@uxmaltech/collab-cli 0.1.0

package/dist/commands/init.js

@@ -0,0 +1,830 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.registerInitCommand = registerInitCommand;
+const node_fs_1 = __importDefault(require("node:fs"));
+const node_path_1 = __importDefault(require("node:path"));
+const command_context_1 = require("../lib/command-context");
+const compose_validator_1 = require("../lib/compose-validator");
+const config_1 = require("../lib/config");
+const ecosystem_1 = require("../lib/ecosystem");
+const compose_renderer_1 = require("../lib/compose-renderer");
+const errors_1 = require("../lib/errors");
+const mode_1 = require("../lib/mode");
+const parsers_1 = require("../lib/parsers");
+const orchestrator_1 = require("../lib/orchestrator");
+const github_auth_1 = require("../lib/github-auth");
+const prompt_1 = require("../lib/prompt");
+const preflight_1 = require("../lib/preflight");
+const preconditions_1 = require("../lib/preconditions");
+const shared_1 = require("./infra/shared");
+const shared_2 = require("./mcp/shared");
+const assistant_setup_1 = require("../stages/assistant-setup");
+const canon_sync_1 = require("../stages/canon-sync");
+const canon_ingest_1 = require("../stages/canon-ingest");
+const graph_seed_1 = require("../stages/graph-seed");
+const repo_scaffold_1 = require("../stages/repo-scaffold");
+const repo_analysis_1 = require("../stages/repo-analysis");
+const repo_analysis_fileonly_1 = require("../stages/repo-analysis-fileonly");
+const agent_skills_setup_1 = require("../stages/agent-skills-setup");
+const ci_setup_1 = require("../stages/ci-setup");
+const domain_gen_1 = require("../stages/domain-gen");
+const canon_resolver_1 = require("../lib/canon-resolver");
+const providers_1 = require("../lib/providers");
+const service_health_1 = require("../lib/service-health");
+function parseComposeMode(value, fallback = 'consolidated') {
+    if (!value) {
+        return fallback;
+    }
+    if (value === 'consolidated' || value === 'split') {
+        return value;
+    }
+    throw new errors_1.CliError(`Invalid compose mode '${value}'. Use 'consolidated' or 'split'.`);
+}
+// Use parseNumber from lib/parsers instead of local toNumber
+function inferComposeMode(config) {
+    const infraPath = node_path_1.default.resolve(config.workspaceDir, config.compose.infraFile);
+    const mcpPath = node_path_1.default.resolve(config.workspaceDir, config.compose.mcpFile);
+    if (node_fs_1.default.existsSync(infraPath) && node_fs_1.default.existsSync(mcpPath)) {
+        return 'split';
+    }
+    return 'consolidated';
+}
+async function resolveWizardSelection(options, config) {
+    const defaults = {
+        mode: (0, mode_1.parseMode)(options.mode, config.mode),
+        composeMode: parseComposeMode(options.composeMode, inferComposeMode(config)),
+    };
+    if (options.yes) {
+        if (!options.mode) {
+            process.stderr.write('Info: Non-interactive mode defaults to file-only. Use --mode indexed for graph/vector features.\n');
+        }
+        return {
+            ...defaults,
+            mode: options.mode ? (0, mode_1.parseMode)(options.mode) : 'file-only',
+            composeMode: options.composeMode ? parseComposeMode(options.composeMode) : 'consolidated',
+        };
+    }
+    const mode = options.mode
+        ? (0, mode_1.parseMode)(options.mode)
+        : await (0, prompt_1.promptChoice)('Select setup mode:', [
+            { value: 'file-only', label: 'file-only (skip infra + MCP startup)' },
+            { value: 'indexed', label: 'indexed (start infra + MCP and enable retrieval)' },
+        ], defaults.mode);
+    // Skip compose-mode prompt when mode is file-only — no Docker/MCP
+    // infrastructure is used, so compose configuration is irrelevant.
