<?php

/**
 * Copyright (C) 2026 Moko Consulting <hello@mokoconsulting.tech>
 *
 * This file is part of a Moko Consulting project.
 *
 * SPDX-License-Identifier: GPL-3.0-or-later
 *
 * FILE INFORMATION
 * DEFGROUP: MokoStandards.Enterprise
 * INGROUP: MokoStandards
 * REPO: https://git.mokoconsulting.tech/MokoConsulting/moko-platform
 * PATH: /lib/Enterprise/RepositorySynchronizer.php
 * BRIEF: Repository synchronization enterprise library
 */

declare(strict_types=1);

namespace MokoEnterprise;

use Exception;
use RuntimeException;

/**
 * Repository Synchronizer
 *
 * Enterprise library for synchronizing files across multiple repositories
 * based on configuration and override files.
 */
class RepositorySynchronizer
{
    private const SYNC_DEFINITION_DIR = 'definitions/sync';
    /** Override file path — resolved at runtime via adapter's getMetadataDir(). */
    private const SYNC_OVERRIDE_FILE_SUFFIX  = 'override.tf';
    private const STANDARDS_VERSION   = '04.06.00';
    private const STANDARDS_MAJOR     = '04';     // Major only — version branch is version/XX
    private const STANDARDS_MINOR     = '04.06';  // Major.Minor for sync branch naming
    private const VERSION_BRANCH      = 'version/' . self::STANDARDS_MAJOR;
    private const SYNC_BRANCH         = 'chore/sync-mokostandards-v' . self::STANDARDS_MINOR;

    private GitPlatformAdapter $adapter;
    private AuditLogger $logger;
    private MetricsCollector $metrics;
    private CheckpointManager $checkpoints;
    private DefinitionParser $definitionParser;
    private MokoStandardsParser $manifestParser;

    /**
     * Constructor
     *
     * @param ApiClient $apiClient Raw API client (kept for backward compatibility)
     * @param AuditLogger $logger Audit logger
     * @param MetricsCollector $metrics Metrics collector
     * @param CheckpointManager|null $checkpoints Checkpoint manager
     * @param DefinitionParser|null $definitionParser Definition parser
     * @param GitPlatformAdapter|null $adapter Platform adapter (auto-created from ApiClient if null)
     */
    public function __construct(
        ApiClient $apiClient,
        AuditLogger $logger,
        MetricsCollector $metrics,
        ?CheckpointManager $checkpoints = null,
        ?DefinitionParser $definitionParser = null,
        ?GitPlatformAdapter $adapter = null
    ) {
        $this->adapter          = $adapter ?? new MokoGiteaAdapter($apiClient);
        $this->logger           = $logger;
        $this->metrics          = $metrics;
        $this->checkpoints      = $checkpoints      ?? new CheckpointManager('.checkpoints');
        $this->definitionParser = $definitionParser ?? new DefinitionParser();
        $this->manifestParser   = new MokoStandardsParser();
    }

    /**
     * Get list of repositories for an organization
     *
     * @param string $org Organization name
     * @param bool $skipArchived Whether to skip archived repositories
     * @return array Array of repository information
     */
    public function getRepositories(string $org, bool $skipArchived = false): array
    {
        $repos = $this->adapter->listOrgRepos($org, $skipArchived);
        $this->metrics->setGauge('repositories_found', count($repos));
        return $repos;
    }

    /**
     * Check if repository has override file
     *
     * @param string $org Organization name
     * @param string $repo Repository name
     * @return bool True if override file exists
     */
    public function hasOverrideFile(string $org, string $repo): bool
    {
        try {
            $overridePath = $this->adapter->getMetadataDir() . '/' . self::SYNC_OVERRIDE_FILE_SUFFIX;
            $override = $this->adapter->getFileContents($org, $repo, $overridePath);
            return $override !== '';
        } catch (Exception $e) {
            return false;
        }
    }

    /**
     * Process single repository
     *
     * @param string $org Organization name
     * @param string $repo Repository name
     * @param bool $dryRun Whether to perform a dry run
     * @param bool $force Force update even if no changes
     * @return int|false PR number on success, false if skipped/failed
     * @throws SynchronizationNotImplementedException When synchronization logic is not implemented
     */
    public function processRepository(string $org, string $repo, bool $dryRun = false, bool $force = false): int|false
    {
        $txn = $this->logger->startTransaction("process_repo_{$repo}");

        try {
            // Check for override file
            if ($this->hasOverrideFile($org, $repo)) {
                $this->logger->logInfo("Repository {$repo} has override file, parsing configuration");
                // Override file exists - in full implementation would parse it
                // For now, skip repos with overrides
                $this->metrics->increment('repos_with_overrides');
                $txn->end('success');
                return false;
            }

            if ($dryRun) {
                $this->logger->logInfo("DRY-RUN: Would update repository {$repo}");
                $txn->end('success');
                return 0;
            }

            // Execute synchronization
            $result = $this->synchronizeRepository($org, $repo, $force);

            if ($result !== false) {
                $this->metrics->increment('repos_synced');
                $txn->end('success');
            } else {
                $txn->end('failure');
            }

            return $result;
        } catch (Exception $e) {
            $txn->end('failure');
            $this->logger->logError("Failed to process repository {$repo}: " . $e->getMessage());
            throw $e;
        }
    }

    /**
     * Synchronize files to a repository
     *
     * @param string $org Organization name
     * @param string $repo Repository name
     * @param bool $force Force override protected files
     * @return int|false PR number on success, false if skipped/failed
     */
    private function synchronizeRepository(string $org, string $repo, bool $force): int|false
    {
        $this->logger->logInfo("Starting synchronization for {$org}/{$repo}");

        // Resolve repo root (three levels up from this file: Enterprise/ → lib/ → root)
        // API repo root (definitions, sync code)
        $repoRoot = dirname(dirname(__DIR__));
        // MokoStandards repo root (templates, configs)
        $standardsRoot = getenv('MOKOSTANDARDS_ROOT') ?: dirname($repoRoot) . '/MokoStandards';

        // Detect platform from repo metadata
        $repoInfo = $this->adapter->getRepo($org, $repo);
        $platform = $this->detectPlatform($repoInfo);
        $this->logger->logInfo("Detected platform for {$repo}: {$platform}");

        // Load file list from the Terraform definition for this platform
        $filesToSync = $this->definitionParser->parseForPlatform($platform, $repoRoot);

        // Append shared workflows — the parser can't extract them from nested
        // subdirectories blocks due to heredoc interference in .tf files.
        $sharedFiles = $this->getSharedWorkflows($platform, $repoRoot);

        // Deduplicate by destination — shared workflows take precedence over parser entries
        $seen = [];
        foreach ($filesToSync as $f) {
            $seen[$f['destination']] = true;
        }
        foreach ($sharedFiles as $f) {
            if (!isset($seen[$f['destination']])) {
                $filesToSync[] = $f;
            }
        }

