@cleocode/core 2026.9.20 → 2026.9.22

package/dist/init.js

@@ -30,23 +30,47 @@
  * @task T4707
  * @epic T4663
  */
-import { existsSync, readdirSync, readFileSync } from 'node:fs';
-import { copyFile, lstat, mkdir, readFile, symlink, unlink, writeFile } from 'node:fs/promises';
+import { copyFileSync, existsSync, constants as fsConstants, readdirSync, readFileSync, realpathSync, statSync, } from 'node:fs';
+import { appendFile, copyFile, lstat, mkdir, readFile, symlink, unlink, writeFile, } from 'node:fs/promises';
 import { platform } from 'node:os';
-import { basename, dirname, join } from 'node:path';
+import { basename, dirname, join, relative, resolve } from 'node:path';
 import { ExitCode } from '@cleocode/contracts';
+import { isAbsolutePath } from '@cleocode/paths';
 import { classifyProject } from './discovery.js';
 import { CleoError } from './errors.js';
-import { ensureGitHooks } from './hooks.js';
+import { resolveGitDir, resolveHooksDir } from './git/hooks-install.js';
+import { ensureGitHooks, MANAGED_HOOKS } from './hooks.js';
 import { ensureInjection } from './injection.js';
 import { writeMemoryBridge } from './memory/memory-bridge.js';
 import { migrateAgentOutputs } from './migration/agent-outputs.js';
 import { pushWarning } from './output.js';
-import { getAgentsHome, getCleoDirAbsolute, getCleoHome, getProjectRoot, resolveCleoDir, } from './paths.js';
+import { getAgentsHome, getCleoDir, getCleoDirAbsolute, getCleoHome, getProjectRoot, isGitLinkedCheckout, linkedWorktreeMainRoot, recordProjectEncounter, resolveCleoDir, worktreeScope, } from './paths.js';
+import { captureProjectScope } from './project-scope.js';
 // Shared utility imports
 import { ensureBrainDb, ensureCleoGitRepo, ensureCleoOsHub, ensureCleoStructure, ensureConfig, ensureGitignore, ensureProjectContext, ensureProjectGitInitialCommit, ensureProjectInfo, ensureWorktreeInclude, getPackageRoot, removeCleoFromRootGitignore, } from './scaffold.js';
 import { ensureGlobalSchemas } from './schema-management.js';
 import { readJson } from './store/json.js';
+/**
+ * Stable machine-readable codes for `cleo init` refusals (T12562). Carried in
+ * `CleoError.details.codeName` so the CLI and the dispatch engine can surface
+ * them instead of a generic `E_INTERNAL` / "use force=true".
+ *
+ * @task T12562
+ */
+export const INIT_ERROR_CODES = {
+    /** cwd is the initialized project root; `--force` re-initializes it. */
+    alreadyInitialized: 'E_ALREADY_INITIALIZED',
+    /** cwd is inside an ancestor project; init changed nothing. */
+    ancestorProject: 'E_INIT_ANCESTOR_PROJECT',
+    /** `--force` resolved to a root other than cwd. */
+    forceNotCwd: 'E_INIT_FORCE_NOT_CWD',
+    /** cwd is inside a linked git worktree; its project is the main checkout. */
+    inWorktree: 'E_INIT_IN_WORKTREE',
+    /** cwd is a submodule / separate-git-dir checkout under a CLEO project. */
+    gitlinkUnsupported: 'E_INIT_GITLINK_UNSUPPORTED',
+    /** The pre-`--force` snapshot could not be taken; nothing was changed. */
+    snapshotFailed: 'E_INIT_SNAPSHOT_FAILED',
+};
 // ── Helpers ──────────────────────────────────────────────────────────
 /**
  * Symlink type for directory symlinks.
@@ -285,7 +309,7 @@ export async function initCoreSkills(created, warnings) {
             const req = createRequire(import.meta.url);
             const skillsPkgMain = req.resolve('@cleocode/skills/package.json');
             const skillsPkgRoot = dirname(skillsPkgMain);
-            if (existsSync(join(skillsPkgRoot, 'skills.json'))) {
+            if (existsSync(join(skillsPkgRoot, 'skills', 'manifest.json'))) {
                 ctSkillsRoot = skillsPkgRoot;
             }
         }
@@ -296,13 +320,13 @@ export async function initCoreSkills(created, warnings) {
             try {
                 // Workspace monorepo fallback (packages/skills/)
                 const bundledPath = join(packageRoot, 'packages', 'skills');
-                if (existsSync(join(bundledPath, 'skills.json'))) {
+                if (existsSync(join(bundledPath, 'skills', 'manifest.json'))) {
                     ctSkillsRoot = bundledPath;
                 }
                 else {
                     // node_modules fallback
                     const ctSkillsPath = join(packageRoot, 'node_modules', '@cleocode', 'skills');
-                    if (existsSync(join(ctSkillsPath, 'skills.json'))) {
+                    if (existsSync(join(ctSkillsPath, 'skills', 'manifest.json'))) {
                         ctSkillsRoot = ctSkillsPath;
                     }
                 }
@@ -322,15 +346,17 @@ export async function initCoreSkills(created, warnings) {
         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);
+        // T12653: the manifest (generated from SKILL.md frontmatter) is the only
+        // skills index. Install every skill that declares `metadata.install:
+        // harness`; `internal` skills never reach a harness (D11157).