+    const composeMode = mode === 'file-only'
+        ? parseComposeMode(options.composeMode, 'consolidated')
+        : options.composeMode
+            ? parseComposeMode(options.composeMode)
+            : await (0, prompt_1.promptChoice)('Select compose generation mode:', [
+                { value: 'consolidated', label: 'consolidated (single docker-compose.yml)' },
+                { value: 'split', label: 'split (infra + mcp compose files)' },
+            ], defaults.composeMode);
+    return {
+        mode,
+        composeMode,
+    };
+}
+function renderMcpSnippet(provider, config) {
+    const workspace = config.workspaceDir;
+    const mcpUrl = 'http://127.0.0.1:7337/mcp';
+    switch (provider) {
+        case 'codex':
+            return {
+                filename: 'codex-mcp-config.toml',
+                content: [
+                    '# Generated by collab-cli',
+                    '[mcp_servers.collab_architecture]',
+                    'transport = "http"',
+                    `url = "${mcpUrl}"`,
+                    '',
+                    '# If MCP_API_KEYS is configured, set a bearer token header in your client.',
+                    '# headers = { Authorization = "Bearer <token>" }',
+                    '',
+                    `# Workspace: ${workspace}`,
+                    '',
+                ].join('\n'),
+            };
+        case 'claude':
+            return {
+                filename: 'claude-mcp-config.json',
+                content: JSON.stringify({
+                    _comment: 'Generated by collab-cli — merge into your Claude Code MCP settings',
+                    mcpServers: {
+                        'collab-architecture': {
+                            type: 'url',
+                            url: mcpUrl,
+                        },
+                    },
+                }, null, 2) + '\n',
+            };
+        case 'gemini':
+            return {
+                filename: 'gemini-mcp-config.json',
+                content: JSON.stringify({
+                    _comment: 'Generated by collab-cli — merge into your Gemini MCP settings',
+                    mcpServers: {
+                        'collab-architecture': {
+                            type: 'url',
+                            url: mcpUrl,
+                        },
+                    },
+                }, null, 2) + '\n',
+            };
+        case 'copilot':
+            // Copilot doesn't use MCP config snippets
+            return null;
+    }
+}
+// ────────────────────────────────────────────────────────────────
+// GitHub auth & business canon helpers
+// ────────────────────────────────────────────────────────────────
+function buildGitHubAuthStage(effectiveConfig, logger, options) {
+    return {
+        id: 'github-auth',
+        title: 'Authorize GitHub access',
+        recovery: [
+            'Set COLLAB_GITHUB_CLIENT_ID env var if OAuth App is not configured.',
+            'Use --github-token <token> to provide a token directly.',
+            'Run collab init --resume after fixing GitHub access.',
+        ],
+        run: async () => {
+            // Skip if no business canon is configured — GitHub auth is only needed for private repos
+            if (!effectiveConfig.canons?.business) {
+                logger.info('No business canon configured; skipping GitHub authorization.');
+                return;
+            }
+            // Check for pre-existing valid token
+            const existing = (0, github_auth_1.loadGitHubAuth)(effectiveConfig.collabDir);
+            if (existing) {
+                const valid = await (0, github_auth_1.isGitHubAuthValid)(existing);
+                if (valid) {
+                    logger.info('GitHub authorization already configured and valid.');
+                    return;
+                }
+                logger.info('Existing GitHub token is invalid or expired. Re-authorizing...');
+            }
+            // --github-token flag: store directly
+            if (options.githubToken) {
+                (0, github_auth_1.storeGitHubToken)(effectiveConfig.collabDir, options.githubToken);
+                logger.info('GitHub token stored from --github-token flag.');
+                return;
+            }
+            // --yes without token: fail
+            if (options.yes) {
+                throw new errors_1.CliError('GitHub authorization required. Use --github-token <token> in non-interactive mode.');
+            }
+            // Interactive: run Device Flow
+            await (0, github_auth_1.runGitHubDeviceFlow)(effectiveConfig.collabDir, (msg) => logger.info(msg));
+        },
+    };
+}
+function parseBusinessCanonOption(value) {
+    if (!value || value === 'none' || value === 'skip') {
+        return undefined;
+    }
+    if (!value.includes('/')) {
+        throw new errors_1.CliError(`Invalid business canon format "${value}". Use "owner/repo" or "none" to skip.`);
+    }
+    return {
+        business: {
