@cleocode/core 2026.4.9 → 2026.4.11

package/dist/init.js

@@ -0,0 +1,852 @@
+/**
+ * Core init logic - project initialization and maintenance.
+ *
+ * Single source of truth for all init operations. CLI delegates here
+ * (shared-core pattern).
+ *
+ * Handles:
+ *   1. .cleo/ directory structure creation
+ *   2. Core data files (config.json, tasks.db)
+ *   3. Schema file installation (~/.cleo/schemas/)
+ *   4. Sequence counter (SQLite schema_meta)
+ *   5. Project info (.cleo/project-info.json)
+ *   6. CAAMP injection into agent instruction files (AGENTS.md hub pattern)
+ *   7. (removed — was MCP server installation)
+ *   8. Agent definition installation (cleo-subagent)
+ *   9. Core skill installation via CAAMP
+ *  10. NEXUS project registration
+ *  11. Project type detection (--detect)
+ *  12. Injection refresh
+ *  13. Git hook installation (commit-msg, pre-commit)
+ *  14. GitHub issue/PR templates (.github/ directory)
+ *
+ * @task T4681
+ * @task T4682
+ * @task T4684
+ * @task T4685
+ * @task T4686
+ * @task T4687
+ * @task T4689
+ * @task T4706
+ * @task T4707
+ * @epic T4663
+ */
+import { existsSync, readdirSync, readFileSync } from 'node:fs';
+import { copyFile, lstat, mkdir, readFile, symlink, unlink, writeFile } from 'node:fs/promises';
+import { platform } from 'node:os';
+import { basename, dirname, join } from 'node:path';
+import { ExitCode } from '@cleocode/contracts';
+import { classifyProject } from './discovery.js';
+import { CleoError } from './errors.js';
+import { ensureGitHooks } from './hooks.js';
+import { ensureInjection } from './injection.js';
+import { writeMemoryBridge } from './memory/memory-bridge.js';
+import { migrateAgentOutputs } from './migration/agent-outputs.js';
+import { getAgentsHome, getCleoDirAbsolute, getProjectRoot } from './paths.js';
+// Shared utility imports
+import { ensureBrainDb, ensureCleoGitRepo, ensureCleoOsHub, ensureCleoStructure, ensureConfig, ensureGitignore, ensureProjectContext, ensureProjectInfo, getPackageRoot, removeCleoFromRootGitignore, } from './scaffold.js';
+import { ensureGlobalSchemas } from './schema-management.js';
+import { readJson } from './store/json.js';
+// ── Helpers ──────────────────────────────────────────────────────────
+/**
+ * Symlink type for directory symlinks.
+ * On Windows, use 'junction' (no admin privileges required).
+ * On Unix, use 'dir'.
+ */
+const DIR_SYMLINK_TYPE = platform() === 'win32' ? 'junction' : 'dir';
+// ── Init-specific operations ─────────────────────────────────────────
+/**
+ * Resolve the absolute path to the bundled `seed-agents/` directory inside
+ * the `@cleocode/agents` package.
+ *
+ * Mirrors the multi-candidate resolution pattern used by
+ * {@link initAgentDefinition} so the same code path works across all layouts:
+ *   1. **npm install** — `require.resolve('@cleocode/agents/package.json')`
+ *      finds the package under `node_modules/@cleocode/agents/`.
+ *   2. **Workspace dev (bundled CLI)** — walks up from `getPackageRoot()`
+ *      (which resolves to `packages/cleo/dist/` or `packages/core/`) to find
+ *      `packages/agents/seed-agents/`.
+ *   3. **Monorepo dev (source)** — falls back to `packages/agents/seed-agents/`
+ *      relative to `getPackageRoot()`.
+ *
+ * @returns Absolute path to an existing `seed-agents/` directory, or `null`
+ *          if no candidate exists. Returning `null` lets callers skip the
+ *          seed install gracefully without crashing.