+        // scripts/lint-emitted-skills.mjs mirrors this selection — change both.
+        const manifestPath = join(ctSkillsRoot, 'skills', 'manifest.json');
+        const manifest = JSON.parse(readFileSync(manifestPath, 'utf-8'));
+        const skills = manifest.skills ?? [];
+        const harnessSkills = skills.filter((s) => s.install === 'harness');
         const installed = [];
-        for (const skill of coreSkills) {
-            const skillSourceDir = dirname(join(ctSkillsRoot, skill.path));
+        for (const skill of harnessSkills) {
+            const skillSourceDir = join(ctSkillsRoot, 'skills', skill.name);
             if (!existsSync(skillSourceDir)) {
                 continue;
             }
@@ -353,11 +379,49 @@ export async function initCoreSkills(created, warnings) {
         if (installed.length > 0) {
             created.push(`skills: ${installed.length} core skills installed`);
         }
+        // T12678: record what CLEO installed, then remove bundled skills CLEO no
+        // longer installs (internal or retired) — only where CLEO owns them.
+        await pruneAfterInstall(ctSkillsRoot, installed, providers, created, warnings);
     }
     catch (err) {
         warnings.push(`Core skill install: ${err instanceof Error ? err.message : String(err)}`);
     }
 }
+/**
+ * Write the bundled-install ledger and prune skills the bundled manifest no
+ * longer installs (T12678). Best-effort: failures become warnings.
+ *
+ * @param ctSkillsRoot - `@cleocode/skills` package root.
+ * @param installed - Skills installed by this run.
+ * @param providers - Installed harness providers.
+ * @param created - Accumulator for created/removed messages.
+ * @param warnings - Accumulator for warnings.
+ */
+async function pruneAfterInstall(ctSkillsRoot, installed, providers, created, warnings) {
+    try {
+        const { resolveProviderSkillsDirs } = await import('@cleocode/caamp');
+        const { resolveSkillsRoot } = await import('./skills/skill-root.js');
+        const { defaultPruneRegistry, pruneBundledSkills, recordBundledInstalls } = await import('./skills/prune-bundled.js');
+        const skillsRoot = resolveSkillsRoot();
+        await recordBundledInstalls(skillsRoot, installed);
+        const receipt = await pruneBundledSkills({
+            bundledSkillsDir: join(ctSkillsRoot, 'skills'),
+            skillsRoot,
+            providerSkillDirs: providers.flatMap((p) => resolveProviderSkillsDirs(p, 'global')),
+            registry: await defaultPruneRegistry(),
+            receiptPath: join(skillsRoot, '.prune-receipts.jsonl'),
+        });
+        const moved = receipt.actions.filter((a) => a.action === 'quarantined');
+        if (moved.length > 0) {
+            created.push(`skills: quarantined ${moved.length} entries no longer installed (${[...new Set(moved.map((a) => a.name))].join(', ')}); restore with cleo skills doctor restore ${receipt.quarantineId}`);
+        }
+        for (const e of receipt.errors)
+            warnings.push(`Skill prune: ${e}`);
+    }
+    catch (err) {
+        warnings.push(`Skill prune: ${err instanceof Error ? err.message : String(err)}`);
+    }
+}
 /**
  * Register/reconcile project with NEXUS.
  * Uses nexusReconcile for idempotent handshake — auto-registers if new,
@@ -365,7 +429,7 @@ export async function initCoreSkills(created, warnings) {
  * @task T4684
  * @task T5368
  */
-export async function initNexusRegistration(projectRoot, created, warnings) {
+export async function initNexusRegistration(projectRoot, created, warnings, opts = {}) {
     try {
         const { shouldAutoRegisterProject } = await import('./nexus/registry-hygiene.js');
         if (!shouldAutoRegisterProject(projectRoot, getCleoHome())) {
@@ -373,8 +437,26 @@ export async function initNexusRegistration(projectRoot, created, warnings) {
             warnings.push('NEXUS registration skipped: project is under a temp directory (register explicitly with `cleo nexus register`)');
             return;
         }
+        if (opts.maintenance) {
+            // T12470: a maintenance command (`cleo upgrade` / `self-update`) is not
+            // an explicit registration. It goes through the encounter, which never
+            // mints an identity and never moves an existing row to this checkout.