        $defCount = count($filesToSync) - count($sharedFiles);
        $sharedAdded = count($filesToSync) - $defCount;
        $sharedTotal = count($sharedFiles);
        $this->logger->logInfo(
            "Loaded " . count($filesToSync) . " sync entries for {$platform}"
            . " (def={$defCount}, shared={$sharedAdded}/{$sharedTotal} added, "
            . ($sharedTotal - $sharedAdded) . " deduped)"
        );
        // Log shared workflow destinations for debugging
        foreach ($sharedFiles as $sf) {
            $dest = $sf['destination'] ?? '?';
            $added = !isset($seen[$dest]) ? 'ADDED' : 'DEDUPED';
            $this->logger->logInfo("  shared: {$dest} [{$added}]");
        }

        if (empty($filesToSync)) {
            $this->logger->logWarning("No syncable entries found in definition for platform '{$platform}', skipping {$repo}");
            return false;
        }

        // Check if there's already a PR open for this repo.
        // With --force, proceed anyway — createSyncPR() will reset the branch
        // and update the existing PR body rather than creating a duplicate.
        $existingPR = $this->checkForExistingPR($org, $repo);
        if ($existingPR && !$force) {
            $this->logger->logInfo("PR #{$existingPR} already exists for {$repo}, skipping (use --force to re-sync)");
            return false;
        }
        if ($existingPR && $force) {
            $this->logger->logInfo("PR #{$existingPR} already exists for {$repo} — force flag set, re-syncing");
        }

        // Create PR with file updates driven by the definition
        // Use API repo root ($repoRoot) — templates live here, not in $standardsRoot
        $result   = $this->createSyncPR($org, $repo, $platform, $filesToSync, $repoRoot, $force);
        $prNumber = $result['number'] ?? null;
        $summary  = $result['summary'] ?? [];

        if ($prNumber) {
            $this->logger->logInfo("Successfully created PR #{$prNumber} for {$repo}");

            // Generate / update definitions/sync/{repo}.def.tf AFTER the sync so it
            // reflects exactly what was pushed in this run.
            $this->generateRepositoryDefinition($org, $repo, $platform, $repoInfo, $summary);

            return (int) $prNumber;
        }

        return false;
    }

    /**
     * Check if there's already an open PR for sync
     */
    private function checkForExistingPR(string $org, string $repo): ?int
    {
        try {
            $prs = $this->adapter->listPullRequests($org, $repo, [
                'state' => 'open',
                'head'  => "{$org}:" . self::SYNC_BRANCH,
            ]);

            if (!empty($prs) && is_array($prs)) {
                return $prs[0]['number'] ?? null;
            }
        } catch (Exception $e) {
            $this->logger->logWarning("Failed to check for existing PR: " . $e->getMessage());
        }

        return null;
    }

    /**
     * Generate / update the repository tracking definition after a successful sync.
     *
     * Writes definitions/sync/{repo}.def.tf with:
     *  - the base platform definition as a foundation
     *  - a sync_record block recording what was actually pushed (files created/updated/skipped)
     *  - full timestamps and platform metadata
     *
     * @param string $org
     * @param string $repo
     * @param string $platform   Detected platform slug (e.g. 'dolibarr')
     * @param array  $repoInfo   Raw GitHub API repository object
     * @param array  $summary    Sync result from createSyncPR: {copied[], skipped[], total}
     * @return bool
     */
    private function generateRepositoryDefinition(
        string $org,
        string $repo,
        string $platform,
        array $repoInfo,
        array $summary
    ): bool {
        try {
            $this->logger->logInfo("Writing sync tracking definition for {$org}/{$repo}");

            $timestamp   = date('c');
            $description = addslashes($repoInfo['description'] ?? '');
            $defaultBranch = $repoInfo['default_branch'] ?? 'main';

            // Resolve repo root relative to this file's location
            $repoRoot    = dirname(dirname(__DIR__));
            $baseDefPath = "{$repoRoot}/definitions/default/{$platform}.tf";
            if (!file_exists($baseDefPath)) {
                $baseDefPath = "{$repoRoot}/definitions/default/generic.tf";
            }
            $baseDefinition = file_get_contents($baseDefPath) ?: '';

            // Extract definition version from the source .tf metadata block
            $definitionVersion = 'unknown';
            if (preg_match('/\bversion\s*=\s*"([^"]+)"/', $baseDefinition, $vm)) {
                $definitionVersion = $vm[1];
            }

            // Cache the nullable sub-arrays once to avoid repeated null-coalescing
            $copiedItems  = $summary['copied']  ?? [];
            $skippedItems = $summary['skipped'] ?? [];
            $totalCount   = (int) ($summary['total'] ?? 0);

            // Build the synced_files list
            $syncedEntries  = '';
            foreach ($copiedItems as $item) {
                $action = addslashes($item['action'] ?? 'synced');
                $file   = addslashes($item['file']   ?? '');
                $syncedEntries .= "    { path = \"{$file}\" action = \"{$action}\" },\n";
            }

            $skippedEntries = '';
            foreach ($skippedItems as $item) {
                $file   = addslashes($item['file']   ?? '');
                $reason = addslashes($item['reason'] ?? '');
                $skippedEntries .= "    { path = \"{$file}\" reason = \"{$reason}\" },\n";
            }

            $createdCount = count(array_filter($copiedItems, fn($i) => ($i['action'] ?? '') === 'created'));
            $updatedCount = count(array_filter($copiedItems, fn($i) => ($i['action'] ?? '') === 'updated'));
            $skippedCount = count($skippedItems);

            // Assemble the definition file using PHP 7.3+ flexible heredoc:
            // the closing marker is indented, so PHP strips that many leading spaces automatically.
            $definition = <<<HCL
/**
 * Repository Sync Tracking Definition: {$org}/{$repo}
 *
 * Auto-generated by MokoStandards bulk sync on {$timestamp}
 * Platform : {$platform}
 * Description: {$description}
 *
 * DO NOT EDIT MANUALLY — this file is regenerated on every successful sync.
 * To change what gets synced, edit definitions/default/{$platform}.tf
 * and re-run the bulk-repo-sync workflow.
 */

locals {
  sync_record = {
    metadata = {
      repo              = "{$org}/{$repo}"
      default_branch    = "{$defaultBranch}"
      detected_platform = "{$platform}"
      description       = "{$description}"
      sync_timestamp    = "{$timestamp}"
      source_repo       = "mokoconsulting-tech/MokoStandards"
      base_definition   = "definitions/default/{$platform}.tf"
    }

    sync_stats = {
      total_files   = {$totalCount}
      created_files = {$createdCount}
      updated_files = {$updatedCount}
      skipped_files = {$skippedCount}
    }

    synced_files = [
{$syncedEntries}  ]

    skipped_files = [
{$skippedEntries}  ]
  }
}

# ---- Base platform definition (reference copy) ----
{$baseDefinition}
HCL;

            $defFilePath = "{$repoRoot}/" . self::SYNC_DEFINITION_DIR . "/{$repo}.def.tf";

            if (!is_dir(dirname($defFilePath))) {
                mkdir(dirname($defFilePath), 0755, true);
            }

            file_put_contents($defFilePath, $definition);
            $this->logger->logInfo("Wrote sync tracking definition: {$defFilePath}");
            $this->metrics->increment('definitions_generated');

            return true;
        } catch (Exception $e) {
            $this->logger->logError("Failed to write tracking definition for {$repo}: " . $e->getMessage());
            return false;
        }
    }

