count > 0
        let root = get_root(cfg)
        let root_for_db = config.get_root(cfg)
        if str.length(root_for_db) > 0
            if not database.init_db_rooted(root_for_db)
                color.print_error("Failed to initialize database in " + root_for_db)
                return ec.EXIT_DB_ERROR()
            end if
        else
            if not database.init_db()
                color.print_error("Failed to initialize package database")
                return ec.EXIT_DB_ERROR()
            end if
        end if

        mut di = 0
        while di < direct_count
            if not install_package(direct_files[di], cfg, root_for_db, opts)
                color.print_error("Failed to install: " + direct_files[di])
                return ec.EXIT_INSTALL_FAILED()
            end if
            di = di + 1
        end while

        if pkg_count == 0
            return ec.EXIT_SUCCESS()
        end if
    end if

    // Resolve dependencies for all packages
    // Use rooted resolver if installing to alternate root
    mut install_order: [string] = new [string](512)
    let root_for_resolve = config.get_root(cfg)
    mut install_count = 0
    if str.length(root_for_resolve) > 0
        install_count = resolver.get_install_order_rooted(packages, pkg_count, install_order, 512, root_for_resolve)
    else
        install_count = resolver.get_install_order(packages, pkg_count, install_order, 512)
    end if

    // When force/reinstall is set, add requested packages that the resolver
    // skipped (because they're already installed) back into the install order
    if opts.force and install_count < pkg_count
        mut fi = 0
        while fi < pkg_count
            let pkg = packages[fi]
            if not array_contains(install_order, install_count, pkg)
                install_order[install_count] = pkg
                install_count = install_count + 1
            end if
            fi = fi + 1
        end while
    end if

    if install_count == 0 and pkg_count > 0
        color.print_warning("No packages to install (all already installed or not found)")
        return ec.EXIT_SUCCESS()
    end if

    // Separate new installs from already-installed (for display)
    mut to_install: [string] = new [string](512)
    mut install_idx = 0

    mut dep_idx = 0
    while dep_idx < install_count
        to_install[install_idx] = install_order[dep_idx]
        install_idx = install_idx + 1
        dep_idx = dep_idx + 1
    end while

    // Ask for confirmation (unless -y flag)
    mut empty_upgrade: [string] = new [string](1)
    if not prompt.confirm_install(to_install, install_idx, empty_upgrade, 0, opts)
        color.print_info("Installation cancelled")
        return ec.EXIT_CANCELLED()
    end if

    // Dry-run: show what would be done and exit
    if opts.dry_run
        color.print_info("Dry run — no changes made")
        return ec.EXIT_SUCCESS()
    end if

    // Get root path for installation
    let root = get_root(cfg)

    // Initialize database in the target root
    let root_for_db = config.get_root(cfg)
    if str.length(root_for_db) > 0
        if not database.init_db_rooted(root_for_db)
            color.print_error("Failed to initialize database in " + root_for_db)
            return ec.EXIT_DB_ERROR()
        end if
    else
        if not database.init_db()
            color.print_error("Failed to initialize package database")
            return ec.EXIT_DB_ERROR()
        end if
    end if

    // Install all packages in resolved order (dependencies first)
    i = 0
    while i < install_count
        let pkg_arg = install_order[i]

        // Install this package
        if not install_package(pkg_arg, cfg, root_for_db, opts)
            color.print_error("Failed to install: " + pkg_arg)
            color.print_error("Aborting installation - dependency failed")
            return ec.EXIT_INSTALL_FAILED()
        end if

        i = i + 1
    end while

    return ec.EXIT_SUCCESS()
end execute

// Helper to check if array contains a string
fn array_contains(arr: [string], count: int, s: string): bool
    mut i = 0
    while i < count
        if str.equals(arr[i], s)
            return true
        end if
        i = i + 1
    end while
    return false
end array_contains

proc print_usage()
    println("Usage: coral install <package...>")
    println("")
    println("Install one or more packages.")
    println("")
    println("Arguments:")
    println("  <package>    Package name or path to .pkg.tar.xz file")
    println("")
    println("Options:")
    println("  -y, --yes    Don't ask for confirmation")
    println("  --force      Force reinstall if already installed")
    println("")
    println("Examples:")
    println("  coral install vim")
    println("  coral install /path/to/package.pkg.tar.xz")
    println("  coral install vim nano htop")
end print_usage

fn install_package(pkg_arg: string, cfg: config.Config, root_path: string, opts: types.GlobalOptions): bool
    // Determine if this is a file path or package name
    let pkg_path = resolve_package_path(pkg_arg, cfg)

    if str.length(pkg_path) == 0
        color.print_error("Package not found: " + pkg_arg)
        return false
    end if

    // Verify signature if required (for local packages not already verified by resolve_package_path)
    let require_signed = config.get_require_signed_packages(cfg)
    if require_signed
        let sig_path = pkg_path + ".sig"
        if file.fileExists(sig_path)
            color.print_info("Verifying package signature...")
            let verify_result = signing.verify_package(pkg_path, sig_path)
            if not verify_result.success or not verify_result.valid
                color.print_error("Signature verification failed: " + verify_result.error)
                return false
            end if
            color.print_success("Signature verified (key: " + verify_result.keyid + ")")
        else
            color.print_error("Package signature required but not found: " + sig_path)
            return false
        end if
    end if

    color.print_action("Installing " + pkg_arg + "...")

    // Create extraction directory
    let extract_dir = create_extract_dir(cfg)
    if str.length(extract_dir) == 0
        color.print_error("Failed to create extraction directory")
        return false
    end if

    // Extract package
    color.print_info("Extracting package...")
    let result = package.extract_package(pkg_path, extract_dir)
    if not result.success
        color.print_error(result.error)
        cleanup_extract_dir(extract_dir)
        return false
    end if

    // Read package info
    let info = package.read_pkginfo(extract_dir)
    if str.length(info.name) == 0
        color.print_error("Failed to read package info")
        cleanup_extract_dir(extract_dir)
        return false
    end if

    color.print_info("Package: " + info.name + " " + info.version)

    // Check for conflicts with installed packages
    if info.conflicts_count > 0
        mut ci = 0
        while ci < info.conflicts_count
            let conflict = info.conflicts[ci]
            if check_installed(conflict, root_path)
                color.print_error("Package " + info.name + " conflicts with installed package: " + conflict)
                if not opts.force
                    color.print_error("Use --force to override conflict check")
                    cleanup_extract_dir(extract_dir)
                    return false
                end if
                color.print_warning("Proceeding despite conflict (--force specified)")
            end if
            ci = ci + 1
        end while
    end if

    // Check if already installed (in target root)
    let already_installed = check_installed(info.name, root_path)
    mut is_upgrade = false
    mut old_version = ""

    if already_installed
        // Get old package info to check version
        let old_pkg = get_old_installed(info.name, root_path)
        old_version = old_pkg.info.version

        if not str.equals(old_version, info.version)
            // Different version — upgrade
            is_upgrade = true
            color.print_info("Upgrading " + info.name + " " + old_version + " -> " + info.version)
        else
            // Same version — skip or reinstall with --force
            if not opts.force
                color.print_warning(info.name + " " + info.version + " is already installed (use --force to reinstall)")
                cleanup_extract_dir(extract_dir)
                return true
            end if
            color.print_info("Reinstalling " + info.name + "...")
        end if
    end if

    let install_root = get_root(cfg)
    // Resolve script execution context; abort early if confinement is required but impossible.
    // Defense-in-depth: main.reef already bars non-root for all non-query commands, so this abort
    // is currently unreachable via the CLI. Kept so confinement fails safely if that global gate is
    // ever relaxed.
    if package.script_wants_chroot(install_root, config.get_chroot_scripts(cfg)) and not priv.is_root()
        color.print_error("--root " + install_root + " runs maintainer scripts confined to the target via chroot, which requires root privileges.")
        color.print_error("Re-run as root, or pass --no-chroot-scripts to run them on the host (unconfined).")
        cleanup_extract_dir(extract_dir)
        return false
    end if
    let script_ctx = package.resolve_script_ctx(install_root, config.get_chroot_scripts(cfg), priv.is_root())

    if is_upgrade
        // Upgrade flow: pre-upgrade → remove old files → install new files → post-upgrade

        // Run pre-upgrade from stored scripts (old package)
        let old_scripts = database.get_scripts_dir(info.name)
        if database.has_stored_scripts(info.name)
            color.print_info("Running pre-upgrade script...")
            if not package.run_stored_pre_upgrade(script_ctx, old_scripts, old_version, info.version)
                color.print_error("Pre-upgrade script failed, aborting")
                cleanup_extract_dir(extract_dir)
                return false
            end if
        end if

        // Remove old files
        color.print_info("Removing old version files...")
        mut old_files: [string] = new [string](4096)
        let old_file_count = get_old_files(info.name, old_files, 4096, root_path)
        if old_file_count > 0
            package.remove_files(old_files, old_file_count, install_root)
        end if

        // Load old manifest for config file checksum protection
        mut old_manifest_entries: [mtree.ManifestEntry] = new [mtree.ManifestEntry](8192)
        let old_manifest_count = load_old_manifest(info.name, root_path, old_manifest_entries, 8192)

        // Install new files (with upgrade config protection)
        color.print_info("Installing files...")
        if old_manifest_count > 0
            if not package.install_files_upgrade(extract_dir, install_root, old_manifest_entries, old_manifest_count)
                color.print_error("Failed to install files")
                cleanup_extract_dir(extract_dir)
                return false
            end if
        else
            if not package.install_files(extract_dir, install_root)
                color.print_error("Failed to install files")
                cleanup_extract_dir(extract_dir)
                return false
            end if
        end if

        // Run post-upgrade from new package's scripts
        if package.has_scripts(extract_dir)
            color.print_info("Running post-upgrade script...")
            if not package.run_post_upgrade(script_ctx, extract_dir, old_version, info.version)
                color.print_warning("Post-upgrade script failed")
            end if
        end if
    else
        // Fresh install flow

        // Run pre-install script (abort on failure)
        if package.has_scripts(extract_dir)
            color.print_info("Running pre-install script...")
            if not package.run_pre_install(script_ctx, extract_dir, info.version)
                color.print_error("Pre-install script failed")
                cleanup_extract_dir(extract_dir)
                return false
            end if
        end if

        // Install files to target root
        color.print_info("Installing files...")
        if not package.install_files(extract_dir, install_root)
            color.print_error("Failed to install files")
            cleanup_extract_dir(extract_dir)
            return false
        end if

        // Run post-install script (warn on failure, don't abort)
        if package.has_scripts(extract_dir)
            color.print_info("Running post-install script...")
            if not package.run_post_install(script_ctx, extract_dir, info.version)
                color.print_warning("Post-install script failed")
            end if
        end if
    end if

    // Register in database (use rooted version if root is set)
    color.print_info("Registering package...")
    if not register_installed_fast_rooted(info, extract_dir, root_path)
        color.print_error("Failed to register package in database")
        // Files are installed but not registered - warn but don't fail
    end if

    // Store scripts for later use (removal)
    if package.has_scripts(extract_dir)
        if not store_scripts_rooted(info.name, extract_dir, root_path)
            color.print_warning("Failed to store scripts for removal")
        end if
    end if

    // Store config files list for upgrade handling
    if not store_config_files_rooted(info.name, extract_dir, root_path)
        color.print_warning("Failed to store config files list")
    end if

    // Update package database indexes
    if not pkgdb.rebuild_indexes_rooted(root_path)
        color.print_warning("Failed to update package indexes")
    end if

    // Cleanup
    cleanup_extract_dir(extract_dir)

    color.print_success("Installed " + info.name + " " + info.version)
    return true
end install_package

// Check if package is installed, using rooted check if root is set
fn check_installed(name: string, root_path: string): bool
    if str.length(root_path) > 0
        return database.is_installed_rooted(name, root_path)
    end if
    return database.is_installed(name)
end check_installed

// Register package using rooted version if root is set
fn register_installed_fast_rooted(info: types.PackageInfo, extract_dir: string, root_path: string): bool
    mut files: [string] = new [string](1)
    mut pkg = new_installed_pkg(info, files, 0)

    if str.length(root_path) > 0
        return database.register_from_extract_dir_rooted(pkg, extract_dir, root_path)
    end if
    return database.register_from_extract_dir(pkg, extract_dir)
end register_installed_fast_rooted

// Store scripts using rooted version if root is set
fn store_scripts_rooted(name: string, extract_dir: string, root_path: string): bool
    if str.length(root_path) > 0
        return database.store_scripts_rooted(name, extract_dir, root_path)
    end if
    return database.store_scripts(name, extract_dir)
end store_scripts_rooted

// Store config files using rooted version if root is set
fn store_config_files_rooted(name: string, extract_dir: string, root_path: string): bool
    if str.length(root_path) > 0
        return database.store_config_files_rooted(name, extract_dir, root_path)
    end if
    return database.store_config_files(name, extract_dir)
end store_config_files_rooted

// Find package file - either direct path, repository, or search in packages directory
fn resolve_package_path(pkg_arg: string, cfg: config.Config): string
    // If it's a file path that exists, use it directly
    if file.fileExists(pkg_arg)
        return pkg_arg
    end if

    // Search in local packages cache first
    let packages_dir = config.get_packages_dir(cfg)

    // Find all matching packages and select highest version
    let entries = res.unwrap_or(dir.list_dir(packages_dir), new [string](0))
    let entry_count = entries.length()

    // Collect all matching package files
    mut best_file = ""
    mut best_version = ""
    mut best_release = 0

    mut i = 0
    while i < entry_count
        let entry = entries[i]
        // Check if entry starts with package name and has correct suffix
        if str.starts_with(entry, pkg_arg + "-") and str.ends_with(entry, ".pkg.tar.xz")
            // Extract version from filename
            let entry_version = ver.extract_version_from_filename(entry, pkg_arg)
            let entry_release = ver.extract_release_from_filename(entry)

            // Compare with current best
            if str.length(best_file) == 0
                // First match
                best_file = entry
                best_version = entry_version
                best_release = entry_release
            else
                // Compare versions
                let cmp = ver.compare_versions(entry_version, best_version)
                if cmp > 0
                    // Entry has higher version
                    best_file = entry
                    best_version = entry_version
                    best_release = entry_release
                elif cmp == 0 and entry_release > best_release
                    // Same version but higher release
                    best_file = entry
                    best_version = entry_version
                    best_release = entry_release
                end if
            end if
        end if
        i = i + 1
    end while

    // Return the best matching package
    if str.length(best_file) > 0
        return path.join_path(packages_dir, best_file)
    end if

    // Also try with .pkg.tar.xz appended
    let direct_path = path.join_path(packages_dir, pkg_arg + ".pkg.tar.xz")
    if file.fileExists(direct_path)
        return direct_path
    end if