+            const outcome = await recordProjectEncounter(projectRoot);
+            if (outcome === 'recorded')
+                created.push('NEXUS registration (encounter recorded)');
+            return;
+        }
         const { nexusReconcile } = await import('./nexus/registry.js');
-        const result = await nexusReconcile(projectRoot);
+        const result = await nexusReconcile(projectRoot, {
+            ...(opts.forceRebind ? { forceRebind: true } : {}),
+        });
+        if (result.status === 'candidate') {
+            warnings.push(`NEXUS registration: this project is registered at ${result.oldPath}, which still exists; ` +
+                'this checkout was recorded as a candidate and the registry was NOT repointed. ' +
+                'If this checkout should own the registration, run `cleo doctor project-identity --resolve` ' +
+                'or re-run with `--force-rebind`.');
+            return;
+        }
         if (result.status === 'auto_registered') {
             created.push('NEXUS registration (auto-registered new project)');
         }
@@ -539,6 +621,345 @@ export async function installHandoffRedirectStubs(projectRoot, created) {
     }
 }
 // ── Public API ───────────────────────────────────────────────────────
+/**
+ * Canonicalize a path for identity comparison, tolerating a missing path.
+ *
+ * @param path - Absolute path.
+ * @returns The realpath, or the resolved path when it cannot be read.
+ */
+function canonicalPath(path) {
+    try {
+        return realpathSync(path);
+    }
+    catch {
+        return resolve(path);
+    }
+}
+/**
+ * Report whether `child` lies strictly below `parent` (by canonical path).
+ *
+ * @param child - Candidate descendant.
+ * @param parent - Candidate ancestor.
+ * @returns `true` when `child` is inside `parent` and not equal to it.
+ */
+function isStrictlyInside(child, parent) {
+    const rel = relative(canonicalPath(parent), canonicalPath(child));
+    return rel !== '' && !rel.startsWith('..') && !isAbsolutePath(rel);
+}
+/**
+ * The CLEO project that encloses a gitlink checkout (submodule or
+ * separate-git-dir), or `undefined` when none does (T12562 · T12558 round 5).
+ *
+ * The walk starts at the gitlink's PARENT directory, never at the checkout
+ * itself: a `.cleo/` inside the checkout — tracked files, or the tombstone a
+ * reroot leaves — must not make it look self-contained, because project-root
+ * resolution walks past a gitlink root and would still use the enclosing
+ * store. A relocation refusal met on the way up is not an enclosing project.
+ *
+ * @param gitlinkRoot - Root of the gitlink checkout (its `.git` is a file).
+ * @returns The enclosing project root, or `undefined`.
+ */
+function enclosingProjectOfGitlink(gitlinkRoot) {
+    const parent = dirname(gitlinkRoot);
+    if (parent === gitlinkRoot)
+        return undefined;
+    try {
+        const root = getProjectRoot(parent);
+        return existsSync(join(root, '.cleo')) && isStrictlyInside(gitlinkRoot, root)
+            ? root
+            : undefined;
+    }
+    catch {
+        return undefined;
+    }
+}
+/**
+ * Find the nearest git checkout boundary at or above `start`.
+ *
+ * @param start - Absolute directory to start from.
+ * @returns The nearest boundary, or `null` when no `.git` entry exists above.
+ */
+function findGitBoundary(start) {
+    let current = start;
+    while (true) {
+        const gitPath = join(current, '.git');
+        try {
+            const st = statSync(gitPath);
+            if (st.isDirectory())
+                return { root: current, kind: 'repo' };
+            if (st.isFile()) {
+                // A linked worktree shares its main checkout's project; a submodule or
+                // separate-git-dir gitlink is its own repository.
+                if (!isGitLinkedCheckout(current))
+                    return { root: current, kind: 'submodule' };
+                const mainRoot = linkedWorktreeMainRoot(current);
+                return { root: current, kind: 'worktree', ...(mainRoot ? { mainRoot } : {}) };
+            }
+        }
+        catch {
+            // No `.git` here — keep walking.
+        }
+        const parent = dirname(current);
+        if (parent === current)
+            return null;
+        current = parent;
+    }
+}
+/**
+ * Choose the directory `cleo init` acts on (T12562).
+ *
+ * Every other command walks up from a subdirectory to the enclosing project,
+ * and keeps doing so. `init` is different because it CREATES a project, so the
+ * walk must not silently redirect it: from a child git repository nested under
+ * an initialized CLEO root the walk found the parent, and the guard then
+ * advised `--force` against the parent's store.
+ *
+ * Resolution order:
+ * 1. `--here` targets the working directory ({@link initProject} still refuses
+ *    it inside a linked worktree).
+ * 2. An active worktree scope, an absolute `CLEO_DIR` or `CLEO_ROOT` /
+ *    `CLEO_PROJECT_ROOT` pins the target explicitly (unchanged behaviour).
+ * 3. A working directory that is its own git root (`.git` is a directory)
+ *    targets itself: a nested repository is a separate project. A gitlink
+ *    checkout (linked worktree, submodule, separate-git-dir) does not, because
+ *    project-root resolution cannot use a store there.