    /**
     * Detect platform from repository info
     */
    /** Repos that are the full Dolibarr platform, not individual modules. */
    private const CRM_PLATFORM_REPOS = ['MokoDolibarr', 'MokoDoliMods'];

    /**
     * Detect platform from the .mokostandards manifest (authoritative), falling
     * back to name/topic/description heuristics when the manifest is missing or
     * unparseable.
     */
    private function detectPlatform(array $repoInfo): string
    {
        $org  = $repoInfo['full_name'] ? explode('/', $repoInfo['full_name'])[0] : '';
        $name = $repoInfo['name'] ?? '';

        // ── 1. Try reading the XML .mokostandards manifest ────────────��─
        $manifestPlatform = $this->readManifestPlatform($org, $name);
        if ($manifestPlatform !== null) {
            $this->logger->logInfo("Platform for {$name} from .mokostandards manifest: {$manifestPlatform}");
            return $manifestPlatform;
        }

        // ── 2. Fallback: heuristic detection ────────────────────────────
        return $this->detectPlatformByHeuristics($repoInfo);
    }

    /**
     * Read the platform slug from the remote .mokostandards manifest.
     * Checks .mokogitea/.mokostandards, .github/.mokostandards, and root .mokostandards.
     *
     * @return string|null Platform slug or null if not found/parseable
     */
    private function readManifestPlatform(string $org, string $repo): ?string
    {
        $metaDir = $this->adapter->getMetadataDir();
        $paths = [
            "{$metaDir}/.mokostandards",
            '.mokostandards',
        ];
        if ($metaDir === '.mokogitea') {
            $paths[] = '.github/.mokostandards';
        }

        foreach ($paths as $path) {
            try {
                $file = $this->adapter->getFileContents($org, $repo, $path);
                $content = base64_decode($file['content'] ?? '');
                $platform = $this->manifestParser->extractPlatform($content);
                if ($platform !== null && in_array($platform, MokoStandardsParser::VALID_PLATFORMS, true)) {
                    return $platform;
                }
            } catch (Exception $e) {
                $this->adapter->getApiClient()->resetCircuitBreaker();
            }
        }

        return null;
    }

    /**
     * Heuristic platform detection from repo name, topics, and description.
     * Used as fallback when .mokostandards manifest is missing or unparseable.
     */
    private function detectPlatformByHeuristics(array $repoInfo): string
    {
        $name = $repoInfo['name'] ?? '';
        $nameLower = strtolower($name);
        $description = strtolower($repoInfo['description'] ?? '');
        $topics = $repoInfo['topics'] ?? [];

        // Explicit platform repos — full Dolibarr installation, not a module
        if (in_array($name, self::CRM_PLATFORM_REPOS, true)) {
            return 'platform';
        }
        if (in_array('dolibarr-platform', $topics)) {
            return 'platform';
        }

        // Check topics first — templates before generic joomla
        if (in_array('joomla', $topics)) {
            return 'joomla';
        }
        if (in_array('joomla', $topics) || in_array('joomla-extension', $topics)) {
            return 'joomla';
        }
        if (in_array('dolibarr', $topics) || in_array('dolibarr-module', $topics)) {
            return 'dolibarr';
        }

        // Check name patterns — templates before generic joomla
        if (str_contains($nameLower, 'template') && (str_contains($nameLower, 'joomla') || str_contains($nameLower, 'tpl'))) {
            return 'joomla';
        }
        if (str_contains($nameLower, 'joomla') || str_contains($nameLower, 'waas')) {
            return 'joomla';
        }
        if (str_contains($nameLower, 'doli') || str_contains($nameLower, 'crm')) {
            return 'dolibarr';
        }

        // Check description patterns
        if (
            str_contains($description, 'joomla template') || str_contains($description, 'joomla 5 template')
            || str_contains($description, 'joomla 4 template')
        ) {
            return 'joomla';
        }
        if (str_contains($description, 'joomla') || str_contains($description, 'component')) {
            return 'joomla';
        }
        if (str_contains($description, 'dolibarr') || str_contains($description, 'module')) {
            return 'dolibarr';
        }

        // Default
        return 'generic';
    }

    /**
     * Create a PR with sync updates driven by the flat entry list from DefinitionParser.
     *
     * @param string $org
     * @param string $repo
     * @param string $platform  Detected platform slug (e.g. 'dolibarr')
     * @param array<int, array{source?: string, inline_content?: string, destination: string, always_overwrite: bool}> $filesToSync
     * @param string $repoRoot  Absolute path to the MokoStandards repository root
     * @param bool   $force     When true, overwrite files even when always_overwrite = false
     * @return array{number: ?int, summary: array}
     */
    private function createSyncPR(string $org, string $repo, string $platform, array $filesToSync, string $repoRoot, bool $force): array
    {
        $nullResult = ['number' => null, 'summary' => []];

        try {
            $repoInfo      = $this->adapter->getRepo($org, $repo);
            $defaultBranch = $repoInfo['default_branch'] ?? 'main';

            // Collect all branches to sync — default branch + any additional branches
            $branchesToSync = [$defaultBranch];
            try {
                $allBranches = $this->adapter->listBranches($org, $repo);
                foreach ($allBranches as $branch) {
                    $name = $branch['name'] ?? '';
                    if ($name !== '' && $name !== $defaultBranch) {
                        $branchesToSync[] = $name;
                    }
                }
            } catch (\Throwable $e) {
                $this->logger->logWarning("Could not list branches for {$repo}, syncing default only: " . $e->getMessage());
            }

            $this->logger->logInfo(
                "Syncing files to {$org}/{$repo} across "
                . count($branchesToSync) . " branch(es): "
                . implode(', ', $branchesToSync)
            );

            // Sync to each branch
            $combinedSummary = ['copied' => [], 'skipped' => [], 'total' => 0];
            foreach ($branchesToSync as $branchName) {
                $this->logger->logInfo("  Syncing branch: {$branchName}");
                $branchSummary = $this->syncFilesToBranch($org, $repo, $platform, $filesToSync, $repoRoot, $force, $branchName, null);
                // Merge summaries — only count first branch's copied files to avoid duplicates in tracking
                if ($branchName === $defaultBranch) {
                    $combinedSummary = $branchSummary;
                }
            }
            $summary = $combinedSummary;

            // Ensure composer.json requires mokoconsulting-tech/enterprise (default branch only)
            $this->ensureComposerEnterprise($org, $repo, $defaultBranch, $summary);

            // Migrate .mokostandards to XML manifest (default branch only)
            $this->migrateMokoStandards($org, $repo, $defaultBranch, $platform, $repoInfo, $summary);

            if (count($summary['copied']) === 0) {
                $this->logger->logWarning("No files were created/updated for {$repo}");
                return $nullResult;
            }