+ *
+ * @task T283
+ * @epic T280
+ */
+export async function resolveSeedAgentsDir() {
+    // Primary: resolve via Node module resolution (@cleocode/agents)
+    try {
+        const { createRequire } = await import('node:module');
+        const req = createRequire(import.meta.url);
+        const agentsPkgMain = req.resolve('@cleocode/agents/package.json');
+        const agentsPkgRoot = dirname(agentsPkgMain);
+        const candidate = join(agentsPkgRoot, 'seed-agents');
+        if (existsSync(candidate)) {
+            return candidate;
+        }
+    }
+    catch {
+        // Not resolvable via require.resolve — fall through to bundled path
+    }
+    // Walk a series of candidate paths relative to getPackageRoot(), which
+    // can resolve to several different locations depending on whether we're
+    // running from packages/core/dist, packages/cleo/dist, or installed under
+    // node_modules/@cleocode/.
+    const packageRoot = getPackageRoot();
+    const candidates = [
+        // Workspace fallback: bundled alongside core under packages/agents/seed-agents
+        join(packageRoot, 'agents', 'seed-agents'),
+        // Sibling-package layout (e.g. node_modules/@cleocode/core -> ../agents)
+        join(packageRoot, '..', 'agents', 'seed-agents'),
+        // Bundled CLI: packages/cleo/dist -> ../../agents/seed-agents
+        join(packageRoot, '..', '..', 'agents', 'seed-agents'),
+        // Bundled CLI dist subdir: packages/cleo/dist/cli -> ../../../packages/agents
+        join(packageRoot, '..', '..', 'packages', 'agents', 'seed-agents'),
+        // Monorepo workspace from repo root
+        join(packageRoot, '..', '..', '..', 'packages', 'agents', 'seed-agents'),
+    ];
+    return candidates.find((p) => existsSync(p)) ?? null;
+}
+/**
+ * Install cleo-subagent agent definition to ~/.agents/agents/.
+ * @task T4685
+ */
+export async function initAgentDefinition(created, warnings) {
+    // Resolve agents package via require.resolve, then workspace/bundled fallback
+    let agentSourceDir = null;
+    try {
+        const { createRequire } = await import('node:module');
+        const req = createRequire(import.meta.url);
+        const agentsPkgMain = req.resolve('@cleocode/agents/package.json');
+        const agentsPkgRoot = dirname(agentsPkgMain);
+        const candidate = join(agentsPkgRoot, 'cleo-subagent');
+        if (existsSync(candidate)) {
+            agentSourceDir = candidate;
+        }
+    }
+    catch {
+        // Not resolvable via require.resolve — fall through to bundled path
+    }
+    if (!agentSourceDir) {
+        const packageRoot = getPackageRoot();
+        const bundled = join(packageRoot, 'agents', 'cleo-subagent');
+        if (existsSync(bundled)) {
+            agentSourceDir = bundled;
+        }
+    }
+    if (!agentSourceDir) {
+        warnings.push('agents/cleo-subagent/ not found in package, skipping agent definition install');
+        return;
+    }
+    const globalAgentsDir = join(getAgentsHome(), 'agents', 'cleo-subagent');
+    await mkdir(dirname(globalAgentsDir), { recursive: true });
+    try {
+        // Check if symlink already exists and points to correct target
+        try {
+            const stat = await lstat(globalAgentsDir);
+            if (stat.isSymbolicLink()) {
+                const { readlink } = await import('node:fs/promises');
+                const currentTarget = await readlink(globalAgentsDir);
+                if (currentTarget === agentSourceDir) {
+                    return; // Symlink intact and pointing to correct location
+                }
+                // Stale symlink — remove and recreate
+                await unlink(globalAgentsDir);
+            }
+            else if (stat.isDirectory()) {
+                return; // Copied dir, leave as-is
+            }
+        }
+        catch {
+            // Doesn't exist, proceed to create
+        }
+        // Create symlink from ~/.agents/agents/cleo-subagent -> package agents/cleo-subagent/
+        await symlink(agentSourceDir, globalAgentsDir, DIR_SYMLINK_TYPE);
+        created.push('agent: cleo-subagent (symlinked)');
+    }
+    catch (_err) {
+        // If symlink fails (e.g., permissions), try copying
+        try {
+            await mkdir(globalAgentsDir, { recursive: true });
+            const files = readdirSync(agentSourceDir);
+            for (const file of files) {
+                await copyFile(join(agentSourceDir, file), join(globalAgentsDir, file));
+            }
+            created.push('agent: cleo-subagent (copied)');
+        }
+        catch (copyErr) {
+            warnings.push(`Agent definition install: ${copyErr instanceof Error ? copyErr.message : String(copyErr)}`);
+        }
+    }
+}
+/**
+ * No-op. Kept for API compatibility.