+            repo: value,
+            branch: 'main',
+            localDir: 'business',
+        },
+    };
+}
+async function resolveBusinessCanon(options, logger) {
+    // CLI flag takes priority
+    if (options.businessCanon) {
+        return parseBusinessCanonOption(options.businessCanon);
+    }
+    // --yes without --business-canon: mandatory error
+    if (options.yes) {
+        throw new errors_1.CliError('--business-canon is required with --yes. Use --business-canon owner/repo or --business-canon none.');
+    }
+    // Interactive prompt
+    const repo = await (0, prompt_1.promptText)('Business architecture canon repo (owner/repo, empty to skip):');
+    if (!repo) {
+        logger.info('No business canon configured.');
+        return undefined;
+    }
+    if (!repo.includes('/')) {
+        throw new errors_1.CliError(`Invalid format "${repo}". Use "owner/repo".`);
+    }
+    const branch = await (0, prompt_1.promptText)('Business canon branch:', 'main');
+    return {
+        business: {
+            repo,
+            branch: branch || 'main',
+            localDir: 'business',
+        },
+    };
+}
+// ────────────────────────────────────────────────────────────────
+// Shared inline stages used by both pipelines
+// ────────────────────────────────────────────────────────────────
+function buildPreflightStage(executor, logger, mode) {
+    return {
+        id: 'preflight',
+        title: 'Run preflight checks',
+        recovery: [
+            'Install missing dependencies reported by preflight.',
+            'Run collab init --resume after fixing prerequisites.',
+        ],
+        run: () => {
+            const checks = (0, preflight_1.runPreflightChecks)(executor, { mode });
+            (0, preflight_1.assertPreflightChecks)(checks, logger);
+        },
+    };
+}
+function buildConfigStage(effectiveConfig, executor, logger, configExistedBefore, force) {
+    return {
+        id: 'environment-setup',
+        title: 'Write local collab configuration',
+        recovery: [
+            'Verify write permissions for .collab and workspace directory.',
+            'Run collab init --resume once permissions are fixed.',
+        ],
+        run: () => {
+            if (configExistedBefore && !force) {
+                logger.info('Existing configuration detected; preserving it. Use --force to overwrite.');
+                return;
+            }
+            executor.ensureDirectory(effectiveConfig.collabDir);
+            executor.writeFile(effectiveConfig.configFile, `${(0, config_1.serializeUserConfig)(effectiveConfig)}\n`, { description: 'write collab config' });
+        },
+    };
+}
+function parseRepos(value) {
+    if (!value)
+        return null;
+    return value.split(',').map((r) => r.trim()).filter(Boolean);
+}
+async function resolveWorkspace(workspaceDir, options, logger) {
+    const name = (0, config_1.deriveWorkspaceName)(workspaceDir);
+    // Explicit --repos flag takes priority
+    const explicit = parseRepos(options.repos);
+    if (explicit && explicit.length > 0) {
+        const type = explicit.length >= 2 ? 'multi-repo' : 'mono-repo';
+        logger.info(`Workspace mode: ${explicit.length} repo(s) specified: ${explicit.join(', ')}`);
+        return { name, type, repos: explicit };
+    }
+    // Auto-detect workspace layout
+    const layout = (0, config_1.detectWorkspaceLayout)(workspaceDir);
+    if (layout) {
+        if (options.yes) {
+            logger.info(`Workspace auto-detected (${layout.type}): ${layout.repos.length} repo(s) found: ${layout.repos.join(', ')}`);
+            return { name, type: layout.type, repos: layout.repos };
+        }
+        // Interactive: for multi-repo let user confirm/select repos
+        if (layout.type === 'multi-repo') {
+            const selected = await (0, prompt_1.promptMultiSelect)('This directory contains multiple git repositories. Select repos to include:', layout.repos.map((r) => ({ value: r, label: r })), layout.repos);
+            if (selected.length === 0)
+                return null;
+            return { name, type: 'multi-repo', repos: selected };
+        }
+        // mono-repo auto-detected
+        logger.info(`Mono-repo workspace detected: ${layout.repos.join(', ')}`);
+        return { name, type: 'mono-repo', repos: layout.repos };
+    }
+    // No repos found
+    if (options.yes) {
+        // Non-interactive with no repos → treat cwd as mono-repo
+        logger.info('No repos discovered; initializing as mono-repo workspace.');
+        return { name, type: 'mono-repo', repos: ['.'] };
+    }
+    return null;
+}
+// ────────────────────────────────────────────────────────────────
+// Workspace pipeline builders
+// ────────────────────────────────────────────────────────────────
+function buildWorkspaceStages(effectiveConfig, executor, logger, configExistedBefore, options) {
+    return [
+        buildPreflightStage(executor, logger),
+        buildConfigStage(effectiveConfig, executor, logger, configExistedBefore, options.force),