+ * 4. Otherwise the existing resolution applies. A plain (non-git)
+ *    subdirectory of a CLEO project therefore still resolves to that ancestor;
+ *    {@link initProject} reports it by absolute path and never wipes it.
+ *
+ * @param opts - `here` forces the working directory; `cwd` overrides `process.cwd()`.
+ * @returns The chosen target.
+ *
+ * @example
+ * ```ts
+ * resolveInitTarget(); // { projectRoot: '/repo/child', source: 'git-root', isCwd: true, ... }
+ * ```
+ *
+ * @task T12562
+ */
+export function resolveInitTarget(opts = {}) {
+    const cwd = resolve(opts.cwd ?? process.cwd()); // CWD-OK: init creates the project at cwd (T12562)
+    const cleoDirEnv = getCleoDir();
+    const relativeCleoDir = isAbsolutePath(cleoDirEnv) ? '.cleo' : cleoDirEnv;
+    const envPinned = isAbsolutePath(cleoDirEnv) ||
+        Boolean(process.env['CLEO_ROOT'] ?? process.env['CLEO_PROJECT_ROOT']);
+    const pinned = envPinned || worktreeScope.getStore() !== undefined;
+    const gitBoundary = findGitBoundary(cwd);
+    let cleoDir;
+    let source;
+    if (opts.here) {
+        cleoDir = resolve(cwd, relativeCleoDir);
+        source = 'here';
+    }
+    else if (pinned) {
+        // T9803/D009: `bootstrap` is the only sanctioned cwd-relative fallback.
+        cleoDir = getCleoDirAbsolute(opts.cwd, { bootstrap: true });
+        source = 'pinned';
+    }
+    else if (gitBoundary?.kind === 'repo' && gitBoundary.root === cwd) {
+        cleoDir = resolve(cwd, relativeCleoDir);
+        source = 'git-root';
+    }
+    else {
+        cleoDir = getCleoDirAbsolute(opts.cwd, { bootstrap: true });
+        source = 'resolved';
+    }
+    // `cleoDir` is `<root>/.cleo` by default, so its parent is the project root.
+    // This also respects an absolute `CLEO_DIR` used by the init-e2e suite.
+    const projectRoot = dirname(cleoDir);
+    let enclosingProjectRoot;
+    if (gitBoundary?.kind === 'submodule') {
+        enclosingProjectRoot = enclosingProjectOfGitlink(gitBoundary.root);
+    }
+    return {
+        cleoDir,
+        projectRoot,
+        cwd,
+        source,
+        isCwd: canonicalPath(projectRoot) === canonicalPath(cwd),
+        envPinned,
+        gitBoundary,
+        ...(enclosingProjectRoot ? { enclosingProjectRoot } : {}),
+    };
+}
+/**
+ * Return the stable init refusal code carried by `err`, if any (T12562).
+ *
+ * @param err - Error thrown by core `initProject`.
+ * @returns One of {@link INIT_ERROR_CODES}, or `undefined`.
+ *
+ * @example
+ * ```ts
+ * initErrorCodeName(err); // 'E_INIT_ANCESTOR_PROJECT'
+ * ```
+ *
+ * @task T12562
+ */
+export function initErrorCodeName(err) {
+    if (!(err instanceof CleoError))
+        return undefined;
+    const codeName = err.details?.['codeName'];
+    const known = Object.values(INIT_ERROR_CODES);
+    return typeof codeName === 'string' && known.includes(codeName) ? codeName : undefined;
+}
+/**
+ * Build a `cleo init` refusal carrying its stable code in `details.codeName`.
+ *
+ * @param codeName - One of {@link INIT_ERROR_CODES}.
+ * @param message - Self-contained message; the CLI prints only this line.
+ * @param fix - Copy-paste remedy.
+ * @param details - Extra structured context.
+ * @returns The error to throw.
+ */
+function initRefusal(codeName, message, fix, details) {
+    return new CleoError(ExitCode.GENERAL_ERROR, message, {
+        fix,
+        details: { field: 'cwd', codeName, ...details },
+    });
+}
+/** What `--force` resets, stated once for every message that mentions it. */
+const FORCE_RESETS = '--force resets .cleo/config.json and .cleo/project-info.json to defaults and rewrites ' +
+    '.cleo/.gitignore and the managed git hooks (commit-msg, pre-commit, pre-push); it deletes ' +
+    'no task, brain or conduit data. It first snapshots the databases (VACUUM INTO) and those ' +
+    'files into .cleo/backups/sqlite/ and refuses if the snapshot fails.';
+/**
+ * Refuse any init that could touch a project other than the one the operator
+ * is standing in (T12562). Every refusal changes nothing.
+ *
+ * @param target - The resolved target.
+ * @param opts - The caller's init options.
+ * @param alreadyInitialized - Whether the target already holds a project.