+ * @task T4706
+ */
+export async function initMcpServer(_projectRoot, _created, _warnings) {
+    // No-op: removed
+}
+/**
+ * Install CLEO core skills to the canonical skills directory via CAAMP.
+ * @task T4707
+ * @task T4689
+ */
+export async function initCoreSkills(created, warnings) {
+    try {
+        const { getInstalledProviders, installSkill, registerSkillLibraryFromPath } = await import('@cleocode/caamp');
+        const providers = getInstalledProviders();
+        if (providers.length === 0) {
+            return;
+        }
+        // Find skills package via require.resolve, then workspace path, then node_modules fallback
+        const packageRoot = getPackageRoot();
+        let ctSkillsRoot = null;
+        try {
+            // Primary: resolve via Node module resolution (@cleocode/skills)
+            const { createRequire } = await import('node:module');
+            const req = createRequire(import.meta.url);
+            const skillsPkgMain = req.resolve('@cleocode/skills/package.json');
+            const skillsPkgRoot = dirname(skillsPkgMain);
+            if (existsSync(join(skillsPkgRoot, 'skills.json'))) {
+                ctSkillsRoot = skillsPkgRoot;
+            }
+        }
+        catch {
+            // Not resolvable via require.resolve — try workspace and node_modules fallbacks
+        }
+        if (!ctSkillsRoot) {
+            try {
+                // Workspace monorepo fallback (packages/skills/)
+                const bundledPath = join(packageRoot, 'packages', 'skills');
+                if (existsSync(join(bundledPath, 'skills.json'))) {
+                    ctSkillsRoot = bundledPath;
+                }
+                else {
+                    // node_modules fallback
+                    const ctSkillsPath = join(packageRoot, 'node_modules', '@cleocode', 'skills');
+                    if (existsSync(join(ctSkillsPath, 'skills.json'))) {
+                        ctSkillsRoot = ctSkillsPath;
+                    }
+                }
+            }
+            catch {
+                // not found
+            }
+        }
+        if (!ctSkillsRoot) {
+            warnings.push('skills package not found, skipping core skill installation');
+            return;
+        }
+        // Register bundled skill library with CAAMP
+        try {
+            registerSkillLibraryFromPath(ctSkillsRoot);
+        }
+        catch {
+            warnings.push('Failed to register skill library with CAAMP');
+        }
+        // Read the skills catalog to find core skills
+        const catalogPath = join(ctSkillsRoot, 'skills.json');
+        const catalog = JSON.parse(readFileSync(catalogPath, 'utf-8'));
+        const skills = catalog.skills ?? [];
+        // Install core and recommended skills (tier 0, 1, 2)
+        const coreSkills = skills.filter((s) => s.tier <= 2);
+        const installed = [];
+        for (const skill of coreSkills) {
+            const skillSourceDir = dirname(join(ctSkillsRoot, skill.path));
+            if (!existsSync(skillSourceDir)) {
+                continue;
+            }
+            try {
+                const result = await installSkill(skillSourceDir, skill.name, providers, true);
+                if (result.success) {
+                    installed.push(skill.name);
+                }
+            }
+            catch {
+                // Skill may already be installed, continue
+            }
+        }
+        if (installed.length > 0) {
+            created.push(`skills: ${installed.length} core skills installed`);
+        }
+    }
+    catch (err) {
+        warnings.push(`Core skill install: ${err instanceof Error ? err.message : String(err)}`);
+    }
+}
+/**
+ * Register/reconcile project with NEXUS.
+ * Uses nexusReconcile for idempotent handshake — auto-registers if new,
+ * updates path if moved, confirms identity if unchanged.