+        buildGitHubAuthStage(effectiveConfig, logger, options),
+        assistant_setup_1.assistantSetupStage,
+        canon_sync_1.canonSyncStage,
+    ];
+}
+function buildPerRepoStages(mode) {
+    const analysisStage = mode === 'indexed' ? repo_analysis_1.repoAnalysisStage : repo_analysis_fileonly_1.repoAnalysisFileOnlyStage;
+    return [
+        repo_scaffold_1.repoScaffoldStage,
+        analysisStage,
+        ci_setup_1.ciSetupStage,
+        agent_skills_setup_1.agentSkillsSetupStage,
+    ];
+}
+function buildInfraStages(effectiveConfig, executor, logger, options, composeMode) {
+    const health = {
+        timeoutMs: (0, parsers_1.parseNumber)(options.timeoutMs, 5_000),
+        retries: (0, parsers_1.parseNumber)(options.retries, 15),
+        retryDelayMs: (0, parsers_1.parseNumber)(options.retryDelayMs, 2_000),
+    };
+    return [
+        {
+            id: 'compose-generation',
+            title: 'Generate and validate compose files',
+            recovery: [
+                'Run collab compose validate to inspect configuration errors.',
+                'Run collab init --resume after fixing compose inputs.',
+            ],
+            run: () => {
+                const generation = (0, compose_renderer_1.generateComposeFiles)({
+                    config: effectiveConfig,
+                    mode: composeMode,
+                    outputDirectory: options.outputDir,
+                    logger,
+                    executor,
+                });
+                for (const warning of generation.driftWarnings) {
+                    logger.warn(warning);
+                }
+                (0, compose_validator_1.assertComposeFilesValid)(generation.files.map((file) => file.filePath), effectiveConfig.workspaceDir, executor);
+            },
+        },
+        {
+            id: 'infra-start',
+            title: 'Start infrastructure services',
+            recovery: [
+                'Run collab infra status to inspect Qdrant and Nebula.',
+                'Run collab init --resume after infra services are healthy.',
+            ],
+            run: async () => {
+                // Check if infra is already running (e.g. from a workspace-level init)
+                const env = (0, service_health_1.loadRuntimeEnv)(effectiveConfig);
+                const probe = await (0, service_health_1.waitForInfraHealth)(env, { ...health, retries: 1 });
+                if (probe.ok) {
+                    logger.info('Infrastructure already running — skipping docker compose up.');
+                    (0, service_health_1.logServiceHealth)(logger, 'infra health', probe);
+                    return;
+                }
+                const selection = (0, shared_1.resolveInfraComposeFile)(effectiveConfig, options.outputDir, undefined);
+                await (0, shared_1.runInfraCompose)(logger, executor, effectiveConfig, selection, 'up', { health });
+            },
+        },
+        {
+            id: 'mcp-start',
+            title: 'Start MCP service',
+            recovery: [
+                'Run collab mcp status to inspect MCP runtime.',
+                'Run collab init --resume after MCP health endpoint responds.',
+            ],
+            run: async () => {
+                // Check if MCP is already running (e.g. from a workspace-level init)
+                const env = (0, service_health_1.loadRuntimeEnv)(effectiveConfig);
+                const probe = await (0, service_health_1.waitForMcpHealth)(env, { ...health, retries: 1 });
+                if (probe.ok) {
+                    logger.info('MCP service already running — skipping docker compose up.');
+                    (0, service_health_1.logServiceHealth)(logger, 'mcp health', probe);
+                    return;
+                }
+                const selection = (0, shared_2.resolveMcpComposeFile)(effectiveConfig, options.outputDir, undefined);
+                await (0, shared_2.runMcpCompose)(logger, executor, effectiveConfig, selection, 'up', { health });
+            },
+        },
+        {
+            id: 'mcp-client-config',
+            title: 'Generate MCP client config snippets',
+            recovery: [
+                'Verify permissions in .collab directory.',
+                'Run collab init --resume to regenerate MCP config snippets.',
+            ],
+            run: () => {
+                if (options.skipMcpSnippets) {
+                    logger.info('Skipping MCP snippet generation by user choice.');
+                    return;
+                }
+                const enabled = (0, providers_1.getEnabledProviders)(effectiveConfig);
+                if (enabled.length === 0) {
+                    logger.info('No providers configured; skipping MCP snippet generation.');
+                    return;
+                }
+                for (const provider of enabled) {
+                    const snippet = renderMcpSnippet(provider, effectiveConfig);