+ * @throws {CleoError} With `details.codeName` from {@link INIT_ERROR_CODES}.
+ */
+function assertInitTargetAllowed(target, opts, alreadyInitialized) {
+    const { cwd, projectRoot: root, gitBoundary: git } = target;
+    const additiveMapOnly = opts.mapCodebase === true && !opts.force;
+    // A linked worktree shares its main checkout's project (D009 / T9803): a
+    // `.cleo/` inside it is an orphan store. Only an explicit env pin, or the
+    // additive map of the already-initialized main project, may proceed.
+    if (git?.kind === 'worktree' && !target.envPinned) {
+        const main = git.mainRoot;
+        const mapsMain = main !== undefined &&
+            additiveMapOnly &&
+            alreadyInitialized &&
+            canonicalPath(root) === canonicalPath(main);
+        if (!mapsMain) {
+            const whose = main ? ` of ${main}` : '';
+            throw initRefusal(INIT_ERROR_CODES.inWorktree, `${cwd} is inside a linked git worktree${whose}. A worktree shares its main ` +
+                `checkout's CLEO project, so there is nothing to init here, and a .cleo/ inside a ` +
+                'worktree would be an orphan store. Nothing was changed.' +
+                (main ? ` If ${main} is not a CLEO project yet, run \`cleo init\` there.` : ''), main
+                ? `cd ${JSON.stringify(main)} && cleo init`
+                : 'Run `cleo init` in the main checkout (`git worktree list` names it).', { resolvedRoot: root, worktreeRoot: git.root, ...(main ? { mainRoot: main } : {}) });
+        }
+    }
+    // A submodule / separate-git-dir checkout under a CLEO project: project-root
+    // resolution walks past a gitlink root, so a store created here would be
+    // ignored and every later command would use the superproject's store.
+    const enclosing = target.enclosingProjectRoot;
+    if (git?.kind === 'submodule' &&
+        enclosing !== undefined &&
+        !target.envPinned &&
+        !(additiveMapOnly && !opts.here)) {
+        throw initRefusal(INIT_ERROR_CODES.gitlinkUnsupported, `${git.root} is a submodule / separate-git-dir checkout inside the CLEO project at ` +
+            `${enclosing}. CLEO resolves this checkout to ${enclosing}, so every command run here ` +
+            `already uses that project's store; a separate store for a gitlink checkout is not ` +
+            'supported yet (tracked separately). Nothing was changed.', `Use the project at ${enclosing} (run cleo from anywhere inside it).`, { resolvedRoot: root, repositoryRoot: git.root, enclosingProjectRoot: enclosing });
+    }
+    // An uninitialized repository between cwd and the ancestor project is the
+    // project the operator most likely meant: point there, not at cwd.
+    const nestedRepo = git?.kind === 'repo' && isStrictlyInside(git.root, root) ? git.root : undefined;
+    // Never advise --force against a root other than cwd (T12562 AC2).
+    const separateProjectFix = nestedRepo
+        ? `cd ${JSON.stringify(nestedRepo)} && cleo init`
+        : `cd ${JSON.stringify(cwd)} && cleo init --here`;
+    if (opts.force && !target.isCwd) {
+        throw initRefusal(INIT_ERROR_CODES.forceNotCwd, `Refusing --force: it would re-initialize ${root}, which is not the current directory ` +
+            `(${cwd}). --force only ever acts on the current directory's own project. ` +
+            'Nothing was changed.', separateProjectFix, { field: 'force', resolvedRoot: root });
+    }
+    if (!alreadyInitialized || opts.force || additiveMapOnly)
+        return;
+    if (target.isCwd) {
+        throw initRefusal(INIT_ERROR_CODES.alreadyInitialized, `Project already initialized at ${root}. DANGER ZONE: ${FORCE_RESETS}`, 'cleo init --force', { resolvedRoot: root });
+    }
+    if (nestedRepo) {
+        throw initRefusal(INIT_ERROR_CODES.ancestorProject, `${cwd} is inside the git repository ${nestedRepo}, which is not a CLEO project yet; ` +
+            `the nearest CLEO project is ${root}. Nothing was changed. To make that repository ` +
+            `its own project, run \`cleo init\` in ${nestedRepo}.`, separateProjectFix, { resolvedRoot: root, repositoryRoot: nestedRepo });
+    }
+    throw initRefusal(INIT_ERROR_CODES.ancestorProject, `${cwd} is inside the CLEO project already initialized at ${root}. Nothing was ` +
+        `changed. To create a separate project in ${cwd}, run \`cleo init --here\` there.`, separateProjectFix, { resolvedRoot: root, source: target.source });
+}
+/**
+ * Every managed git hook a forced re-init could overwrite, as snapshot sources.
+ *
+ * `ensureGitHooks({ force })` writes `<root>/.git/hooks`. The hooks git
+ * actually runs may live elsewhere (a gitlink checkout's git dir, or a custom
+ * `core.hooksPath`), so that directory is resolved too and snapshotted when it
+ * differs (T12562).