+ * @task T4684
+ * @task T5368
+ */
+export async function initNexusRegistration(projectRoot, created, warnings) {
+    try {
+        const { nexusReconcile } = await import('./nexus/registry.js');
+        const result = await nexusReconcile(projectRoot);
+        if (result.status === 'auto_registered') {
+            created.push('NEXUS registration (auto-registered new project)');
+        }
+        else if (result.status === 'path_updated') {
+            created.push(`NEXUS registration (path updated: ${result.oldPath} → ${result.newPath})`);
+        }
+        else if (result.status === 'ok') {
+            created.push('NEXUS registration (project verified and active)');
+        }
+    }
+    catch (err) {
+        const errStr = String(err);
+        if (errStr.includes('NEXUS_PROJECT_EXISTS')) {
+            warnings.push('NEXUS registration: Project already registered');
+        }
+        else if (errStr.includes('NEXUS_REGISTRY_CORRUPT')) {
+            warnings.push(`NEXUS registration: Identity conflict - ${err instanceof Error ? err.message : errStr}. Run 'cleo nexus unregister' and re-register.`);
+        }
+        else {
+            warnings.push(`NEXUS registration: ${err instanceof Error ? err.message : errStr}`);
+        }
+    }
+}
+// ── GitHub Templates ─────────────────────────────────────────────────
+/**
+ * Install GitHub issue and PR templates to .github/ if a git repo exists
+ * but .github/ISSUE_TEMPLATE/ is not yet present.
+ *
+ * Idempotent: skips files that already exist. Never overwrites existing
+ * templates — the project owner's customisations take precedence.
+ *
+ * @param projectRoot  Absolute path to the project root.
+ * @param created      Array to push "created: ..." log entries into.
+ * @param skipped      Array to push "skipped: ..." log entries into.
+ */
+export async function installGitHubTemplates(projectRoot, created, skipped) {
+    // Only apply when a .git directory is present (i.e. this is a git repo)
+    if (!existsSync(join(projectRoot, '.git'))) {
+        return;
+    }
+    const githubDir = join(projectRoot, '.github');
+    const issueTemplateDir = join(githubDir, 'ISSUE_TEMPLATE');
+    // Locate bundled templates shipped alongside the package
+    const packageRoot = getPackageRoot();
+    const templateSrcDir = join(packageRoot, 'templates', 'github');
+    if (!existsSync(templateSrcDir)) {
+        // Templates not bundled — skip silently (e.g. development builds)
+        return;
+    }
+    // Ensure .github/ISSUE_TEMPLATE/ directory tree exists
+    await mkdir(issueTemplateDir, { recursive: true });
+    // ── ISSUE_TEMPLATE files ─────────────────────────────────────────
+    const issueSrcDir = join(templateSrcDir, 'ISSUE_TEMPLATE');
+    if (existsSync(issueSrcDir)) {
+        const issueFiles = readdirSync(issueSrcDir);
+        for (const file of issueFiles) {
+            const dest = join(issueTemplateDir, file);
+            if (existsSync(dest)) {
+                skipped.push(`.github/ISSUE_TEMPLATE/${file}`);
+                continue;
+            }
+            const content = readFileSync(join(issueSrcDir, file), 'utf-8');
+            await writeFile(dest, content, 'utf-8');
+            created.push(`.github/ISSUE_TEMPLATE/${file}`);
+        }
+    }
+    // ── pull_request_template.md ─────────────────────────────────────
+    const prTemplateSrc = join(templateSrcDir, 'pull_request_template.md');
+    const prTemplateDest = join(githubDir, 'pull_request_template.md');
+    if (existsSync(prTemplateSrc)) {
+        if (existsSync(prTemplateDest)) {
+            skipped.push('.github/pull_request_template.md');
+        }
+        else {
+            const content = readFileSync(prTemplateSrc, 'utf-8');
+            await writeFile(prTemplateDest, content, 'utf-8');
+            created.push('.github/pull_request_template.md');
+        }
+    }
+}
+// ── Public API ───────────────────────────────────────────────────────
+/**
+ * Run update-docs only: refresh all injections without reinitializing.
+ * Re-injects CLEO-INJECTION.md into all detected agent instruction files.
+ *
+ * @task T4686
+ */
+export async function updateDocs() {
+    const cleoDir = getCleoDirAbsolute();
+    const projRoot = getProjectRoot();
+    const created = [];
+    const warnings = [];
+    // Re-inject into all provider instruction files (and AGENTS.md hub)
+    try {
+        const result = await ensureInjection(projRoot);
+        if (result.action !== 'skipped') {
+            created.push(`injection: ${result.details ?? result.action}`);
+        }
+    }
+    catch (err) {
+        warnings.push(`CAAMP injection: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    return {
+        initialized: true,
+        directory: cleoDir,
+        created,
+        skipped: [],
+        warnings,
+        updateDocsOnly: true,
+    };
+}
+/**
+ * Run full project initialization.