+                    if (!snippet)
+                        continue;
+                    const target = node_path_1.default.join(effectiveConfig.collabDir, snippet.filename);
+                    executor.writeFile(target, snippet.content, {
+                        description: `write ${providers_1.PROVIDER_DEFAULTS[provider].label} MCP config snippet`,
+                    });
+                }
+                logger.info(`Generated MCP snippets for: ${enabled.map((k) => providers_1.PROVIDER_DEFAULTS[k].label).join(', ')}`);
+            },
+        },
+        graph_seed_1.graphSeedStage,
+        canon_ingest_1.canonIngestStage,
+    ];
+}
+// ────────────────────────────────────────────────────────────────
+// File-only pipeline (8 stages)
+// ────────────────────────────────────────────────────────────────
+function buildFileOnlyPipeline(effectiveConfig, executor, logger, configExistedBefore, options) {
+    return [
+        buildPreflightStage(executor, logger), // 1
+        buildConfigStage(effectiveConfig, executor, logger, configExistedBefore, options.force), // 2
+        buildGitHubAuthStage(effectiveConfig, logger, options), // 3
+        assistant_setup_1.assistantSetupStage, // 4
+        canon_sync_1.canonSyncStage, // 5
+        repo_scaffold_1.repoScaffoldStage, // 6
+        repo_analysis_fileonly_1.repoAnalysisFileOnlyStage, // 7
+        ci_setup_1.ciSetupStage, // 8
+        agent_skills_setup_1.agentSkillsSetupStage, // 9
+    ];
+}
+// ────────────────────────────────────────────────────────────────
+// Indexed pipeline (15 stages)
+// ────────────────────────────────────────────────────────────────
+function buildIndexedPipeline(effectiveConfig, executor, logger, configExistedBefore, options, composeMode) {
+    return [
+        // Phase A — Local setup (shared with file-only)
+        buildPreflightStage(executor, logger, 'indexed'), // 1
+        buildConfigStage(effectiveConfig, executor, logger, configExistedBefore, options.force), // 2
+        buildGitHubAuthStage(effectiveConfig, logger, options), // 3
+        assistant_setup_1.assistantSetupStage, // 4
+        canon_sync_1.canonSyncStage, // 5
+        repo_scaffold_1.repoScaffoldStage, // 6
+        repo_analysis_1.repoAnalysisStage, // 7
+        ci_setup_1.ciSetupStage, // 8
+        agent_skills_setup_1.agentSkillsSetupStage, // 9
+        // Phase B — Infrastructure + Phase C — Ingestion  (9-14)
+        ...buildInfraStages(effectiveConfig, executor, logger, options, composeMode),
+    ];
+}
+// ────────────────────────────────────────────────────────────────
+// Standalone infra phase  (collab init infra)
+// ────────────────────────────────────────────────────────────────
+async function runInfraOnly(context, options) {
+    // Build an indexed config — infra always implies indexed mode.
+    // If a config already exists we honour it; otherwise bootstrap one.
+    const effectiveConfig = {
+        ...(0, config_1.defaultCollabConfig)(context.config.workspaceDir),
+        ...context.config,
+        mode: 'indexed',
+    };
+    // Persist config so subsequent commands (infra status, mcp status) work.
+    const configExists = node_fs_1.default.existsSync(effectiveConfig.configFile);
+    if (!configExists) {
+        context.executor.ensureDirectory(effectiveConfig.collabDir);
+        context.executor.writeFile(effectiveConfig.configFile, `${(0, config_1.serializeUserConfig)(effectiveConfig)}\n`, { description: 'write collab config (infra bootstrap)' });
+    }
+    const composeMode = parseComposeMode(options.composeMode, inferComposeMode(effectiveConfig));
+    context.logger.phaseHeader('Infrastructure', 'Docker + MCP services');
+    const infraStages = buildInfraStages(effectiveConfig, context.executor, context.logger, options, composeMode);
+    await (0, orchestrator_1.runOrchestration)({
+        workflowId: 'init:infra',
+        config: effectiveConfig,
+        executor: context.executor,
+        logger: context.logger,
+        resume: options.resume,
+        mode: 'indexed (infra)',
+        stageOptions: { outputDir: options.outputDir },
+    }, infraStages);
+    // Summary
+    context.logger.phaseHeader('Infrastructure Ready');
+    context.logger.summaryFooter([
+        { label: 'Phase', value: 'infra only' },
+        { label: 'Compose mode', value: composeMode },
+        { label: 'Dry-run', value: context.executor.dryRun ? 'yes' : 'no' },
+        { label: 'Config', value: effectiveConfig.configFile },
+    ]);
+}
+// ────────────────────────────────────────────────────────────────
+// Repo domain generation  (collab init --repo=<package>)
+// ────────────────────────────────────────────────────────────────
+/**
+ * Resolves and validates the path to a repository package.
+ *
+ * Resolution order:
+ *   1. Absolute path → use directly
+ *   2. Relative path from workspace dir → resolve
+ *   3. Name within workspace → join with workspaceDir
+ *
+ * @throws {CliError} When the path is not found or is not a directory.