    // Try to build from source if configured
    if config.get_fallback_to_source(cfg)
        let port_result = port.find(pkg_arg)
        if port_result.success
            color.print_info("No binary package found for " + pkg_arg + ", building from source...")
            let build_cmd = "coral build -y " + pkg_arg
            let build_pid = process.process_spawn_shell(build_cmd)
            if build_pid > 0
                let build_exit = process.process_wait(build_pid)
                if build_exit == 0
                    // Build succeeded, look for the package it produced
                    let p = port_result.port
                    let built_pkg = p.info.name + "-" + p.info.version + "-" + int_to_str(p.info.release) + ".pkg.tar.xz"
                    let built_path = path.join_path(packages_dir, built_pkg)
                    if file.fileExists(built_path)
                        return built_path
                    end if
                end if
            end if
            color.print_warning("Source build failed for " + pkg_arg + ", trying repositories...")
        end if
    end if

    // Try to find in repositories and download
    let remote_result = repository.find_remote_package(pkg_arg)
    if remote_result.success
        let remote_pkg = remote_result.pkg
        color.print_info("Found " + pkg_arg + " " + remote_pkg.version + " in repository: " + remote_pkg.repo_name)

        // Download the package
        let downloaded_path = repository.download_package(remote_pkg)
        if str.length(downloaded_path) > 0
            // Verify checksum if available
            if str.length(remote_pkg.sha256) > 0
                color.print_info("Verifying checksum...")
                if not checksum.verify_checksum(downloaded_path, remote_pkg.sha256)
                    color.print_error("Checksum verification failed!")
                    return ""
                end if
                color.print_success("Checksum verified")
            end if

            // Verify signature if required or available
            let require_signed = config.get_require_signed_packages(cfg)
            if require_signed or str.length(remote_pkg.signature) > 0
                let sig_path = downloaded_path + ".sig"

                // Download signature file if we don't have it
                if not file.fileExists(sig_path) and str.length(remote_pkg.signature) > 0
                    color.print_info("Downloading signature...")
                    let sig_url = get_sig_url(remote_pkg)
                    if not download_signature(sig_url, sig_path)
                        if require_signed
                            color.print_error("Failed to download package signature")
                            return ""
                        else
                            color.print_warning("Could not download signature, skipping verification")
                        end if
                    end if
                end if

                // Verify signature if we have it
                if file.fileExists(sig_path)
                    color.print_info("Verifying signature...")
                    let verify_result = signing.verify_package(downloaded_path, sig_path)
                    if verify_result.success and verify_result.valid
                        color.print_success("Signature verified (key: " + verify_result.keyid + ")")
                    else
                        if require_signed
                            color.print_error("Signature verification failed: " + verify_result.error)
                            return ""
                        else
                            color.print_warning("Signature verification failed: " + verify_result.error)
                        end if
                    end if
                elif require_signed
                    color.print_error("Package signature required but not available")
                    return ""
                end if
            end if

            return downloaded_path
        end if
    end if

    return ""
end resolve_package_path

// Create a temporary extraction directory
fn create_extract_dir(cfg: config.Config): string
    let work_dir = config.get_work_dir(cfg)
    let pid = process.getpid()
    let extract_dir = path.join_path(work_dir, "install_" + int_to_str(pid))

    if dir.dir_exists(extract_dir)
        // Clean existing
        let cmd = "rm -rf \"" + extract_dir + "\""
        let rm_pid = process.process_spawn_shell(cmd)
        if rm_pid > 0
            process.process_wait(rm_pid)
        end if
    end if

    if not res.is_ok(dir.create_dir_all(extract_dir))
        return ""
    end if

    return extract_dir
end create_extract_dir

// Cleanup extraction directory
fn cleanup_extract_dir(dir_path: string): bool
    if str.length(dir_path) == 0
        return true
    end if

    let cmd = "rm -rf \"" + dir_path + "\""
    let pid = process.process_spawn_shell(cmd)
    if pid < 0
        return false
    end if
    process.process_wait(pid)
    return true
end cleanup_extract_dir

// Get installation root from config (can be overridden with --root)
fn get_root(cfg: config.Config): string
    let root = config.get_root(cfg)
    if str.length(root) == 0
        return "/"
    end if
    return root
end get_root

// Check for file conflicts with other installed packages
// TODO: Implement efficient conflict detection using a file database
fn check_conflicts(files: [string], file_count: int, pkg_name: string): bool
    // Skip conflict checking for performance - file overwrites are handled
    // by the manifest-driven installer and dependencies are managed separately
    return true
end check_conflicts

// Helper to create InstalledPackage
fn new_installed_pkg(info: types.PackageInfo, files: [string], file_count: int): types.InstalledPackage
    mut pkg = types.new_installed_package()
    pkg.info = info
    pkg.install_date = get_date_string()
    pkg.install_reason = "explicit"
    pkg.files = files
    pkg.files_count = file_count
    return pkg
end new_installed_pkg

// Get current date as string (simplified)
fn get_date_string(): string
    // Use date command for simplicity
    // TODO: Use proper time functions when available
    return "2025-01-24"
end get_date_string

// Get installed package info (root-aware)
fn get_old_installed(name: string, root_path: string): types.InstalledPackage
    if str.length(root_path) > 0
        return database.get_installed_rooted(name, root_path)
    end if
    return database.get_installed(name)
end get_old_installed

// Get old file list for a package (root-aware)
fn get_old_files(name: string, files: [string], max_count: int, root_path: string): int
    if str.length(root_path) > 0
        return database.get_files_rooted(name, files, max_count, root_path)
    end if
    return database.get_files(name, files, max_count)
end get_old_files

// Load old manifest from database for upgrade config protection
fn load_old_manifest(name: string, root_path: string, entries: [mtree.ManifestEntry], max_count: int): int
    let manifest_path = database.get_manifest_path(name)
    if not file.fileExists(manifest_path)
        return 0
    end if

    let content = res.unwrap_or(file.readFile(manifest_path), "")
    if str.length(content) == 0
        return 0
    end if

    return mtree.parse_manifest(content, entries, max_count)
end load_old_manifest

// Helper: convert int to string
fn int_to_str(n: int): string
    if n == 0
        return "0"
    end if

    mut negative = false
    mut value = n
    if n < 0
        negative = true
        value = 0 - n
    end if

    mut result = ""
    while value > 0
        let digit = value % 10
        result = str.concat(str.substring("0123456789", digit, 1), result)
        value = value / 10
    end while

    if negative
        result = str.concat("-", result)
    end if

    return result
end int_to_str

// Build signature URL from remote package info
fn get_sig_url(pkg: repository.RemotePackage): string
    mut base_url = pkg.repo_url
    if not str.ends_with(base_url, "/")
        base_url = base_url + "/"
    end if

    // If signature field contains a full URL, use it
    if str.starts_with(pkg.signature, "http")
        return pkg.signature
    end if

    // Otherwise construct from filename
    return base_url + "packages/" + pkg.filename + ".sig"
end get_sig_url

// Download a signature file
fn download_signature(url: string, dest: string): bool
    return uhttp.download(url, dest)
end download_signature

end module
/******************************************************************************
               __               ____                __
              / /   ___  ____ _/ __/_____________ _/ /__
             / /   / _ \/ __ `/ /_/ ___/ ___/ __ `/ / _ \
            / /___/  __/ /_/ / __(__  ) /__/ /_/ / /  __/
           /_____/\___/\__,_/_/ /____/\___/\__,_/_/\___/

   (C)opyright 2025, Leafscale, LLC -  https://www.leafscale.com

   Project: Zygaena
  Filename: key.reef
   Authors: Chris Tusa <chris.tusa@leafscale.com>
   License: <see LICENSE file included with this source code>
Description: Key command - manage signing keys

******************************************************************************/

module commands.key

import sys.args
import sys.process
import io.file
import io.dir
import core.str
import core.signing
import util.color
import exitcodes as ec
import core.result as res

export
    fn execute(): int
end export

fn execute(): int
    let argc = args.count()

    if argc < 3
        print_usage()
        return ec.EXIT_USAGE()
    end if

    let subcommand = args.get(2)

    if subcommand == "list"
        list_keys()
        return ec.EXIT_SUCCESS()
    elif subcommand == "generate"
        if argc < 4
            color.print_error("Missing key name")
            println("Usage: coral key generate <name>")
            return ec.EXIT_USAGE()
        end if
        generate_key(args.get(3))
        return ec.EXIT_SUCCESS()
    elif subcommand == "import"
        if argc < 4
            color.print_error("Missing key file")
            println("Usage: coral key import <file> [name]")
            return ec.EXIT_USAGE()
        end if
        let key_file = args.get(3)
        mut name = ""
        if argc >= 5
            name = args.get(4)
        end if
        import_key(key_file, name)
        return ec.EXIT_SUCCESS()
    elif subcommand == "export"
        if argc < 4
            color.print_error("Missing key name")
            println("Usage: coral key export <name>")
            return ec.EXIT_USAGE()
        end if
        export_key(args.get(3))
        return ec.EXIT_SUCCESS()
    elif subcommand == "delete"
        if argc < 4
            color.print_error("Missing key name")
            println("Usage: coral key delete <name>")
            return ec.EXIT_USAGE()
        end if
        delete_key(args.get(3))
        return ec.EXIT_SUCCESS()
    elif subcommand == "init"
        init_keyring()
        return ec.EXIT_SUCCESS()
    elif subcommand == "trust"
        if argc < 4
            color.print_error("Missing key name")
            println("Usage: coral key trust <name>")
            return ec.EXIT_USAGE()
        end if
        trust_key(args.get(3))
        return ec.EXIT_SUCCESS()
    elif subcommand == "revoke"
        if argc < 4
            color.print_error("Missing key name")
            println("Usage: coral key revoke <name>")
            return ec.EXIT_USAGE()
        end if
        revoke_key(args.get(3))
        return ec.EXIT_SUCCESS()
    else
        color.print_error("Unknown subcommand: " + subcommand)
        print_usage()
        return ec.EXIT_USAGE()
    end if
end execute

proc list_keys()
    color.print_action("Signing keys:")
    println("")

    mut keys: [signing.KeyPair] = new [signing.KeyPair](64)
    let count = signing.list_keys(keys, 64)

    if count == 0
        color.print_info("No keys found")
        println("")
        color.print_info("Generate a key with: coral key generate <name>")
        return
    end if

    mut i = 0
    while i < count
        let key = keys[i]
        print("  ")
        print(key.name)
        if str.length(key.private_key) > 0
            print(" [private+public]")
        else
            print(" [public only]")
        end if
        if key.trusted
            print(" [trusted]")
        end if
        println("")
        i = i + 1
    end while

    println("")
    color.print_info("Total: " + int_to_str(count) + " key(s)")
end list_keys

proc generate_key(name: string)
    color.print_action("Generating Ed25519 keypair: " + name)

    let result = signing.generate_keypair(name)

    if result.success
        color.print_success("Keypair generated successfully")
        println("")
        color.print_info("Private key: " + signing.get_keyring_dir() + "/" + name + ".key")
        color.print_info("Public key:  " + signing.get_keyring_dir() + "/" + name + ".pub")
    else
        color.print_error(result.error)
    end if
end generate_key

proc import_key(key_file: string, name: string)
    if not file.fileExists(key_file)
        color.print_error("Key file not found: " + key_file)
        return
    end if

    // Determine name from filename if not provided
    mut key_name = name
    if str.length(key_name) == 0
        key_name = extract_name(key_file)
    end if

    if str.length(key_name) == 0
        color.print_error("Could not determine key name. Please specify one.")
        return
    end if

    color.print_action("Importing key: " + key_name)

    let key_data = res.unwrap_or(file.readFile(key_file), "")
    let result = signing.import_key(key_data, key_name)

    if result.success
        color.print_success("Key imported successfully")
    else
        color.print_error(result.error)
    end if
end import_key

proc export_key(name: string)
    let keyring = signing.get_keyring_dir()
    let pub_path = keyring + "/" + name + ".pub"

    if not file.fileExists(pub_path)
        color.print_error("Key not found: " + name)
        return
    end if

    color.print_action("Public key for " + name + ":")
    println("")

    let key_data = res.unwrap_or(file.readFile(pub_path), "")
    println(key_data)
end export_key

proc delete_key(name: string)
    let keyring = signing.get_keyring_dir()

    // Check if key exists
    let pub_path = keyring + "/" + name + ".pub"
    let priv_path = keyring + "/" + name + ".key"

    if not file.fileExists(pub_path) and not file.fileExists(priv_path)
        color.print_error("Key not found: " + name)
        return
    end if

    // Ask for confirmation if private key exists
    if file.fileExists(priv_path)
        color.print_warning("This will delete the private key! Are you sure?")
        color.print_info("Use --force to confirm deletion")

        if not args.has_flag("force")
            return
        end if
    end if

    // Delete files
    if file.fileExists(pub_path)
        let cmd1 = "rm -f \"" + pub_path + "\""
        let pid1 = process.process_spawn_shell(cmd1)
        if pid1 > 0
            process.process_wait(pid1)
        end if
    end if

    if file.fileExists(priv_path)
        let cmd2 = "rm -f \"" + priv_path + "\""
        let pid2 = process.process_spawn_shell(cmd2)
        if pid2 > 0
            process.process_wait(pid2)
        end if
    end if

    color.print_success("Deleted key: " + name)
end delete_key

fn extract_name(path: string): string
    // Extract filename without extension
    let len = str.length(path)
    if len == 0
        return ""
    end if

    // Find last slash
    mut start = 0
    mut i = 0
    while i < len
        if path[i] == '/'
            start = i + 1
        end if
        i = i + 1
    end while

    // Find last dot
    mut end_pos = len
    i = len - 1
    while i >= start
        if path[i] == '.'
            end_pos = i
        end if
        i = i - 1
    end while

    if end_pos <= start
        return str.substring(path, start, len - start)
    end if

    return str.substring(path, start, end_pos - start)
end extract_name

// Initialize the keyring directory structure
proc init_keyring()
    color.print_action("Initializing keyring...")

    let keyring = signing.get_keyring_dir()
    let trusted_keys_dir = "/var/lib/coral/trusted-keys"

    // Create keyring directory
    if not dir.dir_exists(keyring)
        if not res.is_ok(dir.create_dir_all(keyring))
            color.print_error("Failed to create keyring directory: " + keyring)
            return
        end if
        color.print_info("Created: " + keyring)
    else
        color.print_info("Keyring already exists: " + keyring)
    end if

    // Create trusted-keys directory
    if not dir.dir_exists(trusted_keys_dir)
        if not res.is_ok(dir.create_dir_all(trusted_keys_dir))
            color.print_error("Failed to create trusted-keys directory")
            return
        end if
        color.print_info("Created: " + trusted_keys_dir)
    else
        color.print_info("Trusted keys directory already exists: " + trusted_keys_dir)
    end if