+ *
+ * Creates the .cleo/ directory structure, installs schemas, templates,
+ * agent definitions, skills, and registers with NEXUS.
+ *
+ * @task T4681
+ * @task T4682
+ * @task T4684
+ * @task T4685
+ * @task T4686
+ * @task T4687
+ * @task T4689
+ * @task T4706
+ * @task T4707
+ */
+export async function initProject(opts = {}) {
+    const cleoDir = getCleoDirAbsolute();
+    const projRoot = getProjectRoot();
+    // Guard: fail if project already initialized (unless --force)
+    const alreadyInitialized = existsSync(cleoDir) &&
+        (existsSync(join(cleoDir, 'tasks.db')) || existsSync(join(cleoDir, 'config.json')));
+    if (alreadyInitialized && !opts.force) {
+        throw new CleoError(ExitCode.GENERAL_ERROR, 'Project already initialized. DANGER ZONE: use --force to wipe and re-init.', { fix: 'cleo init --force' });
+    }
+    const force = !!opts.force;
+    const created = [];
+    const skipped = [];
+    const warnings = [];
+    // Phase 5 — classify the directory BEFORE creating any files so the
+    // classification reflects the real pre-init state of the directory.
+    let classification;
+    try {
+        classification = classifyProject(projRoot);
+    }
+    catch (err) {
+        warnings.push(`Project classification failed: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    // T4681: Create .cleo/ directory structure
+    const structureResult = await ensureCleoStructure(projRoot);
+    if (structureResult.action === 'created') {
+        created.push('.cleo/ directory structure');
+    }
+    // T4681: Create config.json
+    const configResult = await ensureConfig(projRoot, { force });
+    if (configResult.action === 'skipped') {
+        skipped.push('config.json');
+    }
+    else {
+        created.push('config.json');
+    }
+    // Initialize SQLite database (tasks, sessions, archive, audit log all live here)
+    try {
+        const { getDb } = await import('./store/sqlite.js');
+        await getDb(join(cleoDir, '..'));
+        created.push('tasks.db');
+    }
+    catch (err) {
+        // SQLite init failure is not fatal — will be created on first access
+        created.push(`tasks.db (deferred: ${err instanceof Error ? err.message : String(err)})`);
+    }
+    // Initialize brain.db for BRAIN memory system
+    try {
+        const brainResult = await ensureBrainDb(projRoot);
+        if (brainResult.action === 'created') {
+            created.push('brain.db');
+        }
+    }
+    catch (err) {
+        created.push(`brain.db (deferred: ${err instanceof Error ? err.message : String(err)})`);
+    }
+    // Initialize signaldock.db for local agent messaging infrastructure (T223)
+    try {
+        const { ensureSignaldockDb } = await import('./store/signaldock-sqlite.js');
+        const sdResult = await ensureSignaldockDb(projRoot);
+        if (sdResult.action === 'created') {
+            created.push('signaldock.db');
+        }
+    }
+    catch (err) {
+        // Non-fatal — signaldock.db will be created on first agent operation
+        created.push(`signaldock.db (deferred: ${err instanceof Error ? err.message : String(err)})`);
+    }
+    // T4681: Create .cleo/.gitignore (respect force flag)
+    if (force) {
+        // When force is set, always overwrite — ensureGitignore does content-comparison only
+        const gitignoreResult = await ensureGitignore(projRoot);
+        if (gitignoreResult.action === 'skipped') {
+            skipped.push('.gitignore');
+        }
+        else {
+            created.push('.gitignore');
+        }
+    }
+    else {
+        const gitignorePath = join(cleoDir, '.gitignore');
+        if (existsSync(gitignorePath)) {
+            skipped.push('.gitignore');
+        }
+        else {
+            const gitignoreResult = await ensureGitignore(projRoot);
+            if (gitignoreResult.action !== 'skipped') {
+                created.push('.gitignore');
+            }
+            else {
+                skipped.push('.gitignore');
+            }
+        }
+    }
+    // Remove legacy sequence files if they exist (migration)
+    const legacySequencePath = join(cleoDir, '.sequence');
+    try {
+        await unlink(legacySequencePath);
+    }
+    catch {
+        /* ignore if absent */
+    }
+    const legacySequenceJsonPath = join(cleoDir, '.sequence.json');
+    try {
+        await unlink(legacySequenceJsonPath);
+    }
+    catch {
+        /* ignore if absent */
+    }
+    // T4872: Isolated .cleo/.git checkpoint repository
+    try {
+        const gitRepoResult = await ensureCleoGitRepo(projRoot);
+        if (gitRepoResult.action === 'created') {
+            created.push('.cleo/.git (isolated checkpoint repository)');
+        }
+    }
+    catch (err) {
+        warnings.push(`Could not initialize .cleo/.git: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    // T4700: Migrate legacy agent-output directories before proceeding