+ *
+ * @param projRoot - Absolute project root.
+ * @returns `[label, sourcePath]` pairs for the snapshot.
+ */
+function managedHookSnapshotSources(projRoot) {
+    const literal = join(projRoot, '.git', 'hooks');
+    const gitDir = resolveGitDir(projRoot);
+    const effective = gitDir ? resolveHooksDir(projRoot, gitDir) : literal;
+    const dirs = [['git-hook', literal]];
+    if (canonicalPath(effective) !== canonicalPath(literal))
+        dirs.push(['hooks-path', effective]);
+    return dirs.flatMap(([prefix, dir]) => MANAGED_HOOKS.map((h) => [`${prefix}-${h}`, join(dir, h)]));
+}
+/**
+ * Snapshot everything a forced re-init overwrites, and refuse to continue
+ * without a complete snapshot (T12562).
+ *
+ * Uses the `cleo backup add` path ({@link createBackup}): `VACUUM INTO` for the
+ * databases and atomic copies of `config.json` / `project-info.json`, with a
+ * restorable `<backupId>.meta.json` sidecar (`cleo restore backup`). The other
+ * files `--force` rewrites (`.cleo/.gitignore`, `.cleo/project-context.json`,
+ * the managed git hooks) are copied beside it as `<name>.<backupId>`.
+ *
+ * @param projRoot - Absolute project root being re-initialized.
+ * @param cleoDir - Absolute `.cleo/` directory of that root.
+ * @returns The backup id written by THIS run.
+ * @throws {CleoError} `E_INIT_SNAPSHOT_FAILED` when any required file is missing
+ *   from this run's snapshot.
+ */
+async function snapshotBeforeForcedReinit(projRoot, cleoDir) {
+    const { createBackup } = await import('./system/backup.js');
+    const result = await createBackup(projRoot, {
+        type: 'pre-force-init',
+        note: 'taken by `cleo init --force` before it resets project files (T12562)',
+    });
+    const required = ['config.json', 'project-info.json'].filter((f) => existsSync(join(cleoDir, f)));
+    // `tasks.db` is createBackup's label for the live project store (cleo.db).
+    if (existsSync(join(cleoDir, 'cleo.db')) || existsSync(join(cleoDir, 'tasks.db'))) {
+        required.push('tasks.db');
+    }
+    const missing = required.filter((f) => !result.files.includes(f));
+    const extras = [
+        ['.gitignore', join(cleoDir, '.gitignore')],
+        ['project-context.json', join(cleoDir, 'project-context.json')],
+        ...managedHookSnapshotSources(projRoot),
+    ];
+    for (const [label, src] of extras) {
+        if (!existsSync(src))
+            continue;
+        try {
+            copyFileSync(src, join(result.path, `${label}.${result.backupId}`), fsConstants.COPYFILE_EXCL);
+        }
+        catch {
+            missing.push(label);
+        }
+    }
+    if (missing.length > 0) {
+        throw initRefusal(INIT_ERROR_CODES.snapshotFailed, `Refusing --force: the pre-reset snapshot of ${projRoot} is incomplete (missing: ` +
+            `${missing.join(', ')}). Nothing was changed. Run \`cleo backup add\`, then retry.`, 'cleo backup add', { field: 'force', resolvedRoot: projRoot, missing, backupId: result.backupId });
+    }
+    return result.backupId;
+}
 /**
  * Run update-docs only: refresh all injections without reinitializing.
  * Re-injects CLEO-INJECTION.md into all detected agent instruction files.
@@ -569,6 +990,33 @@ export async function updateDocs() {
         updateDocsOnly: true,
     };
 }
+/**
+ * Remove the identity files a relocated project left (or `git checkout`
+ * restored) at `root`, so `cleo init --here --new-identity` mints a new id
+ * instead of adopting the old one: `.cleo/project-id` and
+ * `.cleo/project-info.json` only when they declare `projectId`, and the reroot
+ * tombstone. Nothing else is touched.
+ */
+async function retireRelocatedIdentity(root, projectId) {
+    const { readPortableProjectId } = await import('@cleocode/paths');
+    const tracked = readPortableProjectId(root);
+    if (tracked.status === 'valid' && tracked.projectId === projectId) {
+        await unlink(join(root, '.cleo', 'project-id'));
+    }
+    const infoPath = join(root, '.cleo', 'project-info.json');
+    if (existsSync(infoPath)) {
+        try {
+            const info = JSON.parse(await readFile(infoPath, 'utf-8'));
+            if (info.projectId === projectId)
+                await unlink(infoPath);
+        }
+        catch {
+            // Unparseable: ensureProjectInfo regenerates it.
+        }
+    }
+    const { PROJECT_TOMBSTONE_FILE } = await import('./project-tombstone.js');
+    await unlink(join(root, PROJECT_TOMBSTONE_FILE)).catch(() => undefined);
+}
 /**
  * Run full project initialization.