+ */
+function resolveRepoPath(repoValue, config) {
+    const isDirectory = (p) => {
+        try {
+            return node_fs_1.default.statSync(p).isDirectory();
+        }
+        catch {
+            return false;
+        }
+    };
+    // 1. Absolute path
+    if (node_path_1.default.isAbsolute(repoValue)) {
+        if (!node_fs_1.default.existsSync(repoValue)) {
+            throw new errors_1.CliError(`Repository path not found: ${repoValue}`);
+        }
+        if (!isDirectory(repoValue)) {
+            throw new errors_1.CliError(`Repository path is not a directory: ${repoValue}`);
+        }
+        return repoValue;
+    }
+    // 2. Relative path from workspace dir (respects --cwd)
+    const fromCwd = node_path_1.default.resolve(config.workspaceDir, repoValue);
+    if (isDirectory(fromCwd)) {
+        return fromCwd;
+    }
+    // 3. Name within workspace
+    const fromWorkspace = node_path_1.default.join(config.workspaceDir, repoValue);
+    if (isDirectory(fromWorkspace)) {
+        return fromWorkspace;
+    }
+    throw new errors_1.CliError(`Repository "${repoValue}" not found.\n` +
+        `Searched:\n` +
+        `  - ${fromCwd}\n` +
+        `  - ${fromWorkspace}\n` +
+        `Provide an absolute path, a relative path from cwd, or a repo name within your workspace.`);
+}
+async function runRepoDomainGeneration(context, options) {
+    const repoValue = options.repo;
+    // Build a minimal config — reuse existing if available
+    const effectiveConfig = {
+        ...(0, config_1.defaultCollabConfig)(context.config.workspaceDir),
+        ...context.config,
+    };
+    // Resolve business canon if passed via flag (but don't require it for file-only)
+    const canons = options.businessCanon ? parseBusinessCanonOption(options.businessCanon) : undefined;
+    if (canons) {
+        effectiveConfig.canons = canons;
+    }
+    // Store GitHub token if provided (required for indexed push/sync)
+    if (options.githubToken) {
+        if (context.executor.dryRun) {
+            context.logger.info('[dry-run] Would store GitHub token from --github-token flag.');
+        }
+        else {
+            (0, github_auth_1.storeGitHubToken)(effectiveConfig.collabDir, options.githubToken);
+            context.logger.info('GitHub token stored from --github-token flag.');
+        }
+    }
+    // Resolve mode
+    let mode;
+    if (options.mode) {
+        mode = (0, mode_1.parseMode)(options.mode);
+    }
+    else if (options.yes) {
+        mode = 'file-only';
+    }
+    else {
+        mode = await (0, prompt_1.promptChoice)('Select domain generation mode:', [
+            { value: 'file-only', label: 'file-only (write domain files to local repo only)' },
+            { value: 'indexed', label: 'indexed (write to business canon + ingest into MCP)' },
+        ], 'file-only');
+    }
+    // Validate prerequisites
+    if (mode === 'indexed' && !(0, canon_resolver_1.isBusinessCanonConfigured)(effectiveConfig)) {
+        throw new errors_1.CliError('Business canon is required for indexed mode. ' +
+            'Use --business-canon owner/repo to configure it, or use --mode file-only.');
+    }
+    // Resolve repo path
+    const repoPath = resolveRepoPath(repoValue, effectiveConfig);
+    const repoName = node_path_1.default.basename(repoPath);
+    context.logger.phaseHeader('Domain Generation', `${repoName} (${mode})`);
+    // Build pipeline
+    const stages = mode === 'file-only'
+        ? (0, domain_gen_1.buildFileOnlyDomainPipeline)()
+        : (0, domain_gen_1.buildIndexedDomainPipeline)();
+    // Execute
+    await (0, orchestrator_1.runOrchestration)({
+        workflowId: 'init:repo-domain',
+        config: effectiveConfig,
+        executor: context.executor,
+        logger: context.logger,
+        resume: options.resume,
+        mode: `${mode} (repo domain)`,
+        stageOptions: {
+            _repoPath: repoPath,
+            yes: options.yes,
+            providers: options.providers,
+        },
+    }, stages);
+    // Summary
+    context.logger.phaseHeader('Domain Generation Complete');
+    context.logger.summaryFooter([
+        { label: 'Mode', value: mode },
+        { label: 'Repository', value: repoName },
+        { label: 'Dry-run', value: context.executor.dryRun ? 'yes' : 'no' },
+    ]);
+}
+// ────────────────────────────────────────────────────────────────
+// Command registration
+// ────────────────────────────────────────────────────────────────
+function registerInitCommand(program) {
+    program
+        .command('init')
+        .description('Run onboarding wizard and orchestrate setup stages')