    // Set permissions (keyring should be root-only for private keys)
    let cmd = "chmod 700 \"" + keyring + "\""
    let pid = process.process_spawn_shell(cmd)
    if pid > 0
        process.process_wait(pid)
    end if

    color.print_success("Keyring initialized")
    color.print_info("Generate keys with: coral key generate <name>")
end init_keyring

// Add a key to the trusted keys list
proc trust_key(name: string)
    let keyring = signing.get_keyring_dir()
    let trusted_dir = "/var/lib/coral/trusted-keys"
    let pub_path = keyring + "/" + name + ".pub"

    // Check if key exists
    if not file.fileExists(pub_path)
        color.print_error("Key not found: " + name)
        color.print_info("Import or generate the key first")
        return
    end if

    // Ensure trusted-keys directory exists
    if not dir.dir_exists(trusted_dir)
        if not res.is_ok(dir.create_dir_all(trusted_dir))
            color.print_error("Failed to create trusted-keys directory")
            return
        end if
    end if

    // Check if already trusted
    let trusted_path = trusted_dir + "/" + name + ".pub"
    if file.fileExists(trusted_path)
        color.print_warning("Key already trusted: " + name)
        return
    end if

    // Copy public key to trusted directory
    let cmd = "cp \"" + pub_path + "\" \"" + trusted_path + "\""
    let pid = process.process_spawn_shell(cmd)
    if pid < 0
        color.print_error("Failed to copy key")
        return
    end if

    let exit_code = process.process_wait(pid)
    if exit_code != 0
        color.print_error("Failed to trust key")
        return
    end if

    color.print_success("Trusted key: " + name)
    color.print_info("Packages signed with this key will now be accepted")
end trust_key

// Remove a key from the trusted keys list
proc revoke_key(name: string)
    let trusted_dir = "/var/lib/coral/trusted-keys"
    let trusted_path = trusted_dir + "/" + name + ".pub"

    // Check if key is trusted
    if not file.fileExists(trusted_path)
        color.print_error("Key is not in trusted list: " + name)
        return
    end if

    // Confirm revocation
    if not args.has_flag("force") and not args.has_flag("yes")
        color.print_warning("This will revoke trust for key: " + name)
        color.print_info("Use --force or -y to confirm")
        return
    end if

    // Remove from trusted keys
    let cmd = "rm -f \"" + trusted_path + "\""
    let pid = process.process_spawn_shell(cmd)
    if pid < 0
        color.print_error("Failed to revoke key")
        return
    end if

    let exit_code = process.process_wait(pid)
    if exit_code != 0
        color.print_error("Failed to remove key from trusted list")
        return
    end if

    color.print_success("Revoked trust for key: " + name)
    color.print_info("Packages signed with this key will no longer be accepted")
end revoke_key

// List trusted keys
proc list_trusted_keys()
    let trusted_dir = "/var/lib/coral/trusted-keys"

    if not dir.dir_exists(trusted_dir)
        color.print_info("No trusted keys (directory does not exist)")
        return
    end if

    let entries = res.unwrap_or(dir.list_dir(trusted_dir), new [string](0))
    let count = entries.length()

    if count == 0
        color.print_info("No trusted keys")
        return
    end if

    println("")
    color.print_action("Trusted keys:")
    mut i = 0
    while i < count
        let entry = entries[i]
        if str.ends_with(entry, ".pub")
            let name = str.substring(entry, 0, str.length(entry) - 4)
            println("  " + name)
        end if
        i = i + 1
    end while
end list_trusted_keys

proc print_usage()
    println("Usage: coral key <command> [options]")
    println("")
    println("Manage signing keys for package verification.")
    println("")
    println("Commands:")
    println("  list                List all keys in keyring")
    println("  generate <name>     Generate a new Ed25519 keypair")
    println("  import <file> [name] Import a public key")
    println("  export <name>       Export a public key")
    println("  delete <name>       Delete a key (use --force for private keys)")
    println("")
    println("Trust management:")
    println("  init                Initialize keyring directories")
    println("  trust <name>        Add key to trusted list")
    println("  revoke <name>       Remove key from trusted list")
    println("")
    println("Examples:")
    println("  coral key init")
    println("  coral key generate maintainer")
    println("  coral key import repo.pub community")
    println("  coral key trust community")
end print_usage

// Helper: convert int to string
fn int_to_str(n: int): string
    if n == 0
        return "0"
    end if

    mut negative = false
    mut value = n
    if n < 0
        negative = true
        value = 0 - n
    end if

    mut result = ""
    while value > 0
        let digit = value % 10
        result = str.concat(str.substring("0123456789", digit, 1), result)
        value = value / 10
    end while

    if negative
        result = str.concat("-", result)
    end if

    return result
end int_to_str

end module
/******************************************************************************
               __               ____                __
              / /   ___  ____ _/ __/_____________ _/ /__
             / /   / _ \/ __ `/ /_/ ___/ ___/ __ `/ / _ \
            / /___/  __/ /_/ / __(__  ) /__/ /_/ / /  __/
           /_____/\___/\__,_/_/ /____/\___/\__,_/_/\___/

   (C)opyright 2025, Leafscale, LLC -  https://www.leafscale.com

   Project: Zygaena
  Filename: list.reef
   Authors: Chris Tusa <chris.tusa@leafscale.com>
   License: <see LICENSE file included with this source code>
Description: List installed or available packages

******************************************************************************/

module commands.list

import sys.args
import core.str
import core.config
import core.database
import core.port
import core.portindex
import types
import util.color
import exitcodes as ec

export
    fn execute(opts: types.GlobalOptions): int
end export

fn execute(opts: types.GlobalOptions): int
    let argc = args.count()

    // Load configuration and apply command-line overrides
    let base_cfg = config.load()
    let cfg = config.apply_overrides(base_cfg, opts.root, opts.prefix, opts.no_chroot)
    let root_path = config.get_root(cfg)

    // Show root if set (verbose mode)
    if opts.verbose and str.length(root_path) > 0
        color.print_info("Using root: " + root_path)
    end if

    // Check for --available flag
    if args.has_flag("available") or args.has_flag("a")
        list_available()
        return ec.EXIT_SUCCESS()
    end if

    // Default: list installed packages
    list_installed(root_path)
    return ec.EXIT_SUCCESS()
end execute

proc list_installed(root_path: string)
    mut packages: [string] = new [string](512)
    let pkg_count = list_installed_pkgs(packages, 512, root_path)

    if pkg_count == 0
        color.print_info("No packages installed")
        return
    end if

    color.print_action("Installed packages:")
    println("")

    mut i = 0
    while i < pkg_count
        let pkg_name = packages[i]
        let pkg = get_installed_pkg(pkg_name, root_path)

        // Format: name version
        print("  ")
        print(pkg.info.name)
        print(" ")
        print(pkg.info.version)
        print("-")
        println(int_to_str(pkg.info.release))

        i = i + 1
    end while

    println("")
    color.print_info("Total: " + int_to_str(pkg_count) + " packages")
end list_installed

// Helper functions for rooted operations
fn list_installed_pkgs(names: [string], max_count: int, root_path: string): int
    if str.length(root_path) > 0
        return database.list_installed_rooted(names, max_count, root_path)
    end if
    return database.list_installed(names, max_count)
end list_installed_pkgs

fn get_installed_pkg(name: string, root_path: string): types.InstalledPackage
    if str.length(root_path) > 0
        return database.get_installed_rooted(name, root_path)
    end if
    return database.get_installed(name)
end get_installed_pkg

proc list_available()
    color.print_action("Available ports:")
    println("")

    mut total = 0

    // Try ports index first (fast path)
    if portindex.port_index_exists()
        mut entries: [portindex.PortIndexEntry] = new [portindex.PortIndexEntry](4096)
        let entry_count = portindex.list_all_ports(entries, 4096)

        // Group by category for display
        mut current_cat = ""
        mut i = 0
        while i < entry_count
            let entry = entries[i]
            if not str.equals(entry.category, current_cat)
                if str.length(current_cat) > 0
                    println("")
                end if
                current_cat = entry.category
                color.print_info(current_cat + "/")
            end if

            print("  ")
            print(entry.name)
            print(" ")
            print(entry.version)
            print(" - ")
            println(entry.description)
            total = total + 1

            i = i + 1
        end while
    else
        // Fall back to filesystem scan
        mut cats: [string] = new [string](32)
        let cat_count = port.get_categories(cats, 32)

        mut i = 0
        while i < cat_count
            let category = cats[i]
            mut ports: [string] = new [string](256)
            let port_count = port.list_category(category, ports, 256)

            if port_count > 0
                color.print_info(category + "/")
                mut j = 0
                while j < port_count
                    let port_name = ports[j]
                    let result = port.find(port_name)
                    if result.success
                        let p = result.port
                        print("  ")
                        print(p.info.name)
                        print(" ")
                        print(p.info.version)
                        print(" - ")
                        println(p.info.description)
                    end if
                    j = j + 1
                    total = total + 1
                end while
                println("")
            end if

            i = i + 1
        end while
    end if

    println("")
    color.print_info("Total: " + int_to_str(total) + " ports")
end list_available

// Helper: convert int to string
fn int_to_str(n: int): string
    if n == 0
        return "0"
    end if

    mut negative = false
    mut value = n
    if n < 0
        negative = true
        value = 0 - n
    end if

    mut result = ""
    while value > 0
        let digit = value % 10
        result = str.concat(str.substring("0123456789", digit, 1), result)
        value = value / 10
    end while

    if negative
        result = str.concat("-", result)
    end if

    return result
end int_to_str

end module
/******************************************************************************
               __               ____                __
              / /   ___  ____ _/ __/_____________ _/ /__
             / /   / _ \/ __ `/ /_/ ___/ ___/ __ `/ / _ \
            / /___/  __/ /_/ / __(__  ) /__/ /_/ / /  __/
           /_____/\___/\__,_/_/ /____/\___/\__,_/_/\___/

   (C)opyright 2025, Leafscale, LLC -  https://www.leafscale.com

   Project: Zygaena
  Filename: outdated.reef
   Authors: Chris Tusa <chris.tusa@leafscale.com>
   License: <see LICENSE file included with this source code>
Description: Outdated command - show packages with available updates

******************************************************************************/

module commands.outdated

import sys.args
import core.str
import core.database
import core.port
import types
import util.color
import exitcodes as ec

export
    fn execute(): int
end export

fn execute(): int
    color.print_action("Checking for available updates...")
    println("")

    // Get list of installed packages
    mut installed: [string] = new [string](512)
    let installed_count = database.list_installed(installed, 512)

    if installed_count == 0
        color.print_info("No packages installed")
        return ec.EXIT_SUCCESS()
    end if

    // Check each package for updates
    mut outdated_count = 0
    mut i = 0
    while i < installed_count
        let pkg_name = installed[i]
        let installed_pkg = database.get_installed(pkg_name)

        // Find port
        let port_result = port.find(pkg_name)

        if port_result.success
            let p = port_result.port

            // Compare versions
            let cmp = compare_versions(installed_pkg.info.version, p.info.version)

            if cmp < 0
                // Outdated
                if outdated_count == 0
                    color.print_info("Outdated packages:")
                    println("")
                end if

                print("  ")
                print(pkg_name)
                print(" ")
                print(installed_pkg.info.version)
                print("-")
                print(int_to_str(installed_pkg.info.release))
                print(" -> ")
                print(p.info.version)
                print("-")
                println(int_to_str(p.info.release))

                outdated_count = outdated_count + 1
            end if
        end if

        i = i + 1
    end while

    if outdated_count == 0
        color.print_success("All packages are up to date")
        // Return special code for scripting - no updates available
        if args.has_flag("check")
            return ec.EXIT_NO_UPDATES()
        end if
        return ec.EXIT_SUCCESS()
    else
        println("")
        color.print_info(int_to_str(outdated_count) + " package(s) can be upgraded")
        println("")
        color.print_info("Run 'coral upgrade' to upgrade all packages")
        color.print_info("Run 'coral upgrade <package>' to upgrade specific packages")
        // Return special code for scripting - updates available
        if args.has_flag("check")
            return ec.EXIT_UPDATE_AVAILABLE()
        end if
        return ec.EXIT_SUCCESS()
    end if
end execute

// Compare two version strings
// Returns: -1 if v1 < v2, 0 if equal, 1 if v1 > v2
fn compare_versions(v1: string, v2: string): int
    // Split versions into parts
    mut parts1: [string] = new [string](10)
    mut parts2: [string] = new [string](10)

    let count1 = str.split(v1, '.', parts1, 10)
    let count2 = str.split(v2, '.', parts2, 10)

    // Compare each part
    mut i = 0
    let max_parts = max_int(count1, count2)

    while i < max_parts
        mut n1 = 0
        mut n2 = 0

        if i < count1
            n1 = parse_int(parts1[i])
        end if

        if i < count2
            n2 = parse_int(parts2[i])
        end if

        if n1 < n2
            return 0 - 1
        elif n1 > n2
            return 1
        end if

        i = i + 1
    end while

    return 0
end compare_versions

fn max_int(a: int, b: int): int
    if a > b
        return a
    end if
    return b
end max_int

// Parse integer from string
fn parse_int(s: string): int
    let len = str.length(s)
    if len == 0
        return 0
    end if

    mut result = 0
    mut i = 0

    while i < len
        let c = s[i]
        if c >= '0' and c <= '9'
            result = result * 10 + (c - '0')
        else
            // Stop at non-digit
            return result
        end if
        i = i + 1
    end while

    return result
end parse_int

// Helper: convert int to string
fn int_to_str(n: int): string
    if n == 0
        return "0"
    end if

    mut negative = false
    mut value = n
    if n < 0
        negative = true
        value = 0 - n
    end if

    mut result = ""
    while value > 0
        let digit = value % 10
        result = str.concat(str.substring("0123456789", digit, 1), result)
        value = value / 10
    end while

    if negative
        result = str.concat("-", result)
    end if

    return result
end int_to_str

end module
/******************************************************************************
               __               ____                __
              / /   ___  ____ _/ __/_____________ _/ /__
             / /   / _ \/ __ `/ /_/ ___/ ___/ __ `/ / _ \
            / /___/  __/ /_/ / __(__  ) /__/ /_/ / /  __/
           /_____/\___/\__,_/_/ /____/\___/\__,_/_/\___/

   (C)opyright 2025, Leafscale, LLC -  https://www.leafscale.com

   Project: Zygaena
  Filename: owner.reef
   Authors: Chris Tusa <chris.tusa@leafscale.com>
   License: <see LICENSE file included with this source code>
Description: Owner command - find which package owns a file