  *
@@ -586,43 +1034,109 @@ export async function updateDocs() {
  * @task T4707
  */
 export async function initProject(opts = {}) {
-    // T9803/D009: `cleo init` is the ONLY caller permitted to bootstrap a
-    // missing project root. Passing `{ bootstrap: true }` opts into the
-    // cwd-relative fallback; every other caller must resolve through an
-    // existing root or throw to prevent orphan-`.cleo/` synthesis inside
-    // worktrees.
-    const cleoDir = getCleoDirAbsolute(undefined, { bootstrap: true });
-    // `cleo init` CREATES the project root, so we cannot call getProjectRoot()
-    // here — that walks up looking for an existing `.cleo/` sentinel and throws
-    // `E_NOT_FOUND` when none is present (the whole point of `init` is that
-    // none is present yet). `cleoDir` is `<cwd>/.cleo` by default, so its
-    // parent directory is the project root. This also respects an absolute
-    // `CLEO_DIR` env var used by the init-e2e test suite to pin the target
-    // directory.
-    const projRoot = dirname(cleoDir);
-    // Guard: fail if project already initialized (unless --force)
-    const alreadyInitialized = existsSync(cleoDir) &&
-        (existsSync(join(cleoDir, 'tasks.db')) || existsSync(join(cleoDir, 'config.json')));
-    // T12077: `--map-codebase` is ADDITIVE — it analyses the tree and writes
-    // findings to BRAIN; it scaffolds nothing and wipes nothing. Blocking it
-    // behind this guard made the onboarding path self-contradictory: a fresh
-    // `cleo init` on a brownfield repo returns
-    //
-    //   nextSteps: [{ action: 'Anchor the existing codebase in BRAIN as baseline
-    //                 context', command: 'cleo init --map-codebase' }]
-    //
-    // and running that exact command then failed with "Project already
-    // initialized. DANGER ZONE: use --force to wipe and re-init." The only way
-    // to follow CLEO's own advice was to destroy the project it had just set up.
-    //
-    // Measured on a greenfield sandbox: `cleo init` succeeded, and the very
-    // first recommended follow-up was impossible.
-    const additiveMapOnly = opts.mapCodebase === true;
-    if (alreadyInitialized && !opts.force && !additiveMapOnly) {
-        throw new CleoError(ExitCode.GENERAL_ERROR, 'Project already initialized. DANGER ZONE: use --force to wipe and re-init.', { fix: 'cleo init --force' });
+    // T12562: choose the target explicitly instead of trusting the ancestor
+    // walk. From a child git repo under an initialized CLEO root the walk
+    // resolved the PARENT, the guard below then advised `--force`, and following
+    // that advice re-initialized the parent store.
+    const target = resolveInitTarget({ here: opts.here });
+    const { cleoDir, projectRoot: projRoot } = target;
+    // T12558: relocation state, detected WITHOUT writing or throwing yet.
+    // Resolving from the target reports E_PROJECT_MOVED at a valid reroot
+    // tombstone (at the target or an ancestor it would resolve to); the store
+    // guard's registry arm is checked up front for the same reason.
+    let movedOnResolve;
+    if (!opts.here) {
+        try {
+            getProjectRoot(projRoot);
+        }
+        catch (err) {
+            if (err instanceof CleoError && err.code === ExitCode.PROJECT_MOVED)
+                movedOnResolve = err;
+        }
+    }
+    const { detectRelocatedRoot, allowStoreAtRelocatedRoot } = await import('./store/relocated-store-guard.js');
+    const { resolveDualScopeDbPath } = await import('./store/dual-scope-db.js');
+    const relocated = existsSync(join(cleoDir, 'cleo.db'))
+        ? null
+        : detectRelocatedRoot(projRoot, resolveDualScopeDbPath('global'));
+    // T12562: legacy `tasks.db` counts too, so a forced re-init snapshots it.
+    // T12558: at a relocated root (no store) restored tracked files never count,
+    // so #1605's guard never answers "already initialized — use --force" there.
+    const alreadyInitialized = !relocated &&
+        existsSync(cleoDir) &&
+        (existsSync(join(cleoDir, 'cleo.db')) ||
+            existsSync(join(cleoDir, 'tasks.db')) ||
+            existsSync(join(cleoDir, 'config.json')));
+    // #1605's target refusals (worktree, gitlink, force-not-cwd, ancestor) run
+    // FIRST: a relocation opt-out can never reopen a target CLEO cannot use.
+    assertInitTargetAllowed(target, opts, alreadyInitialized);
+    // T12558: relocation refusals, still before any write.