            // Create tracking issue (no PR — files pushed directly to default branch)
            $issueBody  = $this->generatePRBody($summary);
            $issueTitle = 'chore: MokoStandards v' . self::STANDARDS_MINOR . ' sync — ' . count($summary['copied']) . ' files updated';
            $issueNumber = null;

            try {
                $issueData = $this->adapter->createIssue($org, $repo, $issueTitle, $issueBody, [
                    'labels'    => ['mokostandards', 'type: chore', 'automation'],
                    'assignees' => ['jmiller'],
                ]);
                $issueNumber = $issueData['number'] ?? null;
                $this->logger->logInfo(
                    "Created tracking issue #{$issueNumber} — "
                    . count($summary['copied'])
                    . " files synced directly to {$defaultBranch}"
                );
            } catch (\Exception $e) {
                $this->logger->logWarning("Could not create tracking issue: " . $e->getMessage());
            }

            return ['number' => $issueNumber, 'summary' => $summary];
        } catch (CircuitBreakerOpen | RateLimitExceeded $e) {
            $this->logger->logError("Sync failed: " . $e->getMessage());
            throw $e;
        } catch (Exception $e) {
            $this->logger->logError("Sync failed: " . $e->getMessage());
            return $nullResult;
        }
    }

    /**
     * Replace all {{TOKEN}} placeholders in a template file with repo-specific values.
     *
     * Tokens sourced from GitHub API data (always available):
     *   {{REPO_NAME}}        — repository name
     *   {{REPO_URL}}         — full GitHub URL
     *   {{REPO_DESCRIPTION}} — GitHub repo description
     *   {{PRIMARY_LANGUAGE}} — dominant language from GitHub
     *   {{PLATFORM_TYPE}}    — human-readable platform label
     *
     * Dolibarr-specific tokens (dolibarr platform only):
     *   {{MODULE_NAME}}      — lowercase module name (e.g. mokocrm)
     *   {{MODULE_CLASS}}     — PascalCase class name   (e.g. MokoCRM)
     *   {{MODULE_ID}}        — $this->numero from descriptor (null → left unreplaced)
     *
     * @param string      $content   Raw template content
     * @param string      $repo      Repository name
     * @param string      $org       Organisation name
     * @param string      $platform  Detected platform slug
     * @param array       $repoInfo  Raw GitHub API repository object
     * Merge a git config file (gitignore / gitattributes / ftp_ignore) by
     * ensuring all template lines are present without removing custom entries.
     *
     * Strategy: take the existing remote content, then append any template
     * lines that are missing. Comments and blank lines from the template are
     * included to preserve section structure. Duplicate non-blank lines are
     * never added.
     *
     * @param string $existing  Current file content from the remote repo
     * @param string $template  Template file content from MokoStandards
     * @return string Merged content
     */
    /**
     * Return shared workflow entries that should be synced to all platforms.
     *
     * The .tf definition parser cannot extract workflows from nested
     * subdirectories blocks because heredoc content in CLAUDE.md disrupts
     * bracket matching. This method provides the workflow list directly.
     *
     * @return array<int, array{source: string, destination: string, always_overwrite: bool}>
     */
    /**
     * Ensure the remote composer.json requires mokoconsulting-tech/enterprise.
     * If the package is missing, add it and commit the change to the sync branch.
     */
    /**
     * Sync files to a single branch.
     *
     * @param string $org       Organization name
     * @param string $repo      Repository name
     * @param string $platform  Detected platform type
     * @param array  $filesToSync Files to synchronize
     * @param string $repoRoot  Path to MokoStandards root
     * @param bool   $force     Force overwrite
     * @param string $branchName Target branch
     * @param string|null $moduleId Dolibarr module ID (pre-fetched)
     * @return array Summary of operations
     */
    private function syncFilesToBranch(
        string $org,
        string $repo,
        string $platform,
        array $filesToSync,
        string $repoRoot,
        bool $force,
        string $branchName,
        ?string $moduleId
    ): array {
        $repoInfo = $this->adapter->getRepo($org, $repo);
        $summary = ['copied' => [], 'skipped' => [], 'total' => 0];

        foreach ($filesToSync as $entry) {
            $summary['total']++;
            $targetPath   = $entry['destination'];
            $basename     = strtolower(basename($targetPath));
            $isReadme     = $basename === 'readme.md';
            $isChangelog  = in_array($basename, ['changelog.md', 'changelog'], true);
            $isProtected  = $isReadme || $isChangelog;
            // Protected files are NEVER overwritten, even with --force
            if ($entry['protected'] ?? false) {
                $summary['skipped'][] = ['file' => $targetPath, 'reason' => 'Protected — never overwritten'];
                continue;
            }
            $canOverwrite = !$isProtected && ($force || $entry['always_overwrite']);

            if ($isReadme) {
                $summary['skipped'][] = ['file' => $targetPath, 'reason' => 'README — never overwritten'];
                continue;
            }
            if ($isChangelog) {
                $summary['skipped'][] = ['file' => $targetPath, 'reason' => 'CHANGELOG — never overwritten'];
                continue;
            }

            if (isset($entry['inline_content'])) {
                $content = $entry['inline_content'];
            } else {
                $sourcePath = rtrim($repoRoot, '/') . '/' . ltrim($entry['source'] ?? '', '/');
                if (!file_exists($sourcePath)) {
                    $summary['skipped'][] = ['file' => $targetPath, 'reason' => 'Source file not found'];
                    continue;
                }
                $content = file_get_contents($sourcePath);
                if ($content === false) {
                    $summary['skipped'][] = ['file' => $targetPath, 'reason' => 'Failed to read source'];
                    continue;
                }
            }

            $content = $this->processTemplateContent($content, $repo, $org, $platform, $repoInfo, $moduleId);

            try {
                $existingFile = $this->adapter->getFileContents($org, $repo, $targetPath, $branchName);

                if (!$canOverwrite) {
                    $existingDecoded = base64_decode($existingFile['content'] ?? '');
                    $hasStaleTokens  = (bool) preg_match('/\{\{[A-Z_a-z]+\}\}|\{[A-Z_]{4,}\}/', $existingDecoded);
                    if (!$hasStaleTokens) {
                        $summary['skipped'][] = ['file' => $targetPath, 'reason' => 'Preserved (always_overwrite=false)'];
                        continue;
                    }
                }

                $isGitConfig = in_array(basename($targetPath), ['.gitignore', '.gitattributes', '.ftpignore'], true);
                if ($isGitConfig) {
                    $existingDecoded = base64_decode($existingFile['content'] ?? '');
                    $content = $this->mergeGitConfigFile($existingDecoded, $content);
                }