******************************************************************************/

module commands.owner

import sys.args
import core.str
import core.config
import core.database
import core.pkgdb
import types
import util.color
import exitcodes as ec

export
    fn execute(opts: types.GlobalOptions): int
end export

fn execute(opts: types.GlobalOptions): int
    let argc = args.count()

    // File path should be at cmd_index + 1
    if argc <= opts.cmd_index + 1
        print_usage()
        return ec.EXIT_USAGE()
    end if

    // Load configuration and apply command-line overrides
    let base_cfg = config.load()
    let cfg = config.apply_overrides(base_cfg, opts.root, opts.prefix, opts.no_chroot)
    let root_path = config.get_root(cfg)

    // Show root if set (verbose mode)
    if opts.verbose and str.length(root_path) > 0
        color.print_info("Using root: " + root_path)
    end if

    let file_path = args.get(opts.cmd_index + 1)

    // Find owner (use rooted version if root is set)
    let owner = find_owner(file_path, root_path)

    if str.length(owner) == 0
        color.print_error("No package owns: " + file_path)
        return ec.EXIT_PKG_NOT_FOUND()
    end if

    // Get package info (use rooted version if root is set)
    let pkg = get_installed_pkg(owner, root_path)

    color.print_action("File: " + file_path)
    println("")
    println("Owned by: " + owner + " " + pkg.info.version)
    return ec.EXIT_SUCCESS()
end execute

// Helper functions for rooted operations
// Uses pkgdb for fast indexed lookup with fallback to database scan
fn find_owner(file_path: string, root_path: string): string
    return pkgdb.find_file_owner_rooted(file_path, root_path)
end find_owner

fn get_installed_pkg(name: string, root_path: string): types.InstalledPackage
    if str.length(root_path) > 0
        return database.get_installed_rooted(name, root_path)
    end if
    return database.get_installed(name)
end get_installed_pkg

proc print_usage()
    println("Usage: coral owner <file>")
    println("")
    println("Find which package owns a given file.")
    println("")
    println("Arguments:")
    println("  <file>    Path to the file to look up")
    println("")
    println("Examples:")
    println("  coral owner /usr/bin/vim")
    println("  coral owner /usr/bin/hello")
end print_usage

end module
/******************************************************************************
               __               ____                __
              / /   ___  ____ _/ __/_____________ _/ /__
             / /   / _ \/ __ `/ /_/ ___/ ___/ __ `/ / _ \
            / /___/  __/ /_/ / __(__  ) /__/ /_/ / /  __/
           /_____/\___/\__,_/_/ /____/\___/\__,_/_/\___/

   (C)opyright 2025, Leafscale, LLC -  https://www.leafscale.com

   Project: Zygaena
  Filename: ports.reef
   Authors: Chris Tusa <chris.tusa@leafscale.com>
   License: <see LICENSE file included with this source code>
Description: Ports command - port scaffolding and cache management

******************************************************************************/

module commands.ports

import sys.args
import io.file
import io.dir
import io.path
import core.str
import core.config
import core.portindex
import types
import util.color
import exitcodes as ec
import core.result as res

export
    fn execute(opts: types.GlobalOptions): int
end export

fn execute(opts: types.GlobalOptions): int
    let argc = args.count()

    if argc <= opts.cmd_index + 1
        print_usage()
        return ec.EXIT_USAGE()
    end if

    let subcommand = args.get(opts.cmd_index + 1)

    if subcommand == "new"
        return ports_new(opts)
    elif subcommand == "cache"
        return ports_cache(opts)
    else
        color.print_error("Unknown subcommand: " + subcommand)
        print_usage()
        return ec.EXIT_USAGE()
    end if
end execute

// ============================================================================
// coral ports new <category/name>
// ============================================================================

fn ports_new(opts: types.GlobalOptions): int
    let argc = args.count()

    if argc <= opts.cmd_index + 2
        color.print_error("Missing argument: category/name")
        println("Usage: coral ports new <category/name>")
        return ec.EXIT_USAGE()
    end if

    let arg = args.get(opts.cmd_index + 2)

    // Require slash format
    let slash_idx = str.index_of(arg, "/")
    if slash_idx <= 0
        color.print_error("Invalid format: '" + arg + "'")
        println("Use category/name format, e.g.: coral ports new hammerhead/my-port")
        return ec.EXIT_USAGE()
    end if

    let category = str.substring(arg, 0, slash_idx)
    let name = str.substring(arg, slash_idx + 1, str.length(arg) - slash_idx - 1)

    if str.length(name) == 0
        color.print_error("Port name cannot be empty")
        return ec.EXIT_USAGE()
    end if

    // Get ports directory
    let cfg = config.load()
    let ports_dir = config.get_ports_dir(cfg)

    // Create port directory
    let port_dir = path.join_path(ports_dir, path.join_path(category, name))

    if dir.dir_exists(port_dir)
        color.print_error("Port directory already exists: " + port_dir)
        return ec.EXIT_PKG_ALREADY_INSTALLED()
    end if

    if not res.is_ok(dir.create_dir_all(port_dir))
        color.print_error("Failed to create directory: " + port_dir)
        return ec.EXIT_PERMISSION_DENIED()
    end if

    // Generate package.toml
    let toml_path = path.join_path(port_dir, "package.toml")
    let toml_content = "[package]\nname = \"" + name + "\"\nversion = \"0.1.0\"\nrelease = 1\ndescription = \"\"\nurl = \"\"\nlicense = \"\"\nmaintainer = \"\"\narch = \"x86_64\"\n\n[dependencies]\nruntime = []\nbuild = []\n\n[[source]]\nfile = \"\"\nurls = []\nchecksum = \"SKIP\"\n\n[build]\nparallel = true\njobs = 0\n"

    if not res.is_ok(file.writeFile(toml_path, toml_content))
        color.print_error("Failed to write package.toml")
        return ec.EXIT_PERMISSION_DENIED()
    end if

    // Generate build.sh
    let build_path = path.join_path(port_dir, "build.sh")
    let dollar = "$"
    let build_content = "#!/bin/sh\n# Build script for " + name + "\nset -e\n\n# cd " + name + "-" + dollar + "{VERSION}\n\nMAKE=gmake\nif [ \"" + dollar + "(uname -s)\" != \"SunOS\" ]; then\n    MAKE=make\nfi\n\n# ./configure --prefix=/usr\n# " + dollar + "MAKE " + dollar + "{MAKEFLAGS}\n# " + dollar + "MAKE DESTDIR=\"" + dollar + "{DESTDIR}\" install\n"

    if not res.is_ok(file.writeFile(build_path, build_content))
        color.print_error("Failed to write build.sh")
        return ec.EXIT_PERMISSION_DENIED()
    end if

    color.print_success("Port created: " + category + "/" + name)
    println("")
    println("  Directory: " + port_dir)
    println("  package.toml: " + toml_path)
    println("  build.sh: " + build_path)
    println("")
    color.print_info("Next steps:")
    println("  1. Edit package.toml with package details")
    println("  2. Add source URLs and checksums")
    println("  3. Write the build.sh script")
    println("  4. Test with: coral build " + category + "/" + name)

    return ec.EXIT_SUCCESS()
end ports_new

// ============================================================================
// coral ports cache [status|rebuild]
// ============================================================================

fn ports_cache(opts: types.GlobalOptions): int
    let argc = args.count()

    if argc <= opts.cmd_index + 2
        // Default to status
        return cache_status()
    end if

    let subcmd = args.get(opts.cmd_index + 2)

    if subcmd == "status"
        return cache_status()
    elif subcmd == "rebuild"
        return cache_rebuild()
    else
        color.print_error("Unknown cache subcommand: " + subcmd)
        println("Usage: coral ports cache [status|rebuild]")
        return ec.EXIT_USAGE()
    end if
end ports_cache

fn cache_status(): int
    color.print_action("Ports index status:")
    println("")

    if portindex.port_index_exists()
        let count = portindex.get_port_count()
        println("  Status: built")
        println("  Ports indexed: " + int_to_str(count))
    else
        println("  Status: not built")
        color.print_info("Run 'coral ports cache rebuild' to build the index")
    end if

    return ec.EXIT_SUCCESS()
end cache_status

fn cache_rebuild(): int
    color.print_action("Rebuilding ports index...")
    println("")

    if portindex.rebuild_port_index()
        let count = portindex.get_port_count()
        color.print_success("Ports index rebuilt successfully")
        println("  Ports indexed: " + int_to_str(count))
        return ec.EXIT_SUCCESS()
    else
        color.print_error("Failed to rebuild ports index")
        return ec.EXIT_DB_ERROR()
    end if
end cache_rebuild

// ============================================================================
// Usage
// ============================================================================

proc print_usage()
    println("Usage: coral ports <command> [args]")
    println("")
    println("Port development and cache management.")
    println("")
    println("Commands:")
    println("  new <category/name>   Scaffold a new port")
    println("  cache [status]        Show ports index status")
    println("  cache rebuild         Rebuild ports index")
    println("")
    println("Examples:")
    println("  coral ports new hammerhead/my-port")
    println("  coral ports cache status")
    println("  coral ports cache rebuild")
end print_usage

// Helper: convert int to string
fn int_to_str(n: int): string
    if n == 0
        return "0"
    end if

    mut negative = false
    mut value = n
    if n < 0
        negative = true
        value = 0 - n
    end if

    mut result = ""
    while value > 0
        let digit = value % 10
        result = str.concat(str.substring("0123456789", digit, 1), result)
        value = value / 10
    end while

    if negative
        result = str.concat("-", result)
    end if

    return result
end int_to_str

end module
/******************************************************************************
               __               ____                __
              / /   ___  ____ _/ __/_____________ _/ /__
             / /   / _ \/ __ `/ /_/ ___/ ___/ __ `/ / _ \
            / /___/  __/ /_/ / __(__  ) /__/ /_/ / /  __/
           /_____/\___/\__,_/_/ /____/\___/\__,_/_/\___/

   (C)opyright 2025, Leafscale, LLC -  https://www.leafscale.com

   Project: Zygaena
  Filename: remove.reef
   Authors: Chris Tusa <chris.tusa@leafscale.com>
   License: <see LICENSE file included with this source code>
Description: Remove command - uninstall packages

******************************************************************************/

module commands.remove

import sys.args
import sys.process
import io.file
import io.dir
import io.path
import core.str
import core.config
import core.database
import core.pkgdb
import core.package
import core.port
import util.prompt
import util.mtree
import util.checksum
import types
import util.color
import fs.stat
import fs.ops
import util.priv
import exitcodes as ec
import core.result as res

export
    fn execute(opts: types.GlobalOptions): int
end export

fn execute(opts: types.GlobalOptions): int
    let argc = args.count()

    // Package arguments should be after the command
    if argc <= opts.cmd_index + 1
        print_usage()
        return ec.EXIT_USAGE()
    end if

    // Load configuration and apply command-line overrides
    let base_cfg = config.load()
    let cfg = config.apply_overrides(base_cfg, opts.root, opts.prefix, opts.no_chroot)
    let root_path = config.get_root(cfg)

    // Show root if set (verbose mode)
    if opts.verbose and str.length(root_path) > 0
        color.print_info("Using root: " + root_path)
    end if

    // Collect packages to remove
    mut packages: [string] = new [string](256)
    mut pkg_count = 0

    mut i = opts.cmd_index + 1
    while i < argc and pkg_count < 256
        let pkg_name = args.get(i)

        // Skip flags and their values
        if pkg_name == "--root" or pkg_name == "--prefix"
            i = i + 2  // Skip flag and its value
            continue
        elif pkg_name == "--no-chroot-scripts"
            i = i + 1  // valueless flag: skip only itself
            continue
        end if
        if str.starts_with(pkg_name, "-")
            i = i + 1
            continue
        end if

        // Check if installed (use rooted version if root is set)
        let installed = check_installed(pkg_name, root_path)
        if installed
            packages[pkg_count] = pkg_name
            pkg_count = pkg_count + 1
        else
            color.print_warning(pkg_name + " is not installed")
        end if

        i = i + 1
    end while

    if pkg_count == 0
        color.print_info("No packages to remove")
        return ec.EXIT_SUCCESS()
    end if

    // Check for reverse dependencies (packages that depend on these)
    mut dependents: [string] = new [string](256)
    mut dependent_count = 0

    i = 0
    while i < pkg_count
        let pkg_name = packages[i]
        let count = get_reverse_dependencies(pkg_name, dependents, dependent_count, 256)
        dependent_count = count
        i = i + 1
    end while

    // Warn if there are dependents
    if dependent_count > 0
        color.print_warning("The following installed packages depend on packages being removed:")
        i = 0
        while i < dependent_count
            println("  - " + dependents[i])
            i = i + 1
        end while

        // Require --force to proceed
        if not opts.force
            color.print_error("Use --force to remove packages with dependents")
            return ec.EXIT_DEPS_CONFLICT()
        end if
        color.print_warning("Proceeding with removal (--force specified)")
    end if

    // Ask for confirmation (unless -y flag)
    if not prompt.confirm_remove(packages, pkg_count, dependents, dependent_count, opts)
        color.print_info("Removal cancelled")
        return ec.EXIT_CANCELLED()
    end if

    // Dry-run: show what would be done and exit
    if opts.dry_run
        color.print_info("Dry run — no changes made")
        return ec.EXIT_SUCCESS()
    end if

    // Remove packages
    mut all_success = true
    i = 0
    while i < pkg_count
        if not remove_package(packages[i], root_path, cfg)
            color.print_error("Failed to remove: " + packages[i])
            all_success = false
        end if
        i = i + 1
    end while

    if all_success
        return ec.EXIT_SUCCESS()
    else
        return ec.EXIT_REMOVE_FAILED()
    end if
end execute

// Check if package is installed, using rooted check if root is set
fn check_installed(name: string, root_path: string): bool
    if str.length(root_path) > 0
        return database.is_installed_rooted(name, root_path)
    end if
    return database.is_installed(name)
end check_installed

proc print_usage()
    println("Usage: coral remove <package...>")
    println("")
    println("Remove one or more installed packages.")
    println("")
    println("Arguments:")
    println("  <package>    Name of installed package to remove")
    println("")
    println("Options:")
    println("  -y, --yes    Don't ask for confirmation")
    println("  -f, --force  Remove even if other packages depend on it")
    println("")
    println("Examples:")
    println("  coral remove vim")
    println("  coral remove vim nano htop")
    println("  coral remove --force libfoo")
end print_usage

fn remove_package(pkg_name: string, root_path: string, cfg: config.Config): bool
    // Check if package is installed (use rooted version if root is set)
    if not check_installed(pkg_name, root_path)
        color.print_error(pkg_name + " is not installed")
        return false
    end if

    color.print_action("Removing " + pkg_name + "...")