+    if (movedOnResolve)
+        throw movedOnResolve;
+    if (relocated && !opts.here) {
+        const { projectMovedError } = await import('./project-tombstone.js');
+        throw projectMovedError(projRoot, relocated, undefined, relocated.via);
+    }
+    // `--here` alone would ADOPT the relocated project's id and create a SECOND
+    // store for it — two diverging copies of one project. Only a genuinely
+    // separate project (a new id) may start here.
+    if (relocated && !opts.newIdentity) {
+        throw new CleoError(ExitCode.PROJECT_MOVED, `E_PROJECT_MOVED: ${projRoot} is where project ${relocated.projectId} was rerooted from; \`--here\` alone would create a second store for that same project`, {
+            fix: `cd "${relocated.movedTo}" (the live project). To start a DIFFERENT project here, run \`cleo init --here --new-identity\` (mints a new id; commit the new .cleo/project-id).`,
+            details: {
+                field: 'projectRoot',
+                projectId: relocated.projectId,
+                movedFrom: projRoot,
+                movedTo: relocated.movedTo,
+                evidence: relocated.via,
+            },
+        });
+    }
+    // T12558: `--here --new-identity` at a relocated root — every refusal has
+    // passed. The restored `.cleo/project-id` (and a stale tombstone) belong to
+    // the relocated project; retire them so a new id is minted, not adopted.
+    let retiredProjectId;
+    if (relocated) {
+        allowStoreAtRelocatedRoot(projRoot);
+        retiredProjectId = relocated.projectId;
+        await retireRelocatedIdentity(projRoot, relocated.projectId);
+        const auditPath = join(cleoDir, 'audit', 'relocation-override.jsonl');
+        await mkdir(dirname(auditPath), { recursive: true });
+        await appendFile(auditPath, `${JSON.stringify({
+            timestamp: new Date().toISOString(),
+            action: 'init --here --new-identity',
+            projectRoot: projRoot,
+            projectId: relocated.projectId,
+            movedTo: relocated.movedTo,
+            evidence: relocated.via,
+            newIdentity: true,
+        })}\n`);
     }
     const force = !!opts.force;
+    const scope = captureProjectScope(projRoot, worktreeScope.getStore());
+    let preForceBackupId;
+    if (force && alreadyInitialized) {
+        preForceBackupId = await worktreeScope.run(scope, () => snapshotBeforeForcedReinit(projRoot, cleoDir));
+    }
+    // Pin every ambient `getProjectRoot()` / `getCleoDirAbsolute()` inside the
+    // scaffolding steps to the chosen target, so none of them walks back up to
+    // an ancestor project while the target's `.cleo/` is still being created.
+    return worktreeScope.run(scope, () => scaffoldInitTarget(opts, { cleoDir, projRoot, force, preForceBackupId, retiredProjectId }));
+}
+/**
+ * Run the scaffolding half of {@link initProject} against an already-chosen,
+ * already-guarded target.
+ *
+ * @param opts - The caller's init options.
+ * @param target - Resolved `.cleo/` directory, project root, force flag and pre-force backup id.
+ * @returns The init result.
+ */
+async function scaffoldInitTarget(opts, target) {
+    const { cleoDir, projRoot, force, retiredProjectId } = target;
     const created = [];
+    if (target.preForceBackupId) {
+        created.push(`pre-force snapshot: .cleo/backups/sqlite/*.${target.preForceBackupId} (cleo restore backup)`);
+    }
     const skipped = [];
     const warnings = [];
     // Phase 5 — classify the directory BEFORE creating any files so the
@@ -654,6 +1168,9 @@ export async function initProject(opts = {}) {
         created.push('tasks.db');
     }
     catch (err) {
+        // A relocated root is a refusal, never a store "deferred" behind success.
+        if (err instanceof CleoError && err.code === ExitCode.PROJECT_MOVED)
+            throw 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)})`);
     }
@@ -827,6 +1344,12 @@ export async function initProject(opts = {}) {
         /re-linked|conflict|invalid|coverage missing/.test(projectInfoResult.details)) {
         warnings.push(`Project identity: ${projectInfoResult.details}`);
     }
+    if (retiredProjectId) {
+        warnings.push(`.cleo/project-id changed: this is a NEW project, not ${retiredProjectId} (which lives on elsewhere). Commit the new .cleo/project-id.`);
+        // Both projects are registered under this directory's name; say so rather
+        // than rename either one behind the operator's back.
+        warnings.push(`Project name "${basename(projRoot)}" is now ambiguous: ${retiredProjectId} was registered under the same name. Rename this one with \`cleo project rename <new-name>\`.`);
+    }
     // Project context detection (always run during init)
     try {
         const detectResult = await ensureProjectContext(projRoot, { force: !!opts.detect });
@@ -890,7 +1413,9 @@ export async function initProject(opts = {}) {
     // 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);
+    await initNexusRegistration(projRoot, created, warnings, {
+        ...(opts.forceRebind ? { forceRebind: true } : {}),
+    });
     // T5240: Adapter discovery, activation, and install
     try {
         const { AdapterManager } = await import('./adapters/index.js');