                $this->adapter->createOrUpdateFile(
                    $org,
                    $repo,
                    $targetPath,
                    $content,
                    "chore: update {$targetPath} from MokoStandards",
                    $existingFile['sha'] ?? null,
                    $branchName
                );
                $this->logger->logInfo("Updated: {$targetPath} ({$branchName})");
                $summary['copied'][] = ['file' => $targetPath, 'action' => 'updated'];
            } catch (Exception $e) {
                $this->adapter->getApiClient()->resetCircuitBreaker();
                try {
                    $this->adapter->createOrUpdateFile(
                        $org,
                        $repo,
                        $targetPath,
                        $content,
                        "chore: add {$targetPath} from MokoStandards",
                        null,
                        $branchName
                    );
                    $this->logger->logInfo("Created: {$targetPath} ({$branchName})");
                    $summary['copied'][] = ['file' => $targetPath, 'action' => 'created'];
                } catch (Exception $e2) {
                    if (str_contains($e2->getMessage(), "sha") || str_contains($e2->getMessage(), '422')) {
                        try {
                            $this->adapter->getApiClient()->resetCircuitBreaker();
                            $existing = $this->adapter->getFileContents($org, $repo, $targetPath, $branchName);
                            $this->adapter->createOrUpdateFile(
                                $org,
                                $repo,
                                $targetPath,
                                $content,
                                "chore: update {$targetPath} from MokoStandards",
                                $existing['sha'] ?? null,
                                $branchName
                            );
                            $summary['copied'][] = ['file' => $targetPath, 'action' => 'updated'];
                        } catch (Exception $e3) {
                            $summary['skipped'][] = ['file' => $targetPath, 'reason' => 'API error: ' . $e3->getMessage()];
                            $this->adapter->getApiClient()->resetCircuitBreaker();
                        }
                    } else {
                        $summary['skipped'][] = ['file' => $targetPath, 'reason' => 'API error: ' . $e2->getMessage()];
                    }
                }
            }
        }

        return $summary;
    }

    /**
     * Migrate .mokostandards to the platform metadata dir (.gitea/ or .github/)
     * and convert legacy YAML-like format to the new XML manifest.
     *
     * Handles:
     *  1. Location migration: root or .github/ → .mokogitea/.mokostandards
     *  2. Format migration: legacy "platform: xxx" → XML manifest
     *  3. Update existing XML: refresh <governance><last-synced> timestamp
     */
    private function migrateMokoStandards(
        string $org,
        string $repo,
        string $branchName,
        string $platform,
        array $repoInfo,
        array &$summary
    ): void {
        $metaDir    = $this->adapter->getMetadataDir();
        $targetPath = "{$metaDir}/.mokostandards";

        // ── Collect existing files from all legacy locations ─────────
        $legacySources = ['.mokostandards'];
        if ($metaDir === '.mokogitea') {
            $legacySources[] = '.github/.mokostandards';
        }

        $legacyFiles = []; // path => ['content' => raw, 'sha' => sha]
        foreach ($legacySources as $path) {
            try {
                $file = $this->adapter->getFileContents($org, $repo, $path, $branchName);
                $legacyFiles[$path] = [
                    'content' => base64_decode($file['content'] ?? ''),
                    'sha'     => $file['sha'] ?? '',
                ];
            } catch (Exception $e) {
                $this->adapter->getApiClient()->resetCircuitBreaker();
            }
        }

        // Check if target already exists in metadata dir
        $existingTarget = null;
        try {
            $file = $this->adapter->getFileContents($org, $repo, $targetPath, $branchName);
            $existingTarget = [
                'content' => base64_decode($file['content'] ?? ''),
                'sha'     => $file['sha'] ?? '',
            ];
        } catch (Exception $e) {
            $this->adapter->getApiClient()->resetCircuitBreaker();
        }

        // ── Determine the best existing content to work from ────────
        $currentContent = $existingTarget['content'] ?? null;
        if ($currentContent === null) {
            // Pick from legacy sources (first found)
            foreach ($legacyFiles as $data) {
                $currentContent = $data['content'];
                break;
            }
        }

        // ── Generate the new XML manifest ───────────────────────────
        $xmlContent = $this->generateMokoStandardsXml(
            $org,
            $repo,
            $platform,
            $repoInfo,
            $currentContent
        );

        // ── Write to target path ────────────────────────────────────
        $targetSha = $existingTarget['sha'] ?? null;
        $isNew     = $existingTarget === null;
        $needsUpdate = $isNew || $existingTarget['content'] !== $xmlContent;

        if ($needsUpdate) {
            $action = $isNew ? 'create' : 'update';
            $commitMsg = $isNew
                ? "chore: add XML .mokostandards manifest to {$metaDir}/"
                : "chore: update .mokostandards manifest (XML format)";

            try {
                $this->adapter->createOrUpdateFile(
                    $org,
                    $repo,
                    $targetPath,
                    $xmlContent,
                    $commitMsg,
                    $targetSha,
                    $branchName
                );
                $this->logger->logInfo(ucfirst($action) . "d XML .mokostandards → {$targetPath}");
                $summary['copied'][] = ['file' => $targetPath, 'action' => "{$action}d (XML manifest)"];
            } catch (Exception $e) {
                $this->adapter->getApiClient()->resetCircuitBreaker();
                $this->logger->logWarning("Could not {$action} .mokostandards: " . $e->getMessage());
                return;
            }
        }

        // ── Delete legacy source files ──────────────────────────────
        foreach ($legacyFiles as $path => $data) {
            if ($path === $targetPath || empty($data['sha'])) {
                continue;
            }
            try {
                $this->adapter->deleteFile(
                    $org,
                    $repo,
                    $path,
                    $data['sha'],
                    "chore: remove legacy {$path} (replaced by {$targetPath})",
                    $branchName
                );
                $this->logger->logInfo("Deleted legacy {$path}");
            } catch (Exception $e) {
                $this->adapter->getApiClient()->resetCircuitBreaker();
            }
        }
    }

    /**
     * Generate an XML .mokostandards manifest for a repository.
     *
     * If existing content is valid XML, preserves user-edited sections
     * (build, deploy, scripts, overrides) and only refreshes governance metadata.
     *
     * @param string      $org             Organization name
     * @param string      $repo            Repository name
     * @param string      $platform        Detected platform slug
     * @param array       $repoInfo        Gitea API repo object
     * @param string|null $existingContent Current .mokostandards content (XML or legacy)
     * @return string Well-formed XML content
     */
    private function generateMokoStandardsXml(
        string $org,
        string $repo,
        string $platform,
        array $repoInfo,
        ?string $existingContent
    ): string {
        $params = [
            'name'              => $repoInfo['name'] ?? $repo,
            'org'               => $org,
            'platform'          => $platform,
            'standards_version' => self::STANDARDS_VERSION,
            'description'       => $repoInfo['description'] ?? '',
            'license'           => 'GPL-3.0-or-later',
            'topics'            => $repoInfo['topics'] ?? [],
            'language'          => $repoInfo['language'] ?? MokoStandardsParser::platformLanguage($platform),
            'package_type'      => MokoStandardsParser::platformPackageType($platform),
            'last_synced'       => date('c'),
        ];

        // If existing content is already valid XML, try to preserve user sections
        if ($existingContent !== null && str_contains($existingContent, '<mokostandards')) {
            try {
                $existing = $this->manifestParser->parse($existingContent);

                // Preserve user-edited build, deploy, scripts, overrides by re-emitting
                // the existing XML with only governance fields refreshed.
                // For now, we use the simple generate() which creates identity + governance + build.
                // User-managed sections (deploy, scripts, overrides) are preserved by doing
                // a targeted replacement of governance fields in the existing XML.
                return $this->refreshGovernanceInXml(
                    $existingContent,
                    $platform,
                    self::STANDARDS_VERSION,
                    date('c')
                );
            } catch (\RuntimeException $e) {
                // Existing XML is broken — regenerate from scratch
                $this->logger->logInfo("Existing .mokostandards XML invalid, regenerating: " . $e->getMessage());
            }
        }

        return $this->manifestParser->generate($params);
    }

    /**
     * Refresh only the <governance> fields in an existing XML .mokostandards,
     * preserving all other sections (build, deploy, scripts, overrides).
     */
    private function refreshGovernanceInXml(
        string $xml,
        string $platform,
        string $standardsVersion,
        string $lastSynced
    ): string {
        $dom = new \DOMDocument('1.0', 'UTF-8');
        $dom->preserveWhiteSpace = true;
        $dom->formatOutput = true;

        if (!$dom->loadXML($xml)) {
            // If parsing fails, return as-is
            return $xml;
        }