+        .argument('[phase]', 'Optional phase to run in isolation (e.g. "infra")')
+        .option('-f, --force', 'Overwrite existing .collab/config.json with new wizard selection')
+        .option('--yes', 'Accept wizard defaults and run non-interactively')
+        .option('--resume', 'Resume from the last incomplete wizard stage')
+        .option('--mode <mode>', 'Wizard mode: file-only|indexed')
+        .option('--compose-mode <mode>', 'Compose mode: consolidated|split')
+        .option('--output-dir <directory>', 'Directory used to write compose outputs')
+        .option('--repos <list>', 'Comma-separated repo directories for workspace mode')
+        .option('--repo <package>', 'Generate domain definition from package analysis')
+        .option('--skip-mcp-snippets', 'Skip MCP client config snippet generation')
+        .option('--skip-analysis', 'Skip AI-powered repository analysis stage')
+        .option('--skip-ci', 'Skip CI workflow generation')
+        .option('--providers <list>', 'Comma-separated AI provider list (codex,claude,gemini,copilot)')
+        .option('--business-canon <owner/repo>', 'Business canon repo (owner/repo or "none" to skip)')
+        .option('--github-token <token>', 'GitHub token for non-interactive mode')
+        .option('--timeout-ms <ms>', 'Per-check timeout in milliseconds', '5000')
+        .option('--retries <count>', 'Health check retries', '15')
+        .option('--retry-delay-ms <ms>', 'Delay between retries in milliseconds', '2000')
+        .addHelpText('after', `
+Examples:
+  collab init
+  collab init --yes
+  collab init --yes --mode file-only
+  collab init --yes --mode indexed
+  collab init --repos api,web,shared --yes
+  collab init --repo collab-chat-ai-pkg --mode file-only
+  collab init --repo collab-chat-ai-pkg --mode indexed
+  collab init --resume
+  collab init infra
+  collab init infra --resume
+`)
+        .action(async (phase, options, command) => {
+        const context = (0, command_context_1.createCommandContext)(command);
+        (0, preconditions_1.ensureWritableDirectory)(context.config.workspaceDir);
+        // ── Phase shortcut: collab init infra ───────────────────
+        if (phase === 'infra') {
+            await runInfraOnly(context, options);
+            return;
+        }
+        if (phase) {
+            throw new errors_1.CliError(`Unknown init phase "${phase}". Available phases: infra`);
+        }
+        // ── Repo domain generation: collab init --repo <pkg> ───
+        if (options.repo) {
+            await runRepoDomainGeneration(context, options);
+            // Ecosystem compatibility checks (same as full wizard)
+            const compatibility = await (0, ecosystem_1.checkEcosystemCompatibility)(context.config, {
+                dryRun: context.executor.dryRun,
+            });
+            for (const check of compatibility) {
+                const prefix = check.ok ? '[PASS]' : '[WARN]';
+                context.logger.result(`${prefix} ${check.id}: ${check.detail}`);
+                if (!check.ok && check.fix)
+                    context.logger.result(`       fix: ${check.fix}`);
+            }
+            return;
+        }
+        // ── Full wizard flow ────────────────────────────────────
+        const configExistedBefore = node_fs_1.default.existsSync(context.config.configFile);
+        if (options.force) {
+            context.logger.warn('Force mode enabled: configuration will be overwritten with wizard selections.');
+        }
+        // ── Step 1: Configuration wizard ────────────────────────
+        context.logger.phaseHeader('collab init', 'Configuration');
+        const selections = await resolveWizardSelection(options, context.config);
+        const preserveExisting = configExistedBefore && !options.force;
+        const effectiveConfig = {
+            ...(0, config_1.defaultCollabConfig)(context.config.workspaceDir),
+            ...context.config,
+            mode: preserveExisting ? context.config.mode : selections.mode,
+        };
+        // ── Step 2: Business canon configuration ──────────────────
+        const canons = await resolveBusinessCanon(options, context.logger);
+        if (canons) {
+            effectiveConfig.canons = canons;
+        }
+        const stageOptions = {
+            yes: options.yes,
+            providers: options.providers,
+            outputDir: options.outputDir,
+            skipAnalysis: options.skipAnalysis,
+            skipCi: options.skipCi,
+        };
+        // ── Workspace detection ───────────────────────────────────
+        // Prefer persisted workspace config when it exists (unless
+        // --force or explicit --repos override is provided).