    let install_root = get_actual_root(root_path)
    // Resolve script execution context; abort early if confinement is required but impossible.
    // Defense-in-depth: main.reef already bars non-root for all non-query commands, so this abort
    // is currently unreachable via the CLI. Kept so confinement fails safely if that global gate is
    // ever relaxed.
    if package.script_wants_chroot(install_root, config.get_chroot_scripts(cfg)) and not priv.is_root()
        color.print_error("--root " + install_root + " runs maintainer scripts confined to the target via chroot, which requires root privileges.")
        color.print_error("Re-run as root, or pass --no-chroot-scripts to run them on the host (unconfined).")
        return false
    end if
    let script_ctx = package.resolve_script_ctx(install_root, config.get_chroot_scripts(cfg), priv.is_root())

    // Get package info (use rooted version if root is set)
    let pkg = get_installed_pkg(pkg_name, root_path)
    color.print_info("Package: " + pkg.info.name + " " + pkg.info.version)

    // Get file list from database (use rooted version if root is set)
    mut files: [string] = new [string](4096)
    let file_count = get_files_list(pkg_name, files, 4096, root_path)

    if file_count == 0
        color.print_warning("No files recorded for package")
    else
        color.print_info("Removing " + int_to_str(file_count) + " files...")
    end if

    // Run pre-remove script if present (abort on failure)
    let scripts_dir = database.get_scripts_dir(pkg_name)
    if database.has_stored_scripts(pkg_name)
        color.print_info("Running pre-remove script...")
        if not package.run_stored_pre_remove(script_ctx, scripts_dir, pkg.info.version)
            color.print_error("Pre-remove script failed, aborting removal of " + pkg_name)
            return false
        end if
    end if

    // Load config file list and manifest checksums for config protection
    mut config_files: [string] = new [string](256)
    let config_count = database.get_config_files(pkg_name, config_files, 256)

    mut manifest_entries: [mtree.ManifestEntry] = new [mtree.ManifestEntry](8192)
    mut manifest_count = 0
    let manifest_path = database.get_manifest_path(pkg_name)
    if file.fileExists(manifest_path)
        let manifest_content = res.unwrap_or(file.readFile(manifest_path), "")
        if str.length(manifest_content) > 0
            manifest_count = mtree.parse_manifest(manifest_content, manifest_entries, 8192)
        end if
    end if

    // Remove files (with proper root path, respecting config protection)
    let actual_root = get_actual_root(root_path)
    if not remove_files(files, file_count, actual_root, config_files, config_count, manifest_entries, manifest_count)
        color.print_warning("Some files could not be removed")
        // Continue anyway - unregister from database
    end if

    // Run post-remove script if present (warn on failure, don't abort)
    if database.has_stored_scripts(pkg_name)
        color.print_info("Running post-remove script...")
        if not package.run_stored_post_remove(script_ctx, scripts_dir, pkg.info.version)
            color.print_warning("Post-remove script failed")
        end if
    end if

    // Unregister from database (use rooted version if root is set)
    color.print_info("Unregistering package...")
    if not unregister_pkg(pkg_name, root_path)
        color.print_error("Failed to unregister package from database")
        return false
    end if

    // Update package database indexes
    if not pkgdb.rebuild_indexes_rooted(root_path)
        color.print_warning("Failed to update package indexes")
    end if

    color.print_success("Removed " + pkg_name)
    return true
end remove_package

// Get installed package info, using rooted check if root is set
fn get_installed_pkg(name: string, root_path: string): types.InstalledPackage
    if str.length(root_path) > 0
        return database.get_installed_rooted(name, root_path)
    end if
    return database.get_installed(name)
end get_installed_pkg

// Get files list, using rooted check if root is set
fn get_files_list(name: string, files: [string], max_count: int, root_path: string): int
    if str.length(root_path) > 0
        return database.get_files_rooted(name, files, max_count, root_path)
    end if
    return database.get_files(name, files, max_count)
end get_files_list

// Unregister package, using rooted version if root is set
fn unregister_pkg(name: string, root_path: string): bool
    if str.length(root_path) > 0
        return database.unregister_package_rooted(name, root_path)
    end if
    return database.unregister_package(name)
end unregister_pkg

// Get actual root path (returns "/" if empty)
fn get_actual_root(root_path: string): string
    if str.length(root_path) == 0
        return "/"
    end if
    return root_path
end get_actual_root

// Remove files from system, respecting config file protection
fn remove_files(files: [string], file_count: int, root_path: string, config_files: [string], config_count: int, manifest_entries: [mtree.ManifestEntry], manifest_count: int): bool
    mut all_success = true

    // Remove files in reverse order
    mut i = file_count - 1
    while i >= 0
        let rel_path = files[i]
        let full_path = path.join_path(root_path, rel_path)

        if stat.is_symlink(full_path) or stat.exists(full_path)
            // Check if this is a config file that the user has modified
            if config_count > 0 and package.is_config_file(rel_path, config_files, config_count)
                // Look up the package's sha256 from the manifest
                let pkg_sha = find_manifest_sha256(rel_path, manifest_entries, manifest_count)
                if str.length(pkg_sha) > 0
                    let installed_sha = checksum.sha256_file(full_path)
                    if not str.equals(installed_sha, pkg_sha)
                        // User has modified this config — preserve it
                        color.print_info("Preserving modified config: " + rel_path)
                        i = i - 1
                        continue
                    end if
                end if
            end if

            if not res.is_ok(ops.remove_file(full_path))
                color.print_warning("Failed to remove: " + full_path)
                all_success = false
            end if
        end if

        i = i - 1
    end while

    // Try to remove empty parent directories
    i = file_count - 1
    while i >= 0
        let rel_path = files[i]
        let full_path = path.join_path(root_path, rel_path)
        let parent = path.dirname(full_path)

        if str.length(parent) > str.length(root_path) and dir.dir_exists(parent)
            dir.remove_dir(parent)
        end if

        i = i - 1
    end while

    return all_success
end remove_files

// Look up the sha256 for a given relative path in the manifest entries
fn find_manifest_sha256(rel_path: string, entries: [mtree.ManifestEntry], count: int): string
    mut i = 0
    while i < count
        let epath = mtree.entry_path(entries[i])
        // Compare with and without ./ prefix
        mut entry_rel = epath
        if str.starts_with(epath, "./")
            entry_rel = str.substring(epath, 2, str.length(epath) - 2)
        end if
        if str.equals(entry_rel, rel_path)
            return mtree.entry_sha256(entries[i])
        end if
        i = i + 1
    end while
    return ""
end find_manifest_sha256

// Get packages that depend on the given package
// Returns new total count (existing + new dependents)
fn get_reverse_dependencies(pkg_name: string, dependents: [string], current_count: int, max_count: int): int
    mut count = current_count

    // List all installed packages
    mut installed: [string] = new [string](512)
    let installed_count = database.list_installed(installed, 512)

    mut i = 0
    while i < installed_count and count < max_count
        let other_pkg = installed[i]

        // Skip the package being removed and already listed dependents
        if str.equals(other_pkg, pkg_name)
            i = i + 1
            continue
        end if

        // Check if already in dependents list
        if array_contains(dependents, count, other_pkg)
            i = i + 1
            continue
        end if

        // Try to find this package's port to get its dependencies
        let port_result = port.find(other_pkg)
        if port_result.success
            let p = port_result.port

            // Check runtime dependencies
            if depends_on(p.deps.runtime, p.deps.runtime_count, pkg_name)
                dependents[count] = other_pkg
                count = count + 1
            end if
        end if

        i = i + 1
    end while

    return count
end get_reverse_dependencies

// Check if a dependency list contains the given package
fn depends_on(deps: [string], dep_count: int, pkg_name: string): bool
    mut i = 0
    while i < dep_count
        let dep = deps[i]

        // Handle alternative dependencies (format: base:opt1,opt2)
        let colon_pos = str.index_of_char(dep, ':')
        mut base_dep = dep
        if colon_pos > 0
            base_dep = str.substring(dep, 0, colon_pos)
        end if

        if str.equals(base_dep, pkg_name)
            return true
        end if

        i = i + 1
    end while

    return false
end depends_on

// Helper to check if array contains a string
fn array_contains(arr: [string], count: int, s: string): bool
    mut i = 0
    while i < count
        if str.equals(arr[i], s)
            return true
        end if
        i = i + 1
    end while
    return false
end array_contains

// Helper: convert int to string
fn int_to_str(n: int): string
    if n == 0
        return "0"
    end if

    mut negative = false
    mut value = n
    if n < 0
        negative = true
        value = 0 - n
    end if

    mut result = ""
    while value > 0
        let digit = value % 10
        result = str.concat(str.substring("0123456789", digit, 1), result)
        value = value / 10
    end while

    if negative
        result = str.concat("-", result)
    end if

    return result
end int_to_str

end module
/******************************************************************************
               __               ____                __
              / /   ___  ____ _/ __/_____________ _/ /__
             / /   / _ \/ __ `/ /_/ ___/ ___/ __ `/ / _ \
            / /___/  __/ /_/ / __(__  ) /__/ /_/ / /  __/
           /_____/\___/\__,_/_/ /____/\___/\__,_/_/\___/

   (C)opyright 2025, Leafscale, LLC -  https://www.leafscale.com

   Project: Zygaena
  Filename: repo.reef
   Authors: Chris Tusa <chris.tusa@leafscale.com>
   License: <see LICENSE file included with this source code>
Description: Repo command - manage package repositories

******************************************************************************/

module commands.repo

import sys.args
import sys.process
import io.file
import io.dir
import core.str
import core.repository
import util.color
import exitcodes as ec
import core.result as res

export
    fn execute(): int
end export

fn execute(): int
    let argc = args.count()

    if argc < 3
        print_usage()
        return ec.EXIT_USAGE()
    end if

    let subcommand = args.get(2)

    if subcommand == "list"
        list_repos()
        return ec.EXIT_SUCCESS()
    elif subcommand == "add"
        if argc < 4
            color.print_error("Missing repository URL")
            println("Usage: coral repo add <url> [name]")
            return ec.EXIT_USAGE()
        end if
        let url = args.get(3)
        mut name = ""
        if argc >= 5
            name = args.get(4)
        end if
        add_repo(url, name)
        return ec.EXIT_SUCCESS()
    elif subcommand == "remove"
        if argc < 4
            color.print_error("Missing repository name")
            println("Usage: coral repo remove <name>")
            return ec.EXIT_USAGE()
        end if
        remove_repo(args.get(3))
        return ec.EXIT_SUCCESS()
    elif subcommand == "enable"
        if argc < 4
            color.print_error("Missing repository name")
            return ec.EXIT_USAGE()
        end if
        enable_repo(args.get(3), true)
        return ec.EXIT_SUCCESS()
    elif subcommand == "disable"
        if argc < 4
            color.print_error("Missing repository name")
            return ec.EXIT_USAGE()
        end if
        enable_repo(args.get(3), false)
        return ec.EXIT_SUCCESS()
    elif subcommand == "init"
        if argc < 4
            color.print_error("Missing repository path")
            println("Usage: coral repo init <path>")
            return ec.EXIT_USAGE()
        end if
        init_repo(args.get(3))
        return ec.EXIT_SUCCESS()
    elif subcommand == "rebuild"
        if argc < 4
            color.print_error("Missing repository path")
            println("Usage: coral repo rebuild <path>")
            return ec.EXIT_USAGE()
        end if
        rebuild_repo(args.get(3))
        return ec.EXIT_SUCCESS()
    elif subcommand == "sign"
        if argc < 4
            color.print_error("Missing repository path")
            println("Usage: coral repo sign <path> [keyname]")
            return ec.EXIT_USAGE()
        end if
        let repo_path = args.get(3)
        mut key_name = "default"
        if argc >= 5
            key_name = args.get(4)
        end if
        sign_repo(repo_path, key_name)
        return ec.EXIT_SUCCESS()
    elif subcommand == "verify"
        if argc < 4
            color.print_error("Missing repository path")
            println("Usage: coral repo verify <path>")
            return ec.EXIT_USAGE()
        end if
        verify_repo(args.get(3))
        return ec.EXIT_SUCCESS()
    elif subcommand == "mirror"
        if argc < 5
            color.print_error("Missing source or destination")
            println("Usage: coral repo mirror <source> <dest>")
            return ec.EXIT_USAGE()
        end if
        mirror_repo(args.get(3), args.get(4))
        return ec.EXIT_SUCCESS()
    elif subcommand == "export"
        if argc < 5
            color.print_error("Missing repository path or output")
            println("Usage: coral repo export <path> <output>")
            return ec.EXIT_USAGE()
        end if
        export_repo(args.get(3), args.get(4))
        return ec.EXIT_SUCCESS()
    else
        color.print_error("Unknown subcommand: " + subcommand)
        print_usage()
        return ec.EXIT_USAGE()
    end if
end execute

proc list_repos()
    color.print_action("Configured repositories:")
    println("")

    mut repos: [repository.Repository] = new [repository.Repository](32)
    let count = repository.list_repos(repos, 32)

    if count == 0
        color.print_info("No repositories configured")
        println("")
        color.print_info("Add a repository with: coral repo add <url>")
        return
    end if

    mut i = 0
    while i < count
        let repo = repos[i]
        print("  ")
        print(repo.name)
        print(" - ")
        print(repo.url)
        if not repo.enabled
            print(" [disabled]")
        end if
        if repo.is_signed
            print(" [signed]")
        end if
        println("")
        i = i + 1
    end while

    println("")
    color.print_info("Total: " + int_to_str(count) + " repository(ies)")
end list_repos

proc add_repo(url: string, name: string)
    color.print_action("Adding repository...")