+    try {
+        const migrationResult = migrateAgentOutputs(projRoot, cleoDir);
+        if (migrationResult.migrated) {
+            created.push(`agent-outputs migration: ${migrationResult.summary}`);
+        }
+    }
+    catch {
+        warnings.push('Agent-outputs migration failed (best-effort, run cleo upgrade to retry)');
+    }
+    // T4681: Schema files (~/.cleo/schemas/)
+    try {
+        const schemaResult = ensureGlobalSchemas({ force });
+        const total = schemaResult.installed + schemaResult.updated;
+        if (total > 0) {
+            created.push(`schemas/ (${total} files)`);
+        }
+    }
+    catch (err) {
+        warnings.push(`Schema installation: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    // Git hooks (commit-msg, pre-commit, pre-push)
+    try {
+        const hooksResult = await ensureGitHooks(projRoot, { force });
+        if (hooksResult.action === 'created') {
+            created.push(hooksResult.details ?? 'git hooks installed');
+        }
+        else if (hooksResult.action === 'skipped' && hooksResult.details?.includes('No .git/')) {
+            warnings.push(hooksResult.details);
+        }
+        else if (hooksResult.action === 'skipped' &&
+            hooksResult.details?.includes('not found in package root')) {
+            warnings.push(hooksResult.details);
+        }
+        else if (hooksResult.action === 'repaired' && hooksResult.details?.includes('error')) {
+            // Hook errors reported via details in 'repaired' action
+            const match = hooksResult.details.match(/Installed (\d+)/);
+            if (match && parseInt(match[1], 10) > 0) {
+                created.push(`git hooks (${match[1]} installed)`);
+            }
+            warnings.push(hooksResult.details);
+        }
+    }
+    catch (err) {
+        warnings.push(`Git hook installation: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    // T4684: Project info (.cleo/project-info.json)
+    const projectInfoResult = await ensureProjectInfo(projRoot, { force });
+    if (projectInfoResult.action === 'skipped') {
+        skipped.push('project-info.json');
+    }
+    else {
+        created.push('project-info.json');
+    }
+    // Project context detection (always run during init)
+    try {
+        const detectResult = await ensureProjectContext(projRoot, { force: !!opts.detect });
+        if (detectResult.action !== 'skipped') {
+            created.push('project-context.json');
+        }
+    }
+    catch (err) {
+        warnings.push(`Project detection failed: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    // Codebase analysis and brain.db storage (brownfield auto-mapping)
+    if (opts.mapCodebase) {
+        try {
+            const { mapCodebase } = await import('./codebase-map/index.js');
+            const mapResult = await mapCodebase(projRoot, { storeToBrain: true });
+            created.push(`codebase-map: ${mapResult.stack.languages.length} languages, ${mapResult.architecture.layers.length} layers analyzed`);
+        }
+        catch (err) {
+            warnings.push(`Codebase mapping: ${err instanceof Error ? err.message : String(err)}`);
+        }
+    }
+    // Generate memory-bridge.md from brain.db BEFORE injection so AGENTS.md can reference it
+    try {
+        const bridgeResult = await writeMemoryBridge(projRoot);
+        if (bridgeResult.written) {
+            created.push('memory-bridge.md');
+        }
+    }
+    catch (err) {
+        warnings.push(`Memory bridge: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    // T4682: Inject into agent instruction files via CAAMP (AGENTS.md hub pattern)
+    try {
+        const injectionResult = await ensureInjection(projRoot);
+        if (injectionResult.action !== 'skipped') {
+            // Parse the details to get individual file actions for backward-compatible output
+            if (injectionResult.details) {
+                created.push(`injection: ${injectionResult.details}`);
+            }
+        }
+        else if (injectionResult.details) {
+            warnings.push(injectionResult.details);
+        }
+    }
+    catch (err) {
+        warnings.push(`CAAMP injection: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    // ADR-029: Contributor project dev channel setup
+    try {
+        const { ensureContributorMcp } = await import('./scaffold.js');
+        const devResult = await ensureContributorMcp(projRoot);
+        if (devResult.action !== 'skipped') {
+            created.push(`contributor dev channel: ${devResult.details ?? devResult.action}`);
+        }
+    }
+    catch (err) {
+        warnings.push(`Contributor dev channel: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    // T4685: Agent definition (cleo-subagent)
+    await initAgentDefinition(created, warnings);
+    // Note: Core skills installation is global-only (bootstrapGlobalCleo / installSkillsGlobally).