        $xpath = new \DOMXPath($dom);
        $xpath->registerNamespace('m', MokoStandardsParser::NAMESPACE_URI);

        // Update <platform>
        $nodes = $xpath->query('//m:governance/m:platform');
        if ($nodes->length > 0) {
            $nodes->item(0)->textContent = $platform;
        }

        // Update <standards-version>
        $nodes = $xpath->query('//m:governance/m:standards-version');
        if ($nodes->length > 0) {
            $nodes->item(0)->textContent = $standardsVersion;
        }

        // Update or create <last-synced>
        $nodes = $xpath->query('//m:governance/m:last-synced');
        if ($nodes->length > 0) {
            $nodes->item(0)->textContent = $lastSynced;
        } else {
            $govNodes = $xpath->query('//m:governance');
            if ($govNodes->length > 0) {
                $lastSyncedEl = $dom->createElementNS(
                    MokoStandardsParser::NAMESPACE_URI,
                    'last-synced'
                );
                $lastSyncedEl->textContent = $lastSynced;
                $govNodes->item(0)->appendChild($lastSyncedEl);
            }
        }

        return $dom->saveXML();
    }

    private function ensureComposerEnterprise(string $org, string $repo, string $branchName, array &$summary): void
    {
        try {
            $file = $this->adapter->getFileContents($org, $repo, 'composer.json', $branchName);
        } catch (Exception $e) {
            return; // No composer.json — skip
        }

        $content = base64_decode($file['content'] ?? '');
        $json = json_decode($content, true);
        if (!is_array($json)) {
            return;
        }

        // Don't add self-referencing dependency — skip if this IS the enterprise package
        if (($json['name'] ?? '') === 'mokoconsulting-tech/enterprise') {
            return;
        }

        $expectedConstraint = 'dev-' . self::VERSION_BRANCH;

        // Check if enterprise package is already required with correct constraint
        $currentConstraint = $json['require']['mokoconsulting-tech/enterprise']
            ?? $json['require-dev']['mokoconsulting-tech/enterprise']
            ?? null;

        if ($currentConstraint === $expectedConstraint) {
            return; // Already correct
        }

        // Add or update the enterprise package to point to version branch
        $json['require'] = $json['require'] ?? [];
        $json['require']['mokoconsulting-tech/enterprise'] = $expectedConstraint;

        // Sort require keys for consistency
        ksort($json['require']);

        $newContent = json_encode($json, JSON_PRETTY_PRINT | JSON_UNESCAPED_SLASHES) . "\n";

        try {
            $this->adapter->createOrUpdateFile(
                $org,
                $repo,
                'composer.json',
                $newContent,
                'chore: add mokoconsulting-tech/enterprise dependency',
                $file['sha'] ?? null,
                $branchName
            );
            $this->logger->logInfo("Added mokoconsulting-tech/enterprise to composer.json");
            $summary['copied'][] = ['file' => 'composer.json', 'action' => 'enterprise dependency added'];
        } catch (Exception $e) {
            $this->logger->logWarning("Could not update composer.json: " . $e->getMessage());
        }
    }

    /**
     * Template repo mapping — canonical source for each platform's workflows.
     * The sync engine clones these at runtime to get the latest workflow files.
     */
    private const TEMPLATE_REPOS = [
        'joomla'   => 'MokoConsulting/MokoStandards-Template-Joomla',
        'dolibarr' => 'MokoConsulting/MokoStandards-Template-Dolibarr',
        'generic'  => 'MokoConsulting/MokoStandards-Template-Generic',
        'client'   => 'MokoConsulting/MokoStandards-Template-Client',
    ];

    private function getSharedWorkflows(string $platform, string $repoRoot): array
    {
        $wfDir = $this->adapter->getWorkflowDir();

        // Determine which template repo to source from
        $templateType = match (true) {
            in_array($platform, ['dolibarr', 'platform']) => 'dolibarr',
            in_array($platform, ['joomla', 'joomla']) => 'joomla',
            str_starts_with($platform, 'client') => 'client',
            default => 'generic',
        };

        // Clone template repo to tmp if not already cached
        $templateRepo = self::TEMPLATE_REPOS[$templateType];
        $cacheDir = sys_get_temp_dir() . '/mokostandards-sync/' . basename($templateRepo);

        if (!is_dir($cacheDir)) {
            $gitUrl = $this->adapter->getCloneUrl($templateRepo);
            $this->logger->logInfo("Cloning template: {$templateRepo} → {$cacheDir}");
            $cloneResult = $this->adapter->cloneRepo($templateRepo, $cacheDir, ['depth' => 1]);
            if (!$cloneResult) {
                throw new \RuntimeException("Failed to clone template repo: {$templateRepo}");
            }
        }

        // Read all .yml files from the template's .gitea/workflows/
        $sourceDir = "{$cacheDir}/.gitea/workflows";
        $shared = [];

        if (is_dir($sourceDir)) {
            foreach (glob("{$sourceDir}/*.yml") as $file) {
                $basename = basename($file);
                $shared[] = [$file, "{$wfDir}/{$basename}"];
            }
        }

        // CODEOWNERS — GitHub only; Gitea doesn't enforce it
        if ($this->adapter->getPlatformName() === 'github') {
            $shared[] = ['templates/github/CODEOWNERS', '.github/CODEOWNERS'];
        }

        // Platform-specific gitignore (merged, not replaced)
        $gitignoreMap = [
            'dolibarr'      => 'templates/configs/gitignore.dolibarr',
            'platform'    => 'templates/configs/gitignore.dolibarr',
            'joomla'  => 'templates/configs/.gitignore.joomla',
        ];
        $gitignoreTemplate = $gitignoreMap[$platform] ?? 'templates/configs/gitignore';
        $shared[] = [$gitignoreTemplate, '.gitignore'];

        // Create TODO.md stub if it doesn't exist (gitignored after first commit)
        $entries[] = [
            'inline_content'   => "# TODO\n\n> **Note:** This file is not tracked in "
                . "version control (.gitignore). It is for local task tracking "
                . "only.\n\n## Critical\n -\n\n## Normal\n -\n\n## Low\n -\n",
            'destination'      => 'TODO.md',
            'always_overwrite' => false,
        ];

        // Always create a custom/ subdirectory under the workflow dir with a README
        // so repos have a safe place for custom workflows that sync won't touch.
        $entries[] = [
                'inline_content'   => "# Custom Workflows\n\nPlace repo-specific workflows here.\n\n"
                    . "- **Never overwritten** by MokoStandards bulk sync\n"
                    . "- **Never deleted** by the repository-cleanup workflow\n"
                    . "- Safe for custom CI, notifications, or repo-specific automation\n\n"
                    . "Synced workflows live in the parent `{$wfDir}/` directory.\n",
                'destination'      => "{$wfDir}/custom/README.md",
                'always_overwrite' => false,
        ];

        foreach ($shared as [$source, $dest]) {
            $fullSource = "{$repoRoot}/{$source}";
            if (file_exists($fullSource)) {
                $entries[] = [
                    'source'           => $source,  // relative — RepositorySynchronizer prepends repoRoot
                    'destination'      => $dest,
                    'always_overwrite' => true,
                ];
            }
        }