    // Generate name from URL if not provided
    mut repo_name = name
    if str.length(repo_name) == 0
        repo_name = extract_repo_name(url)
    end if

    if str.length(repo_name) == 0
        color.print_error("Could not determine repository name. Please specify one.")
        return
    end if

    // Create repo file
    let repos_dir = "/etc/coral/repos.d"
    let repo_path = repos_dir + "/" + repo_name + ".repo"

    // Check if it exists
    if file.fileExists(repo_path)
        color.print_error("Repository already exists: " + repo_name)
        return
    end if

    // Ensure directory exists
    if not dir.dir_exists(repos_dir)
        if not res.is_ok(dir.create_dir_all(repos_dir))
            color.print_error("Failed to create repos directory")
            return
        end if
    end if

    // Create repo file content
    mut content = "[repository]\n"
    content = content + "name = \"" + repo_name + "\"\n"
    content = content + "url = \"" + url + "\"\n"
    content = content + "priority = 100\n"
    content = content + "enabled = true\n"
    content = content + "signed = false\n"

    if not res.is_ok(file.writeFile(repo_path, content))
        color.print_error("Failed to write repository file")
        return
    end if

    color.print_success("Added repository: " + repo_name)
end add_repo

proc remove_repo(name: string)
    let repos_dir = "/etc/coral/repos.d"
    let repo_path = repos_dir + "/" + name + ".repo"

    if not file.fileExists(repo_path)
        color.print_error("Repository not found: " + name)
        return
    end if

    // Remove the file
    let cmd = "rm -f \"" + repo_path + "\""
    let pid = process.process_spawn_shell(cmd)
    if pid > 0
        process.process_wait(pid)
    end if

    color.print_success("Removed repository: " + name)
end remove_repo

proc enable_repo(name: string, enable: bool)
    let repos_dir = "/etc/coral/repos.d"
    let repo_path = repos_dir + "/" + name + ".repo"

    if not file.fileExists(repo_path)
        color.print_error("Repository not found: " + name)
        return
    end if

    // Read current content
    let content = res.unwrap_or(file.readFile(repo_path), "")

    // Replace enabled line
    mut new_content = ""
    if enable
        new_content = str.replace(content, "enabled = false", "enabled = true")
    else
        new_content = str.replace(content, "enabled = true", "enabled = false")
    end if

    if not res.is_ok(file.writeFile(repo_path, new_content))
        color.print_error("Failed to update repository file")
        return
    end if

    if enable
        color.print_success("Enabled repository: " + name)
    else
        color.print_success("Disabled repository: " + name)
    end if
end enable_repo

fn extract_repo_name(url: string): string
    // Extract name from URL (e.g., https://repo.example.com/zygaena -> zygaena)
    let len = str.length(url)
    if len == 0
        return ""
    end if

    // Find last slash
    mut last_slash = 0 - 1
    mut i = 0
    while i < len
        if url[i] == '/'
            last_slash = i
        end if
        i = i + 1
    end while

    if last_slash < 0 or last_slash >= len - 1
        return "repo"
    end if

    return str.substring(url, last_slash + 1, len - last_slash - 1)
end extract_repo_name

// Initialize a new repository at the given path
proc init_repo(repo_path: string)
    color.print_action("Initializing repository at " + repo_path)

    // Create the repository directory
    if not dir.dir_exists(repo_path)
        if not res.is_ok(dir.create_dir_all(repo_path))
            color.print_error("Failed to create repository directory")
            return
        end if
    end if

    // Create packages subdirectory
    let packages_dir = repo_path + "/packages"
    if not dir.dir_exists(packages_dir)
        if not res.is_ok(dir.create_dir_all(packages_dir))
            color.print_error("Failed to create packages directory")
            return
        end if
    end if

    // Create repo.toml manifest
    let manifest_path = repo_path + "/repo.toml"
    if file.fileExists(manifest_path)
        color.print_warning("repo.toml already exists, skipping")
    else
        mut content = "# Coral Repository Manifest\n"
        content = content + "# Generated by coral repo init\n\n"
        content = content + "[repository]\n"
        content = content + "name = \"unnamed\"\n"
        content = content + "description = \"A Coral package repository\"\n"
        content = content + "url = \"\"\n"
        content = content + "arch = \"x86_64\"\n"
        content = content + "created = \"2025-01-24\"\n"
        content = content + "signed = false\n\n"
        content = content + "# Packages will be listed below by coral repo rebuild\n"
        content = content + "[packages]\n"

        if not res.is_ok(file.writeFile(manifest_path, content))
            color.print_error("Failed to write repo.toml")
            return
        end if
    end if

    color.print_success("Repository initialized at " + repo_path)
    color.print_info("Place packages in: " + packages_dir)
    color.print_info("Run 'coral repo rebuild " + repo_path + "' to update manifest")
end init_repo

// Rebuild repository manifest by scanning packages
proc rebuild_repo(repo_path: string)
    color.print_action("Rebuilding repository manifest...")

    let packages_dir = repo_path + "/packages"
    if not dir.dir_exists(packages_dir)
        color.print_error("Packages directory not found: " + packages_dir)
        return
    end if

    // Scan for package files
    let entries = res.unwrap_or(dir.list_dir(packages_dir), new [string](0))
    let entry_count = entries.length()

    mut pkg_count = 0
    mut packages_content = ""

    mut i = 0
    while i < entry_count
        let entry = entries[i]
        // Look for .pkg.tar.xz files
        if str.ends_with(entry, ".pkg.tar.xz")
            // Parse package name and version from filename
            // Format: name-version-release.arch.pkg.tar.xz
            let info = parse_package_filename(entry)
            if str.length(info) > 0
                packages_content = packages_content + info + "\n"
                pkg_count = pkg_count + 1
            end if
        end if
        i = i + 1
    end while

    // Generate new repo.toml
    let manifest_path = repo_path + "/repo.toml"
    mut content = "# Coral Repository Manifest\n"
    content = content + "# Rebuilt by coral repo rebuild\n\n"
    content = content + "[repository]\n"
    content = content + "name = \"unnamed\"\n"
    content = content + "description = \"A Coral package repository\"\n"
    content = content + "url = \"\"\n"
    content = content + "arch = \"x86_64\"\n"
    content = content + "created = \"2025-01-24\"\n"
    content = content + "signed = false\n\n"
    content = content + "[packages]\n"
    content = content + packages_content

    if not res.is_ok(file.writeFile(manifest_path, content))
        color.print_error("Failed to write repo.toml")
        return
    end if

    color.print_success("Repository rebuilt: " + int_to_str(pkg_count) + " package(s) found")
end rebuild_repo

// Parse package filename into TOML entry
fn parse_package_filename(filename: string): string
    // Extract name-version-release from filename
    // Example: vim-9.0-1.x86_64.pkg.tar.xz -> vim = { version = "9.0", release = 1 }

    // Remove .pkg.tar.xz suffix
    let base = str.substring(filename, 0, str.length(filename) - 11)

    // Find arch (e.g., .x86_64)
    let arch_pos = str.last_index_of_char(base, '.')
    if arch_pos < 0
        return ""
    end if

    let name_ver_rel = str.substring(base, 0, arch_pos)

    // Find release number (last hyphen)
    let rel_pos = str.last_index_of_char(name_ver_rel, '-')
    if rel_pos < 0
        return ""
    end if
    let release = str.substring(name_ver_rel, rel_pos + 1, str.length(name_ver_rel) - rel_pos - 1)

    // Find version (second to last hyphen)
    let name_ver = str.substring(name_ver_rel, 0, rel_pos)
    let ver_pos = str.last_index_of_char(name_ver, '-')
    if ver_pos < 0
        return ""
    end if

    let name = str.substring(name_ver, 0, ver_pos)
    let version = str.substring(name_ver, ver_pos + 1, str.length(name_ver) - ver_pos - 1)

    return name + " = { version = \"" + version + "\", release = " + release + ", file = \"" + filename + "\" }"
end parse_package_filename

// Sign the repository manifest
proc sign_repo(repo_path: string, key_name: string)
    color.print_action("Signing repository manifest...")

    let manifest_path = repo_path + "/repo.toml"
    if not file.fileExists(manifest_path)
        color.print_error("repo.toml not found in: " + repo_path)
        return
    end if

    // Find the key
    let keyring = "/etc/coral/keys"
    let key_path = keyring + "/" + key_name + ".key"

    if not file.fileExists(key_path)
        color.print_error("Key not found: " + key_name)
        color.print_info("Generate a key with: coral key generate " + key_name)
        return
    end if

    // Sign the manifest using openssl
    let sig_path = repo_path + "/repo.toml.sig"
    let cmd = "openssl pkeyutl -sign -inkey \"" + key_path + "\" -in \"" + manifest_path + "\" -out \"" + sig_path + "\""

    let pid = process.process_spawn_shell(cmd)
    if pid < 0
        color.print_error("Failed to start signing process")
        return
    end if

    let exit_code = process.process_wait(pid)
    if exit_code != 0
        color.print_error("Signing failed")
        return
    end if

    // Update repo.toml to indicate it's signed
    let content = res.unwrap_or(file.readFile(manifest_path), "")
    let new_content = str.replace(content, "signed = false", "signed = true")
    file.writeFile(manifest_path, new_content)

    color.print_success("Repository signed with key: " + key_name)
    color.print_info("Signature: " + sig_path)
end sign_repo

// Verify repository signature
proc verify_repo(repo_path: string)
    color.print_action("Verifying repository signature...")

    let manifest_path = repo_path + "/repo.toml"
    let sig_path = repo_path + "/repo.toml.sig"

    if not file.fileExists(manifest_path)
        color.print_error("repo.toml not found")
        return
    end if

    if not file.fileExists(sig_path)
        color.print_error("No signature found (repo.toml.sig)")
        return
    end if

    // Try to find a matching public key
    let keyring = "/etc/coral/keys"
    if not dir.dir_exists(keyring)
        color.print_error("No keys in keyring")
        return
    end if

    // List all public keys and try each
    let entries = res.unwrap_or(dir.list_dir(keyring), new [string](0))
    let count = entries.length()

    mut i = 0
    mut verified = false
    while i < count and not verified
        let entry = entries[i]
        if str.ends_with(entry, ".pub")
            let key_path = keyring + "/" + entry
            let cmd = "openssl pkeyutl -verify -pubin -inkey \"" + key_path + "\" -in \"" + manifest_path + "\" -sigfile \"" + sig_path + "\" 2>/dev/null"

            let pid = process.process_spawn_shell(cmd)
            if pid > 0
                let exit_code = process.process_wait(pid)
                if exit_code == 0
                    let key_name = str.substring(entry, 0, str.length(entry) - 4)
                    color.print_success("Signature verified with key: " + key_name)
                    verified = true
                end if
            end if
        end if
        i = i + 1
    end while

    if not verified
        color.print_error("Signature verification failed - no matching key found")
    end if
end verify_repo

// Mirror repository to remote destination
proc mirror_repo(source: string, dest: string)
    color.print_action("Mirroring repository...")
    color.print_info("Source: " + source)
    color.print_info("Destination: " + dest)

    // Use rsync for mirroring
    let cmd = "rsync -av --delete \"" + source + "/\" \"" + dest + "/\""

    let pid = process.process_spawn_shell(cmd)
    if pid < 0
        color.print_error("Failed to start rsync")
        return
    end if

    let exit_code = process.process_wait(pid)
    if exit_code != 0
        color.print_error("Mirror sync failed")
        return
    end if

    color.print_success("Repository mirrored to: " + dest)
end mirror_repo

// Export repository for offline distribution (ISO/USB)
proc export_repo(repo_path: string, output_path: string)
    color.print_action("Exporting repository for offline distribution...")

    if not dir.dir_exists(repo_path)
        color.print_error("Repository not found: " + repo_path)
        return
    end if

    // Determine output format based on extension
    if str.ends_with(output_path, ".tar.xz")
        // Create compressed tarball
        let cmd = "gtar -C \"" + repo_path + "\" -cJf \"" + output_path + "\" ."
        let pid = process.process_spawn_shell(cmd)
        if pid < 0
            color.print_error("Failed to create archive")
            return
        end if
        let exit_code = process.process_wait(pid)
        if exit_code != 0
            color.print_error("Archive creation failed")
            return
        end if
    elif str.ends_with(output_path, ".tar.gz")
        let cmd = "gtar -C \"" + repo_path + "\" -czf \"" + output_path + "\" ."
        let pid = process.process_spawn_shell(cmd)
        if pid < 0
            color.print_error("Failed to create archive")
            return
        end if
        let exit_code = process.process_wait(pid)
        if exit_code != 0
            color.print_error("Archive creation failed")
            return
        end if
    else
        // Copy directory
        let cmd = "cp -r \"" + repo_path + "\" \"" + output_path + "\""
        let pid = process.process_spawn_shell(cmd)
        if pid < 0
            color.print_error("Failed to copy repository")
            return
        end if
        let exit_code = process.process_wait(pid)
        if exit_code != 0
            color.print_error("Copy failed")
            return
        end if
    end if

    color.print_success("Repository exported to: " + output_path)
end export_repo

proc print_usage()
    println("Usage: coral repo <command> [options]")
    println("")
    println("Manage package repositories.")
    println("")
    println("Commands:")
    println("  list              List configured repositories")
    println("  add <url> [name]  Add a new repository")
    println("  remove <name>     Remove a repository")
    println("  enable <name>     Enable a repository")
    println("  disable <name>    Disable a repository")
    println("")
    println("Repository maintenance:")
    println("  init <path>       Create a new repository structure")
    println("  rebuild <path>    Scan packages and rebuild manifest")
    println("  sign <path> [key] Sign repository with Ed25519 key")
    println("  verify <path>     Verify repository signature")
    println("  mirror <src> <dst> Sync repository to mirror (rsync)")
    println("  export <path> <out> Export for offline distribution")
    println("")
    println("Examples:")
    println("  coral repo list")
    println("  coral repo add https://repo.zygaena.org/packages")
    println("  coral repo init /var/www/repo/myrepo")
    println("  coral repo rebuild /var/www/repo/myrepo")
    println("  coral repo sign /var/www/repo/myrepo maintainer")
end print_usage

// Helper: convert int to string
fn int_to_str(n: int): string
    if n == 0
        return "0"
    end if

    mut negative = false
    mut value = n
    if n < 0
        negative = true
        value = 0 - n
    end if

    mut result = ""
    while value > 0
        let digit = value % 10
        result = str.concat(str.substring("0123456789", digit, 1), result)
        value = value / 10
    end while

    if negative
        result = str.concat("-", result)
    end if

    return result
end int_to_str

end module
/******************************************************************************
               __               ____                __
              / /   ___  ____ _/ __/_____________ _/ /__
             / /   / _ \/ __ `/ /_/ ___/ ___/ __ `/ / _ \
            / /___/  __/ /_/ / __(__  ) /__/ /_/ / /  __/
           /_____/\___/\__,_/_/ /____/\___/\__,_/_/\___/

   (C)opyright 2025, Leafscale, LLC -  https://www.leafscale.com

   Project: Zygaena
  Filename: search.reef
   Authors: Chris Tusa <chris.tusa@leafscale.com>
   License: <see LICENSE file included with this source code>
Description: Search command - search for packages by name or description