+    // Skills are NOT installed during project-level init — they are installed once globally.
+    // T4684: NEXUS registration (reconcile-based handshake, T5368)
+    await initNexusRegistration(projRoot, created, warnings);
+    // T5240: Adapter discovery, activation, and install
+    try {
+        const { AdapterManager } = await import('./adapters/index.js');
+        const mgr = AdapterManager.getInstance(projRoot);
+        const manifests = mgr.discover();
+        if (manifests.length > 0) {
+            created.push(`adapters: ${manifests.length} adapter(s) discovered`);
+            const detected = mgr.detectActive();
+            if (detected.length > 0) {
+                created.push(`adapters: active provider detected (${detected.join(', ')})`);
+                // Activate and install detected adapters
+                for (const adapterId of detected) {
+                    try {
+                        const adapter = await mgr.activate(adapterId);
+                        const installResult = await adapter.install.install({
+                            projectDir: projRoot,
+                        });
+                        if (installResult.success) {
+                            created.push(`adapter install (${adapterId}): installed`);
+                        }
+                        else {
+                            warnings.push(`adapter install (${adapterId}): failed`);
+                        }
+                    }
+                    catch (err) {
+                        warnings.push(`adapter activate/install (${adapterId}): ${err instanceof Error ? err.message : String(err)}`);
+                    }
+                }
+            }
+        }
+    }
+    catch (err) {
+        warnings.push(`Adapter discovery: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    // GitHub issue/PR templates (.github/ directory)
+    try {
+        await installGitHubTemplates(projRoot, created, skipped);
+    }
+    catch (err) {
+        warnings.push(`GitHub templates: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    // Remove .cleo/ from root .gitignore if present
+    const rootGitignoreResult = await removeCleoFromRootGitignore(projRoot);
+    if (rootGitignoreResult.removed) {
+        warnings.push('.cleo/ was found in root .gitignore and has been removed. CLEO uses .cleo/.gitignore for selective tracking.');
+    }
+    // T283: Optional install of canonical CleoOS seed agent personas
+    if (opts.installSeedAgents) {
+        try {
+            const seedDir = await resolveSeedAgentsDir();
+            if (seedDir && existsSync(seedDir)) {
+                const targetDir = join(projRoot, '.cleo', 'agents');
+                await mkdir(targetDir, { recursive: true });
+                const seeds = readdirSync(seedDir).filter((f) => f.endsWith('.cant'));
+                let installed = 0;
+                for (const seed of seeds) {
+                    const dst = join(targetDir, seed);
+                    if (!existsSync(dst)) {
+                        await copyFile(join(seedDir, seed), dst);
+                        installed++;
+                    }
+                }
+                if (installed > 0) {
+                    created.push(`seed-agents: ${installed} canonical .cant personas installed`);
+                }
+            }
+            else {
+                warnings.push('seed-agents install: bundled seed-agents/ directory not found');
+            }
+        }
+        catch (err) {
+            warnings.push(`seed-agents install failed: ${err instanceof Error ? err.message : String(err)}`);
+        }
+    }
+    // ────────────────────────────────────────────────────────────────────
+    // Phase 5 — Finalize classification report + CleoOS hub bootstrap
+    // (Classification already ran at the TOP of init, before file creation)
+    // ────────────────────────────────────────────────────────────────────
+    if (classification) {
+        created.push(`classification: ${classification.kind} (${classification.signals.length} signals)`);
+    }
+    // Ensure the CleoOS Hub exists globally (idempotent — only writes once)
+    try {
+        const hubResult = await ensureCleoOsHub();
+        if (hubResult.action === 'created') {
+            created.push(`cleoos-hub: ${hubResult.details ?? 'scaffolded'}`);
+        }
+    }
+    catch (err) {
+        warnings.push(`CleoOS hub scaffold failed: ${err instanceof Error ? err.message : String(err)}`);
+    }
+    // Context anchoring: when brownfield and --map-codebase was NOT already run,
+    // surface a hint so the operator knows they can anchor the baseline in BRAIN.