        // Create update.txt stub for Dolibarr repos (plain text version file)
        if ($platform === 'dolibarr') {
            $entries[] = [
                'inline_content'   => '0.0.0',
                'destination'      => 'update.txt',
                'always_overwrite' => false,
            ];
        }

        return $entries;
    }

    /**
     * Required .gitignore entries that MUST exist in every governed repo.
     * The sync validates these exist (appending if missing) without
     * overwriting custom entries. Repos can add their own patterns freely.
     */
    private const REQUIRED_GITIGNORE_ENTRIES = [
        // Secrets & environment
        '.env',
        '.env.local',
        '.env.*.local',
        'secrets/',
        '*.secrets.*',

        // Sublime Text project files
        '*.sublime-project',
        '*.sublime-workspace',
        '*.sublime-settings',

        // SFTP config (Sublime SFTP, VS Code SFTP, etc.)
        'sftp-config*.json',
        'sftp-config.json.template',
        'sftp-settings.json',

        // IDE / editor
        '.idea/',
        '.vscode/*',
        '.claude/',
        '*.code-workspace',

        // OS cruft
        '.DS_Store',
        'Thumbs.db',

        // Task tracking
        'TODO.md',

        // Vendor / dependencies
        '/vendor/',
        'node_modules/',

        // Logs
        '*.log',
    ];

    /**
     * Validate that required .gitignore entries exist in a repo.
     * Returns array of missing entries, empty if all present.
     *
     * @param string $existingContent Current .gitignore content from repo
     * @return array<string> Missing required entries
     */
    public function validateGitignoreEntries(string $existingContent): array
    {
        $existingLines = array_map('trim', explode("\n", $existingContent));
        $existingSet = [];
        foreach ($existingLines as $line) {
            if ($line !== '' && !str_starts_with($line, '#')) {
                $existingSet[$line] = true;
            }
        }

        $missing = [];
        foreach (self::REQUIRED_GITIGNORE_ENTRIES as $entry) {
            if (!isset($existingSet[$entry])) {
                $missing[] = $entry;
            }
        }

        return $missing;
    }

    private function mergeGitConfigFile(string $existing, string $template): string
    {
        $existingLines = array_map('rtrim', explode("\n", $existing));
        $templateLines = array_map('rtrim', explode("\n", $template));

        // Build a set of normalised non-blank, non-comment lines from the remote
        $existingSet = [];
        foreach ($existingLines as $line) {
            $trimmed = trim($line);
            if ($trimmed !== '' && !str_starts_with($trimmed, '#')) {
                $existingSet[$trimmed] = true;
            }
        }

        // Walk the template and collect lines that are missing from the remote
        $missing = [];
        $prevWasMissing = false;
        foreach ($templateLines as $line) {
            $trimmed = trim($line);

            // Blank or comment lines: include them if they precede a missing entry
            // (to preserve section headers). Buffer them and flush when a missing
            // non-blank line is found.
            if ($trimmed === '' || str_starts_with($trimmed, '#')) {
                if ($prevWasMissing) {
                    $missing[] = $line;
                }
                continue;
            }

            if (!isset($existingSet[$trimmed])) {
                // If the previous line was not missing, add a separator + any
                // section header comments that precede this line in the template.
                if (!$prevWasMissing && !empty($missing)) {
                    $missing[] = '';
                }
                $missing[] = $line;
                $prevWasMissing = true;
            } else {
                $prevWasMissing = false;
            }
        }

        if (empty($missing)) {
            return $existing; // nothing to add
        }

        // Append missing lines with a clear separator
        $merged = rtrim($existing) . "\n\n"
            . "# ── MokoStandards sync (auto-appended) ────────────────────────────────\n"
            . implode("\n", $missing) . "\n";

        return $merged;
    }

    /**
     * @param string|null $moduleId  Pre-fetched Dolibarr module numero, or null
     * @return string Processed content
     */
    private function processTemplateContent(
        string $content,
        string $repo,
        string $org = '',
        string $platform = '',
        array $repoInfo = [],
        ?string $moduleId = null
    ): string {
        // Strip .template suffix from workflow file references
        $content = str_replace('.yml.template', '.yml', $content);

        // Map platform slug to human-readable label
        $platformType = match ($platform) {
            'dolibarr'         => 'Dolibarr module',
            'joomla'     => 'Joomla extension',
            'generic' => 'PHP library',
            default              => ucfirst(str_replace('-', ' ', $platform)),
        };

        // Derive Dolibarr module identifiers from the repository name
        $moduleName  = strtolower(preg_replace('/[^a-zA-Z0-9]/', '', $repo));
        $moduleClass = $repo;  // Repo name is the PascalCase class (e.g. MokoCRM)

        // Build replacement map — uppercase tokens take precedence; legacy lowercase kept for compat
        $map = [
            // Uppercase tokens (used in CLAUDE.md / copilot-instructions templates)
            '{{REPO_NAME}}'        => $repoInfo['name']        ?? $repo,
            '{{REPO_URL}}'         => "https://github.com/{$org}/{$repo}",
            '{{REPO_DESCRIPTION}}' => $repoInfo['description'] ?? '',
            '{{PRIMARY_LANGUAGE}}' => $repoInfo['language']    ?? '',
            '{{PLATFORM_TYPE}}'    => $platformType,
            '{{MODULE_NAME}}'      => $moduleName,
            '{{MODULE_CLASS}}'     => $moduleClass,
            '{{WORKFLOW_DIR}}'     => $this->adapter->getWorkflowDir(),
            // Legacy lowercase tokens
            '{{repo_name}}'        => $repoInfo['name']        ?? $repo,
            '{{repo_name_lower}}'  => strtolower($repo),
            '{{org}}'              => $org,
            '{{platform}}'         => $platform,
            '{{standards_version}}' => self::STANDARDS_VERSION,
            '{{standards_minor}}'   => self::STANDARDS_MINOR,
            '{{standards_branch}}'  => self::VERSION_BRANCH,
            // Single-brace tokens — used by GitHub repository templates and older MokoStandards stubs
            '{REPO_NAME}'         => $repoInfo['name']        ?? $repo,
            '{REPO_URL}'          => "https://github.com/{$org}/{$repo}",
            '{REPO_DESCRIPTION}'  => $repoInfo['description'] ?? '',
            '{PRIMARY_LANGUAGE}'  => $repoInfo['language']    ?? '',
            '{PLATFORM_TYPE}'     => $platformType,
            '{MODULE_NAME}'       => $moduleName,
            '{MODULE_CLASS}'      => $moduleClass,
            '{MODULE_ID}'         => '',  // overridden below when moduleId is available
            '{repo_name}'         => $repoInfo['name']        ?? $repo,
            '{repo_name_lower}'   => strtolower($repo),
            '{org}'               => $org,
        ];