******************************************************************************/

module commands.search

import sys.args
import core.str
import core.port
import core.portindex
import core.database
import types
import util.color
import exitcodes as ec

export
    fn execute(): int
end export

fn execute(): int
    let argc = args.count()

    if argc < 3
        print_usage()
        return ec.EXIT_USAGE()
    end if

    let search_term = args.get(2)

    color.print_action("Searching for: " + search_term)
    println("")

    mut total = 0

    // Try ports index first (fast path)
    if portindex.port_index_exists()
        mut results: [portindex.PortIndexEntry] = new [portindex.PortIndexEntry](512)
        let result_count = portindex.search_ports(search_term, results, 512)

        mut i = 0
        while i < result_count
            let entry = results[i]
            print_index_match(entry)
            total = total + 1
            i = i + 1
        end while
    else
        // Fall back to filesystem scan
        mut cats: [string] = new [string](32)
        let cat_count = port.get_categories(cats, 32)

        mut i = 0
        while i < cat_count
            let category = cats[i]
            mut ports: [string] = new [string](256)
            let port_count = port.list_category(category, ports, 256)

            mut j = 0
            while j < port_count
                let port_name = ports[j]
                let result = port.find(port_name)
                if result.success
                    let p = result.port

                    // Check if search term matches name or description
                    if matches_search(p, search_term)
                        print_match(p, category)
                        total = total + 1
                    end if
                end if
                j = j + 1
            end while

            i = i + 1
        end while
    end if

    if total == 0
        color.print_info("No packages found matching: " + search_term)
    else
        println("")
        color.print_info("Found " + int_to_str(total) + " package(s)")
    end if
    return ec.EXIT_SUCCESS()
end execute

fn matches_search(p: types.Port, term: string): bool
    let lower_term = str.to_lower(term)
    let lower_name = str.to_lower(p.info.name)
    let lower_desc = str.to_lower(p.info.description)

    // Check name
    if str.contains(lower_name, lower_term)
        return true
    end if

    // Check description
    if str.contains(lower_desc, lower_term)
        return true
    end if

    return false
end matches_search

proc print_index_match(entry: portindex.PortIndexEntry)
    let is_installed = database.is_installed(entry.name)

    print(entry.category)
    print("/")
    print(entry.name)
    print(" ")
    print(entry.version)
    if is_installed
        print(" [installed]")
    end if
    println("")
    print("    ")
    println(entry.description)
end print_index_match

proc print_match(p: types.Port, category: string)
    // Check if installed
    let is_installed = database.is_installed(p.info.name)

    print(category)
    print("/")
    print(p.info.name)
    print(" ")
    print(p.info.version)
    if is_installed
        print(" [installed]")
    end if
    println("")
    print("    ")
    println(p.info.description)
end print_match

proc print_usage()
    println("Usage: coral search <term>")
    println("")
    println("Search for packages by name or description.")
    println("")
    println("Arguments:")
    println("  <term>    Search term to look for")
    println("")
    println("Examples:")
    println("  coral search vim")
    println("  coral search editor")
    println("  coral search hello")
end print_usage

// Helper: convert int to string
fn int_to_str(n: int): string
    if n == 0
        return "0"
    end if

    mut negative = false
    mut value = n
    if n < 0
        negative = true
        value = 0 - n
    end if

    mut result = ""
    while value > 0
        let digit = value % 10
        result = str.concat(str.substring("0123456789", digit, 1), result)
        value = value / 10
    end while

    if negative
        result = str.concat("-", result)
    end if

    return result
end int_to_str

end module
/******************************************************************************
               __               ____                __
              / /   ___  ____ _/ __/_____________ _/ /__
             / /   / _ \/ __ `/ /_/ ___/ ___/ __ `/ / _ \
            / /___/  __/ /_/ / __(__  ) /__/ /_/ / /  __/
           /_____/\___/\__,_/_/ /____/\___/\__,_/_/\___/

   (C)opyright 2025, Leafscale, LLC -  https://www.leafscale.com

   Project: Zygaena
  Filename: sync.reef
   Authors: Chris Tusa <chris.tusa@leafscale.com>
   License: <see LICENSE file included with this source code>
Description: Sync command - update ports collection from repository

******************************************************************************/

module commands.sync

import sys.args
import sys.process
import io.dir
import io.path
import io.file
import core.str
import core.config
import core.port
import core.portindex
import util.color
import exitcodes as ec
import core.result as res

export
    fn execute(): int
end export

fn execute(): int
    // Load configuration
    let cfg = config.load()
    let ports_dir = config.get_ports_dir(cfg)

    color.print_action("Syncing ports collection...")
    println("")

    // Check if ports directory exists
    if not dir.dir_exists(ports_dir)
        color.print_error("Ports directory does not exist: " + ports_dir)
        color.print_info("You may need to clone the ports repository first:")
        println("  git clone <ports-repo-url> " + ports_dir)
        return ec.EXIT_CONFIG_ERROR()
    end if

    // Check if it's a git repository
    let git_dir = path.join_path(ports_dir, ".git")
    if not dir.dir_exists(git_dir)
        color.print_warning("Ports directory is not a git repository")
        color.print_info("Cannot sync - no version control detected")
        return ec.EXIT_CONFIG_ERROR()
    end if

    // Run git pull
    color.print_info("Updating from remote repository...")

    let cmd = "cd \"" + ports_dir + "\" && git pull"
    let pid = process.process_spawn_shell(cmd)

    if pid < 0
        color.print_error("Failed to start git pull")
        return ec.EXIT_REPO_UNREACHABLE()
    end if

    let exit_code = process.process_wait(pid)

    if exit_code == 0
        color.print_success("Ports collection updated successfully")

        // Rebuild ports index after successful sync
        portindex.rebuild_port_index()

        // Show summary of changes
        show_update_summary(ports_dir)
        return ec.EXIT_SUCCESS()
    else
        color.print_error("Git pull failed with exit code " + int_to_str(exit_code))
        color.print_info("Check your network connection and repository access")
        return ec.EXIT_REPO_UNREACHABLE()
    end if
end execute

proc show_update_summary(ports_dir: string)
    // Count ports in each category (dynamically discovered)
    mut cats: [string] = new [string](32)
    let cat_count = port.get_categories(cats, 32)

    mut total = 0
    mut i = 0
    while i < cat_count
        let cat = cats[i]
        let cat_path = path.join_path(ports_dir, cat)

        if dir.dir_exists(cat_path)
            let entries = res.unwrap_or(dir.list_dir(cat_path), new [string](0))
            let count = entries.length()

            // Count valid ports (directories with package.toml)
            mut port_count = 0
            mut j = 0
            while j < count
                let entry = entries[j]
                if str.length(entry) > 0 and entry[0] != '.'
                    let toml_path = path.join_path(path.join_path(cat_path, entry), "package.toml")
                    if file.fileExists(toml_path)
                        port_count = port_count + 1
                    end if
                end if
                j = j + 1
            end while

            if port_count > 0
                println("  " + cat + ": " + int_to_str(port_count) + " ports")
                total = total + port_count
            end if
        end if

        i = i + 1
    end while

    println("")
    color.print_info("Total: " + int_to_str(total) + " ports available")
end show_update_summary

// Helper: convert int to string
fn int_to_str(n: int): string
    if n == 0
        return "0"
    end if

    mut negative = false
    mut value = n
    if n < 0
        negative = true
        value = 0 - n
    end if

    mut result = ""
    while value > 0
        let digit = value % 10
        result = str.concat(str.substring("0123456789", digit, 1), result)
        value = value / 10
    end while

    if negative
        result = str.concat("-", result)
    end if

    return result
end int_to_str

end module
/******************************************************************************
               __               ____                __
              / /   ___  ____ _/ __/_____________ _/ /__
             / /   / _ \/ __ `/ /_/ ___/ ___/ __ `/ / _ \
            / /___/  __/ /_/ / __(__  ) /__/ /_/ / /  __/
           /_____/\___/\__,_/_/ /____/\___/\__,_/_/\___/

   (C)opyright 2025, Leafscale, LLC -  https://www.leafscale.com

   Project: Zygaena
  Filename: upgrade.reef
   Authors: Chris Tusa <chris.tusa@leafscale.com>
   License: <see LICENSE file included with this source code>
Description: Upgrade command - upgrade installed packages

******************************************************************************/

module commands.upgrade

import sys.args
import sys.process
import io.file
import io.dir
import io.path
import core.str
import core.config
import core.database
import core.port
import core.portindex
import core.package
import types
import util.color
import util.version as ver
import exitcodes as ec
import core.result as res

export
    fn execute(opts: types.GlobalOptions): int
end export

fn execute(opts: types.GlobalOptions): int
    let argc = args.count()

    // Load configuration and apply command-line overrides
    let base_cfg = config.load()
    let cfg = config.apply_overrides(base_cfg, opts.root, opts.prefix, opts.no_chroot)
    let root_path = config.get_root(cfg)

    // Auto-refresh port index if configured
    if config.get_auto_refresh(cfg)
        portindex.rebuild_port_index()
    end if

    // Show root if set (verbose mode)
    if opts.verbose and str.length(root_path) > 0
        color.print_info("Using root: " + root_path)
    end if

    // Count non-flag arguments (package names)
    // Skip flag values (--root, --prefix take a value)
    mut pkg_count = 0
    mut i = opts.cmd_index + 1
    while i < argc
        let arg = args.get(i)
        if arg == "--root" or arg == "--prefix"
            i = i + 2  // Skip flag and its value
            continue
        elif arg == "--no-chroot-scripts"
            i = i + 1  // valueless flag: skip only itself
            continue
        end if
        if not str.starts_with(arg, "-")
            pkg_count = pkg_count + 1
        end if
        i = i + 1
    end while

    if pkg_count == 0
        // No packages specified - upgrade all
        return upgrade_all(cfg)
    else
        // Upgrade specified packages
        mut all_success = true
        i = opts.cmd_index + 1
        while i < argc
            let pkg_name = args.get(i)

            // Skip flags and their values
            if pkg_name == "--root" or pkg_name == "--prefix"
                i = i + 2  // Skip flag and its value
                continue
            elif pkg_name == "--no-chroot-scripts"
                i = i + 1  // valueless flag: skip only itself
                continue
            end if
            if str.starts_with(pkg_name, "-")
                i = i + 1
                continue
            end if

            // Upgrade this package
            if not upgrade_package(pkg_name, cfg)
                color.print_error("Failed to upgrade: " + pkg_name)
                all_success = false
            end if

            i = i + 1
        end while

        if all_success
            return ec.EXIT_SUCCESS()
        else
            return ec.EXIT_UPGRADE_FAILED()
        end if
    end if
end execute

fn upgrade_all(cfg: config.Config): int
    color.print_action("Checking for upgrades...")

    // Get root path for rooted operations
    let root_path = config.get_root(cfg)

    // List all installed packages (use rooted version if root is set)
    mut installed: [string] = new [string](512)
    let installed_count = list_installed_pkgs(installed, 512, root_path)

    if installed_count == 0
        color.print_info("No packages installed")
        return ec.EXIT_SUCCESS()
    end if

    // Check each package for updates
    mut upgradable: [string] = new [string](512)
    mut upgradable_count = 0

    mut i = 0
    while i < installed_count
        let pkg_name = installed[i]

        if has_upgrade(pkg_name, root_path)
            upgradable[upgradable_count] = pkg_name
            upgradable_count = upgradable_count + 1
        end if

        i = i + 1
    end while

    if upgradable_count == 0
        color.print_success("All packages are up to date")
        return ec.EXIT_SUCCESS()
    end if

    color.print_info("Packages to upgrade: " + int_to_str(upgradable_count))

    // List packages to upgrade
    i = 0
    while i < upgradable_count
        let pkg_name = upgradable[i]
        let installed_pkg = get_installed_pkg(pkg_name, root_path)
        let port_result = port.find(pkg_name)

        if port_result.success
            let p = port_result.port
            println("  " + pkg_name + " " + installed_pkg.info.version + " -> " + p.info.version)
        end if

        i = i + 1
    end while

    // Ask for confirmation unless -y flag
    if not args.has_flag("y") and not args.has_flag("yes")
        color.print_info("Use -y flag to skip confirmation and proceed with upgrade")
        return ec.EXIT_CANCELLED()
    end if

    // Dry-run: show what would be done and exit
    if args.has_flag("n") or args.has_flag("dry-run")
        color.print_info("Dry run — no changes made")
        return ec.EXIT_SUCCESS()
    end if

    // Perform upgrades
    mut all_success = true
    i = 0
    while i < upgradable_count
        if not upgrade_package(upgradable[i], cfg)
            color.print_error("Failed to upgrade: " + upgradable[i])
            all_success = false
        end if
        i = i + 1
    end while

    if all_success
        return ec.EXIT_SUCCESS()
    else
        return ec.EXIT_UPGRADE_FAILED()
    end if
end upgrade_all

fn has_upgrade(pkg_name: string, root_path: string): bool
    // Get installed version (use rooted version if root is set)
    let installed_pkg = get_installed_pkg(pkg_name, root_path)
    if str.length(installed_pkg.info.name) == 0
        return false
    end if

    // Find port
    let port_result = port.find(pkg_name)
    if not port_result.success
        return false
    end if

    let p = port_result.port

    // Compare versions using semantic versioning
    return ver.compare_versions(installed_pkg.info.version, p.info.version) < 0
end has_upgrade

// Helper functions for rooted operations
fn list_installed_pkgs(names: [string], max_count: int, root_path: string): int
    if str.length(root_path) > 0
        return database.list_installed_rooted(names, max_count, root_path)
    end if
    return database.list_installed(names, max_count)
end list_installed_pkgs

fn get_installed_pkg(name: string, root_path: string): types.InstalledPackage
    if str.length(root_path) > 0
        return database.get_installed_rooted(name, root_path)
    end if
    return database.get_installed(name)
end get_installed_pkg

fn is_installed_pkg(name: string, root_path: string): bool
    if str.length(root_path) > 0
        return database.is_installed_rooted(name, root_path)
    end if
    return database.is_installed(name)
end is_installed_pkg

fn get_files_list(name: string, files: [string], max_count: int, root_path: string): int
    if str.length(root_path) > 0
        return database.get_files_rooted(name, files, max_count, root_path)
    end if
    return database.get_files(name, files, max_count)
end get_files_list

fn unregister_pkg(name: string, root_path: string): bool
    if str.length(root_path) > 0
        return database.unregister_package_rooted(name, root_path)
    end if
    return database.unregister_package(name)
end unregister_pkg

fn register_pkg(pkg: types.InstalledPackage, root_path: string): bool
    if str.length(root_path) > 0
        return database.register_from_extract_dir_rooted(pkg, "", root_path)
    end if
    return database.register_package(pkg)
end register_pkg

fn get_actual_root(root_path: string): string
    if str.length(root_path) == 0
        return "/"
    end if
    return root_path
end get_actual_root

fn upgrade_package(pkg_name: string, cfg: config.Config): bool
    // Get root path for rooted operations
    let root_path = config.get_root(cfg)

    // Check if installed (use rooted version if root is set)
    if not is_installed_pkg(pkg_name, root_path)
        color.print_error(pkg_name + " is not installed")
        return false
    end if

    // Get installed info (use rooted version if root is set)
    let installed_pkg = get_installed_pkg(pkg_name, root_path)

    // Find port
    let port_result = port.find(pkg_name)
    if not port_result.success
        color.print_error("Port not found: " + pkg_name)
        return false
    end if

    let p = port_result.port

    // Check if upgrade is available using semantic versioning
    let cmp = ver.compare_versions(installed_pkg.info.version, p.info.version)
    if cmp >= 0
        color.print_info(pkg_name + " is already at version " + installed_pkg.info.version)
        return true
    end if

    color.print_action("Upgrading " + pkg_name + " from " + installed_pkg.info.version + " to " + p.info.version + "...")