+    // (We do NOT auto-run mapCodebase here — it's opt-in to avoid blocking init.)
+    if (classification?.kind === 'brownfield' && !opts.mapCodebase) {
+        warnings.push('Brownfield detected — run `cleo init --map-codebase` to anchor the existing codebase in BRAIN (Phase 5 context anchoring).');
+    }
+    // LAFS next-step guidance for autonomous agents
+    const nextSteps = classification?.kind === 'greenfield'
+        ? [
+            {
+                action: 'Start the session and record your first research findings',
+                command: 'cleo session start --scope global',
+            },
+            {
+                action: 'Create the seed epic for Vision/PRD research',
+                command: 'cleo add "Project vision and initial scope" --type epic',
+            },
+            {
+                action: 'Invoke the Conductor Loop once the seed epic is present',
+                command: 'pi /cleo:auto <seedEpicId>',
+            },
+        ]
+        : [
+            {
+                action: 'Anchor the existing codebase in BRAIN as baseline context',
+                command: 'cleo init --map-codebase',
+            },
+            {
+                action: 'Review the detected project context',
+                command: 'cleo admin paths',
+            },
+            {
+                action: 'Start a session scoped to the work you want to continue',
+                command: 'cleo session start --scope global',
+            },
+        ];
+    return {
+        initialized: true,
+        directory: cleoDir,
+        created,
+        skipped,
+        warnings,
+        classification: classification
+            ? {
+                kind: classification.kind,
+                signalCount: classification.signals.length,
+                topLevelFileCount: classification.topLevelFileCount,
+                hasGit: classification.hasGit,
+            }
+            : undefined,
+        nextSteps,
+    };
+}
+/**
+ * Check if auto-init is enabled via environment variable.
+ * @task T4789
+ */
+export function isAutoInitEnabled() {
+    return process.env.CLEO_AUTO_INIT === 'true';
+}
+/**
+ * Check if a project is initialized and auto-init if configured.
+ * Returns { initialized: true } if ready, throws otherwise.
+ * @task T4789
+ */
+export async function ensureInitialized(projectRoot) {
+    const root = projectRoot ?? getProjectRoot();
+    const cleoDir = join(root, '.cleo');
+    const isInit = existsSync(cleoDir) &&
+        (existsSync(join(cleoDir, 'tasks.db')) || existsSync(join(cleoDir, 'config.json')));
+    if (isInit) {
+        return { initialized: true };
+    }
+    if (isAutoInitEnabled()) {
+        await initProject({ name: basename(root) });
+        return { initialized: true };
+    }
+    throw new Error('CLEO project not initialized. Run system.init or set CLEO_AUTO_INIT=true');
+}
+/**
+ * Get the current CLEO/project version.
+ * Checks VERSION file, then package.json.
+ * @task T4789
+ */
+export async function getVersion(projectRoot) {
+    const root = projectRoot ?? getProjectRoot();
+    // Try VERSION file
+    const versionPaths = [join(root, 'VERSION'), join(root, '..', 'VERSION')];
+    for (const versionPath of versionPaths) {
+        try {
+            const content = await readFile(versionPath, 'utf-8');
+            const version = content.trim();
+            if (version) {
+                return { version };
+            }
+        }
+        catch {
+            // Try next path
+        }
+    }
+    // Fallback: package.json
+    const pkg = await readJson(join(root, 'package.json'));
+    if (pkg?.version) {
+        return { version: pkg.version };
+    }
+    return { version: '0.0.0' };
+}
+//# sourceMappingURL=init.js.map