+        const ws = !options.force && !options.repos && context.config.workspace
+            ? context.config.workspace
+            : await resolveWorkspace(context.config.workspaceDir, options, context.logger);
+        if (ws) {
+            // ── WORKSPACE MODE ────────────────────────────────────
+            effectiveConfig.workspace = { name: ws.name, type: ws.type, repos: ws.repos };
+            effectiveConfig.compose = {
+                ...effectiveConfig.compose,
+                projectName: `collab-${ws.name}`,
+            };
+            const repoConfigs = (0, config_1.resolveRepoConfigs)(effectiveConfig);
+            // Phase W — workspace-level stages
+            context.logger.phaseHeader('Workspace Setup', `${ws.repos.length} repositories (${ws.type})`);
+            const workspaceStages = buildWorkspaceStages(effectiveConfig, context.executor, context.logger, configExistedBefore, options);
+            await (0, orchestrator_1.runOrchestration)({
+                workflowId: 'init',
+                config: effectiveConfig,
+                executor: context.executor,
+                logger: context.logger,
+                resume: options.resume,
+                mode: `${selections.mode} (workspace)`,
+                stageOptions,
+            }, workspaceStages);
+            // Phase R — per-repo stages
+            context.logger.phaseHeader('Repository Analysis', `${selections.mode} mode`);
+            const perRepoStages = buildPerRepoStages(selections.mode);
+            for (const [i, rc] of repoConfigs.entries()) {
+                context.logger.repoHeader(rc.name, i + 1, repoConfigs.length);
+                await (0, orchestrator_1.runPerRepoOrchestration)({
+                    workflowId: 'init',
+                    config: effectiveConfig,
+                    executor: context.executor,
+                    logger: context.logger,
+                    resume: options.resume,
+                    stageOptions,
+                }, rc, perRepoStages);
+            }
+            // Phase I — infra stages (indexed only)
+            if (selections.mode === 'indexed') {
+                context.logger.phaseHeader('Infrastructure', 'Docker + MCP services');
+                const infraStages = buildInfraStages(effectiveConfig, context.executor, context.logger, options, selections.composeMode);
+                await (0, orchestrator_1.runOrchestration)({
+                    workflowId: 'init:infra',
+                    config: effectiveConfig,
+                    executor: context.executor,
+                    logger: context.logger,
+                    resume: options.resume,
+                    mode: 'indexed (infra)',
+                    stageOptions,
+                }, infraStages);
+            }
+        }
+        else {
+            // ── SINGLE-REPO MODE (unchanged) ──────────────────────
+            context.logger.phaseHeader('Project Setup', selections.mode);
+            const stages = selections.mode === 'file-only'
+                ? buildFileOnlyPipeline(effectiveConfig, context.executor, context.logger, configExistedBefore, options)
+                : buildIndexedPipeline(effectiveConfig, context.executor, context.logger, configExistedBefore, options, selections.composeMode);
+            await (0, orchestrator_1.runOrchestration)({
+                workflowId: 'init',
+                config: effectiveConfig,
+                executor: context.executor,
+                logger: context.logger,
+                resume: options.resume,
+                mode: selections.mode,
+                stageOptions,
+            }, stages);
+        }
+        // ── Summary ───────────────────────────────────────────
+        context.logger.phaseHeader('Setup Complete');
+        const enabledProviders = (0, providers_1.getEnabledProviders)(effectiveConfig);
+        const providerLabel = enabledProviders.length > 0
+            ? enabledProviders.map((k) => providers_1.PROVIDER_DEFAULTS[k].label).join(', ')
+            : '(none configured)';
+        const summaryEntries = [
+            { label: 'Mode', value: selections.mode },
+            { label: 'Dry-run', value: context.executor.dryRun ? 'yes' : 'no' },
+            { label: 'Config', value: effectiveConfig.configFile },
+            { label: 'Providers', value: providerLabel },
+        ];
+        if (ws) {
+            summaryEntries.splice(1, 0, { label: 'Workspace', value: `${ws.name} (${ws.type})` }, { label: 'Repos', value: ws.repos.join(', ') });
+        }
+        if (selections.mode === 'indexed') {
+            summaryEntries.splice(ws ? 3 : 1, 0, { label: 'Compose mode', value: selections.composeMode });
+        }
+        context.logger.summaryFooter(summaryEntries);
+        // Ecosystem compatibility checks
+        const compatibility = await (0, ecosystem_1.checkEcosystemCompatibility)(effectiveConfig, {
+            dryRun: context.executor.dryRun,
+        });
+        for (const check of compatibility) {
+            const prefix = check.ok ? '[PASS]' : '[WARN]';
+            context.logger.result(`${prefix} ${check.id}: ${check.detail}`);
+            if (!check.ok && check.fix) {
+                context.logger.result(`       fix: ${check.fix}`);
+            }
+        }
+        // ── Next steps guidance ──────────────────────────────
+        context.logger.info('');
+        context.logger.info('Next steps:');
+        if (selections.mode === 'file-only') {
+            context.logger.info('  - Upgrade to indexed mode for graph/vector features:');
+            context.logger.info('      collab init --mode indexed');
+        }
+        if (selections.mode === 'indexed') {
+            context.logger.info('  - Populate graph and vector stores:');
+            context.logger.info('      collab canon rebuild --confirm');
+        }
+        if (ws) {
+            context.logger.info('  - Initialize domain repos:');
+            context.logger.info('      collab init --repo=<package-name>');
+        }
+        context.logger.info('  - Verify full setup health:');
+        context.logger.info('      collab doctor');
+        context.logger.info('  - Finalize and archive when done:');
+        context.logger.info('      collab end');
+        if (!options.force && configExistedBefore) {
+            context.logger.debug('Existing configuration was reused.');
+        }
+    });
+}