        // Only replace {{MODULE_ID}} / {MODULE_ID} if we actually have the value; otherwise leave
        // the placeholder intact so the CLAUDE.md self-repair block can fill it in later.
        if ($moduleId !== null) {
            $map['{{MODULE_ID}}'] = $moduleId;
            $map['{MODULE_ID}']   = $moduleId;
        } else {
            // Remove the empty single-brace placeholder so it doesn't corrupt values
            unset($map['{MODULE_ID}']);
        }

        return strtr($content, $map);
    }

    /**
     * Fetch the Dolibarr module numero ($this->numero) from the module descriptor.
     *
     * Searches the repository tree for src/core/modules/mod*.class.php and extracts
     * the unique module number. Returns null if not found or on any API error.
     *
     * @param string $org  GitHub organisation
     * @param string $repo Repository name
     * @return string|null Module ID string, or null if unavailable
     */
    private function fetchModuleId(string $org, string $repo): ?string
    {
        try {
            $treeEntries = $this->adapter->getTree($org, $repo, 'HEAD', true);
            $paths = array_column($treeEntries, 'path');

            $descriptors = array_values(array_filter(
                $paths,
                static fn(string $p): bool => (bool) preg_match('#src/core/modules/mod\w+\.class\.php$#', $p)
            ));

            if (empty($descriptors)) {
                return null;
            }

            $fileData = $this->adapter->getFileContents($org, $repo, $descriptors[0]);
            $content  = base64_decode(str_replace(["\n", "\r"], '', $fileData['content'] ?? ''));

            if (preg_match('/\$this->numero\s*=\s*(\d+)/', $content, $m)) {
                return $m[1];
            }
        } catch (\Exception $e) {
            $this->logger->logInfo("Could not fetch module ID for {$repo}: " . $e->getMessage());
        }

        return null;
    }

    /**
     * Generate PR body text
     */
    private function generatePRBody(array $summary): string
    {
        $body = "## MokoStandards Synchronization\n\n";
        $body .= "This PR synchronizes workflows, configurations, and scripts from the MokoStandards repository.\n\n";

        // Summary statistics
        $body .= "### Summary\n";
        $body .= "- 🆕 **Created**: " . count(array_filter($summary['copied'], fn($i) => $i['action'] === 'created')) . " files\n";
        $body .= "- 🔄 **Updated**: " . count(array_filter($summary['copied'], fn($i) => $i['action'] === 'updated')) . " files\n";
        $body .= "- ⚠️ **Skipped**: " . count($summary['skipped']) . " files\n";
        $body .= "- 📊 **Total**: " . $summary['total'] . " files processed\n\n";

        // List copied files
        if (!empty($summary['copied'])) {
            $body .= "### Files Copied\n\n";
            foreach ($summary['copied'] as $item) {
                $action = $item['action'] === 'created' ? '🆕' : '🔄';
                $body .= "- {$action} `{$item['file']}`\n";
            }
            $body .= "\n";
        }

        // List skipped files
        if (!empty($summary['skipped'])) {
            $body .= "### Files Skipped\n\n";
            foreach ($summary['skipped'] as $item) {
                $body .= "- ⚠️ `{$item['file']}` - {$item['reason']}\n";
            }
            $body .= "\n";
        }

        $body .= "### Review Notes\n";
        $body .= "- Please review all changes carefully\n";
        $body .= "- Ensure no custom configurations are overwritten\n";
        $body .= "- Test workflows and scripts after merging\n";
        $body .= "- Verify issue templates render correctly\n\n";

        $body .= "---\n";
        $body .= "*This PR was automatically generated by the MokoStandards bulk sync process.*\n";

        return $body;
    }

    /**
     * Synchronize multiple repositories
     *
     * @param string $org Organization name
     * @param array $options Sync options (repo, skipArchived, dryRun, force)
     * @return array Sync results with statistics
     */
    public function synchronize(string $org, array $options = []): array
    {
        $specificRepo = $options['repo'] ?? null;
        $skipArchived = $options['skipArchived'] ?? false;
        $dryRun = $options['dryRun'] ?? false;
        $force = $options['force'] ?? false;

        $txn = $this->logger->startTransaction('bulk_synchronize');

        try {
            // Get list of repositories
            $repos = $this->getRepositories($org, $skipArchived);

            if ($specificRepo) {
                $repos = array_filter($repos, fn($repo) => $repo['name'] === $specificRepo);
            }

            $total = count($repos);
            $results = [
                'total' => $total,
                'success' => 0,
                'skipped' => 0,
                'failed' => 0,
                'repositories' => [],
            ];

            foreach ($repos as $index => $repo) {
                $repoName = $repo['name'];
                $progress = $index + 1;

                try {
                    $updated = $this->processRepository($org, $repoName, $dryRun, $force);

                    if ($updated) {
                        $results['success']++;
                        $this->metrics->increment('repos_updated_total', 1, ['status' => 'success']);
                        $results['repositories'][$repoName] = 'updated';
                    } else {
                        $results['skipped']++;
                        $this->metrics->increment('repos_updated_total', 1, ['status' => 'skipped']);
                        $results['repositories'][$repoName] = 'skipped';
                    }
                } catch (Exception $e) {
                    $results['failed']++;
                    $this->metrics->increment('repos_updated_total', 1, ['status' => 'failed']);
                    $results['repositories'][$repoName] = 'failed: ' . $e->getMessage();
                }

                // Save checkpoint
                $this->checkpoints->saveCheckpoint('bulk_sync', [
                    'processed' => $progress,
                    'total' => $total,
                    'results' => $results,
                ]);
            }

            $txn->end('success');

            return $results;
        } catch (Exception $e) {
            $txn->end('failure');
            throw $e;
        }
    }

    /**
     * Apply labels to a PR or issue, creating any that don't yet exist on the repo.
     *
     * @param string        $org    GitHub organisation
     * @param string        $repo   Repository name
     * @param int           $number PR or issue number
     * @param list<string>  $labels Label names to apply
     */
    public function applyLabels(string $org, string $repo, int $number, array $labels): void
    {
        // Ensure labels exist on the repo before applying
        $existingLabels = $this->adapter->listLabels($org, $repo);
        $existingNames = array_column($existingLabels, 'name');

        foreach ($labels as $label) {
            if (!in_array($label, $existingNames, true)) {
                try {
                    $this->adapter->createLabel(
                        $org,
                        $repo,
                        $label,
                        match ($label) {
                            'mokostandards' => 'B60205',
                            'type: chore'   => 'FEF2C0',
                            'automation'    => '8B4513',
                            default         => 'EDEDED',
                        },
                        match ($label) {
                            'mokostandards' => 'MokoStandards compliance',
                            'type: chore'   => 'Maintenance tasks',
                            'automation'    => 'Automated processes or scripts',
                            default         => '',
                        }
                    );
                } catch (\Exception $createEx) {
/* already exists race — ignore */
                }
            }
        }

        try {
            $this->adapter->addIssueLabels($org, $repo, $number, $labels);
        } catch (\Exception $e) {
            $this->logger->logInfo("Could not apply labels to #{$number}: " . $e->getMessage());
        }
    }
}