    // Look for pre-built package
    let pkg_path = find_package(pkg_name, p.info.version, p.info.release, cfg)

    if str.length(pkg_path) == 0
        color.print_error("Package not found. Build it first with: coral build")
        return false
    end if

    // Remove old version (keep database entry for now)
    mut files: [string] = new [string](4096)
    let file_count = get_files_list(pkg_name, files, 4096, root_path)

    color.print_info("Removing old files...")
    let actual_root = get_actual_root(root_path)
    remove_files(files, file_count, actual_root)

    // Install new version
    color.print_info("Installing new version...")

    // Create extraction directory
    let extract_dir = create_extract_dir(cfg)
    if str.length(extract_dir) == 0
        color.print_error("Failed to create extraction directory")
        return false
    end if

    // Extract package
    let result = package.extract_package(pkg_path, extract_dir)
    if not result.success
        color.print_error(result.error)
        cleanup_extract_dir(extract_dir)
        return false
    end if

    // Read new file list
    mut new_files: [string] = new [string](4096)
    let new_file_count = package.read_footprint(extract_dir, new_files, 4096)

    // Install files to proper root
    if not package.install_files(extract_dir, actual_root)
        color.print_error("Failed to install files")
        cleanup_extract_dir(extract_dir)
        return false
    end if

    // Update database (remove and re-add) using rooted versions if needed
    unregister_pkg(pkg_name, root_path)

    let new_info = package.read_pkginfo(extract_dir)
    mut new_pkg = types.new_installed_package()
    new_pkg.info = new_info
    new_pkg.install_date = "2025-01-24"
    new_pkg.install_reason = "explicit"
    new_pkg.files = new_files
    new_pkg.files_count = new_file_count

    // Register using rooted version if root is set
    if str.length(root_path) > 0
        if not database.register_from_extract_dir_rooted(new_pkg, extract_dir, root_path)
            color.print_warning("Failed to update database")
        end if
    else
        if not database.register_from_extract_dir(new_pkg, extract_dir)
            color.print_warning("Failed to update database")
        end if
    end if

    // Cleanup
    cleanup_extract_dir(extract_dir)

    color.print_success("Upgraded " + pkg_name + " to " + p.info.version)
    return true
end upgrade_package

// Find a package file by name and version
fn find_package(name: string, version: string, release: int, cfg: config.Config): string
    let packages_dir = config.get_packages_dir(cfg)
    let pkg_name = name + "-" + version + "-" + int_to_str(release) + ".pkg.tar.xz"
    let pkg_path = path.join_path(packages_dir, pkg_name)

    if file.fileExists(pkg_path)
        return pkg_path
    end if

    return ""
end find_package

// Remove files from system
fn remove_files(files: [string], file_count: int, root_path: string): bool
    mut i = file_count - 1
    while i >= 0
        let rel_path = files[i]
        let full_path = path.join_path(root_path, rel_path)

        if file.fileExists(full_path)
            let cmd = "rm -f \"" + full_path + "\""
            let pid = process.process_spawn_shell(cmd)
            if pid > 0
                process.process_wait(pid)
            end if
        end if

        i = i - 1
    end while

    return true
end remove_files

// Create extraction directory
fn create_extract_dir(cfg: config.Config): string
    let work_dir = config.get_work_dir(cfg)
    let pid = process.getpid()
    let extract_dir = path.join_path(work_dir, "upgrade_" + int_to_str(pid))

    if dir.dir_exists(extract_dir)
        let cmd = "rm -rf \"" + extract_dir + "\""
        let rm_pid = process.process_spawn_shell(cmd)
        if rm_pid > 0
            process.process_wait(rm_pid)
        end if
    end if

    if not res.is_ok(dir.create_dir_all(extract_dir))
        return ""
    end if

    return extract_dir
end create_extract_dir

// Cleanup extraction directory
fn cleanup_extract_dir(dir_path: string): bool
    if str.length(dir_path) == 0
        return true
    end if

    let cmd = "rm -rf \"" + dir_path + "\""
    let pid = process.process_spawn_shell(cmd)
    if pid < 0
        return false
    end if
    process.process_wait(pid)
    return true
end cleanup_extract_dir

// Helper: convert int to string
fn int_to_str(n: int): string
    if n == 0
        return "0"
    end if

    mut negative = false
    mut value = n
    if n < 0
        negative = true
        value = 0 - n
    end if

    mut result = ""
    while value > 0
        let digit = value % 10
        result = str.concat(str.substring("0123456789", digit, 1), result)
        value = value / 10
    end while

    if negative
        result = str.concat("-", result)
    end if

    return result
end int_to_str

end module
/******************************************************************************
               __               ____                __
              / /   ___  ____ _/ __/_____________ _/ /__
             / /   / _ \/ __ `/ /_/ ___/ ___/ __ `/ / _ \
            / /___/  __/ /_/ / __(__  ) /__/ /_/ / /  __/
           /_____/\___/\__,_/_/ /____/\___/\__,_/_/\___/

   (C)opyright 2025, Leafscale, LLC -  https://www.leafscale.com

   Project: Zygaena
  Filename: verify.reef
   Authors: Chris Tusa <chris.tusa@leafscale.com>
   License: <see LICENSE file included with this source code>
Description: Verify command - check installed package integrity

******************************************************************************/

module commands.verify

import sys.args
import io.file
import io.dir
import io.path
import core.str
import core.config
import core.database
import util.mtree
import util.checksum
import types
import util.color
import exitcodes as ec
import fs.stat
import fs.link
import core.result as res

export
    fn execute(opts: types.GlobalOptions): int
end export

fn execute(opts: types.GlobalOptions): int
    let argc = args.count()

    if argc <= opts.cmd_index + 1
        print_usage()
        return ec.EXIT_USAGE()
    end if

    // Load configuration and apply command-line overrides
    let base_cfg = config.load()
    let cfg = config.apply_overrides(base_cfg, opts.root, opts.prefix, opts.no_chroot)
    let root_path = config.get_root(cfg)

    if opts.verbose and str.length(root_path) > 0
        color.print_info("Using root: " + root_path)
    end if

    let pkg_name = args.get(opts.cmd_index + 1)

    // Check if installed
    if not check_installed(pkg_name, root_path)
        color.print_error(pkg_name + " is not installed")
        return ec.EXIT_PKG_NOT_FOUND()
    end if

    color.print_action("Verifying " + pkg_name + "...")

    // Load manifest from database
    let manifest_path = database.get_manifest_path(pkg_name)
    if not file.fileExists(manifest_path)
        color.print_error("No manifest found for " + pkg_name + " (legacy package without .MANIFEST)")
        return ec.EXIT_PKG_INVALID()
    end if

    let manifest_content = res.unwrap_or(file.readFile(manifest_path), "")
    if str.length(manifest_content) == 0
        color.print_error("Empty manifest for " + pkg_name)
        return ec.EXIT_PKG_INVALID()
    end if

    mut entries: [mtree.ManifestEntry] = new [mtree.ManifestEntry](8192)
    let entry_count = mtree.parse_manifest(manifest_content, entries, 8192)

    if entry_count == 0
        color.print_error("Failed to parse manifest for " + pkg_name)
        return ec.EXIT_PKG_INVALID()
    end if

    // Determine actual root
    let actual_root = get_actual_root(root_path)

    // Verify each entry
    mut missing_count = 0
    mut checksum_fail_count = 0
    mut mode_fail_count = 0
    mut link_fail_count = 0
    mut ok_count = 0

    mut i = 0
    while i < entry_count
        let entry = entries[i]
        let etype = mtree.entry_type(entry)
        let epath = mtree.entry_path(entry)

        mut rel_path = epath
        if str.starts_with(epath, "./")
            rel_path = str.substring(epath, 2, str.length(epath) - 2)
        end if

        let full_path = path.join_path(actual_root, rel_path)

        if str.equals(etype, "dir")
            if not dir.dir_exists(full_path)
                color.print_warning("MISSING dir:  " + rel_path)
                missing_count = missing_count + 1
            else
                // Check mode
                let expected_mode = mtree.entry_mode(entry)
                let actual_mode = res.unwrap_or(stat.file_mode(full_path), 0)
                // Compare lower 12 bits (permissions + setuid/setgid/sticky)
                if (actual_mode % 4096) != (expected_mode % 4096)
                    if opts.verbose
                        color.print_warning("MODE " + rel_path + " (expected " + int_to_octal(expected_mode) + ", got " + int_to_octal(actual_mode) + ")")
                    else
                        color.print_warning("MODE          " + rel_path)
                    end if
                    mode_fail_count = mode_fail_count + 1
                else
                    ok_count = ok_count + 1
                end if
            end if

        elif str.equals(etype, "file")
            if not stat.exists(full_path)
                color.print_warning("MISSING file: " + rel_path)
                missing_count = missing_count + 1
            else
                mut file_ok = true

                // Check sha256
                let expected_sha = mtree.entry_sha256(entry)
                if str.length(expected_sha) > 0
                    let actual_sha = checksum.sha256_file(full_path)
                    if not str.equals(actual_sha, expected_sha)
                        color.print_warning("CHECKSUM      " + rel_path)
                        checksum_fail_count = checksum_fail_count + 1
                        file_ok = false
                    end if
                end if

                // Check mode
                let expected_mode = mtree.entry_mode(entry)
                let actual_mode = res.unwrap_or(stat.file_mode(full_path), 0)
                if (actual_mode % 4096) != (expected_mode % 4096)
                    if opts.verbose
                        color.print_warning("MODE " + rel_path + " (expected " + int_to_octal(expected_mode) + ", got " + int_to_octal(actual_mode) + ")")
                    else
                        color.print_warning("MODE          " + rel_path)
                    end if
                    mode_fail_count = mode_fail_count + 1
                    file_ok = false
                end if

                // Check ownership
                let expected_uid = mtree.name_to_uid(mtree.entry_uname(entry))
                let expected_gid = mtree.name_to_gid(mtree.entry_gname(entry))
                let actual_uid = res.unwrap_or(stat.file_uid(full_path), 0)
                let actual_gid = res.unwrap_or(stat.file_gid(full_path), 0)
                if actual_uid != expected_uid or actual_gid != expected_gid
                    if opts.verbose
                        color.print_warning("OWNER " + rel_path + " (expected " + mtree.entry_uname(entry) + ":" + mtree.entry_gname(entry) + ")")
                    else
                        color.print_warning("OWNER         " + rel_path)
                    end if
                    mode_fail_count = mode_fail_count + 1
                    file_ok = false
                end if

                if file_ok
                    ok_count = ok_count + 1
                end if
            end if

        elif str.equals(etype, "link")
            if not stat.is_symlink(full_path)
                if not stat.exists(full_path)
                    color.print_warning("MISSING link: " + rel_path)
                    missing_count = missing_count + 1
                else
                    color.print_warning("NOT A LINK    " + rel_path)
                    link_fail_count = link_fail_count + 1
                end if
            else
                let expected_target = mtree.entry_link(entry)
                let actual_target = res.unwrap_or(link.readlink(full_path), "")
                if not str.equals(actual_target, expected_target)
                    if opts.verbose
                        color.print_warning("LINK " + rel_path + " -> " + actual_target + " (expected " + expected_target + ")")
                    else
                        color.print_warning("LINK TARGET   " + rel_path)
                    end if
                    link_fail_count = link_fail_count + 1
                else
                    ok_count = ok_count + 1
                end if
            end if
        end if

        i = i + 1
    end while

    // Summary
    println("")
    let total_issues = missing_count + checksum_fail_count + mode_fail_count + link_fail_count
    if total_issues == 0
        color.print_success(pkg_name + ": " + int_to_str(ok_count) + " entries verified, all OK")
        return ec.EXIT_SUCCESS()
    else
        color.print_error(pkg_name + ": " + int_to_str(total_issues) + " issue(s) found")
        if missing_count > 0
            println("  Missing:    " + int_to_str(missing_count))
        end if
        if checksum_fail_count > 0
            println("  Checksum:   " + int_to_str(checksum_fail_count))
        end if
        if mode_fail_count > 0
            println("  Mode/Owner: " + int_to_str(mode_fail_count))
        end if
        if link_fail_count > 0
            println("  Symlinks:   " + int_to_str(link_fail_count))
        end if
        println("  OK:         " + int_to_str(ok_count))
        return ec.EXIT_PKG_CHECKSUM_MISMATCH()
    end if
end execute

fn check_installed(name: string, root_path: string): bool
    if str.length(root_path) > 0
        return database.is_installed_rooted(name, root_path)
    end if
    return database.is_installed(name)
end check_installed

fn get_actual_root(root_path: string): string
    if str.length(root_path) == 0
        return "/"
    end if
    return root_path
end get_actual_root

proc print_usage()
    println("Usage: coral verify <package>")
    println("")
    println("Verify integrity of an installed package against its manifest.")
    println("")
    println("Checks:")
    println("  - Missing files, directories, and symlinks")
    println("  - File checksum (sha256) mismatches")
    println("  - Permission and ownership changes")
    println("  - Broken or incorrect symlink targets")
    println("")
    println("Arguments:")
    println("  <package>    Name of installed package to verify")
    println("")
    println("Options:")
    println("  -v, --verbose    Show expected vs actual values for failures")
    println("")
    println("Examples:")
    println("  coral verify vim")
    println("  coral verify -v openssl")
end print_usage

// Helper: convert int to string
fn int_to_str(n: int): string
    if n == 0
        return "0"
    end if

    mut negative = false
    mut value = n
    if n < 0
        negative = true
        value = 0 - n
    end if

    mut result = ""
    while value > 0
        let digit = value % 10
        result = str.concat(str.substring("0123456789", digit, 1), result)
        value = value / 10
    end while

    if negative
        result = str.concat("-", result)
    end if

    return result
end int_to_str

// Helper: convert int to octal string (for mode display)
fn int_to_octal(n: int): string
    if n == 0
        return "0"
    end if

    mut value = n % 4096
    mut result = ""
    while value > 0
        let digit = value % 8
        result = str.concat(str.substring("01234567", digit, 1), result)
        value = value / 8
    end while

    return result
end int_to_octal

end module