@cleocode/core 2026.6.14 → 2026.6.17

package/dist/gc/cleanup.d.ts

@@ -49,7 +49,11 @@ export interface CleanupResult {
     removed: number;
     /** Absolute paths that were removed (or would be removed). */
     removedPaths: string[];
-    /** Entries that were skipped (dry-run). */
+    /** Number of worktrees quarantined (dirty/unpushed — preserved, not deleted). */
+    quarantined: number;
+    /** Absolute paths that were quarantined (tar archives placed in quarantine dir). */
+    quarantinedPaths: string[];
+    /** Entries that were skipped (dry-run or preserved). */
     skipped: number;
     /** Errors encountered during removal (non-fatal). */
     errors: Array<{
@@ -58,6 +62,11 @@ export interface CleanupResult {
     }>;
     /** Whether this was a dry run. */
     dryRun: boolean;
+    /**
+     * True when pruning was skipped entirely because the preserve set was empty
+     * while worktrees exist (fail-closed guard, T11996).
+     */
+    skippedFailClosed?: boolean;
 }
 /**
  * Options for `pruneOrphanWorktrees`.
@@ -132,18 +141,24 @@ export interface OrphanEntry {
  * Prune orphaned agent worktree directories.
  *
  * Scans `worktreesRoot` (or `worktreesRoot/<projectHash>`) for directories
- * whose names are NOT in `activeTaskIds` and removes them. Uses `rmSync`
- * directly because the worktrees at this point are only filesystem artefacts
- * — the agent has already merged its work via `completeAgentWorktreeViaMerge`.
- * Git worktree de-registration is attempted with `git worktree prune` at the
- * level of the caller (cleo gc or cleo doctor does not need a git root here;
- * individual worktrees have their own `.git` file redirects which become stale
- * and are cleaned up by `git worktree prune` in the primary repo).
+ * whose names are NOT in `activeTaskIds` and removes them.
+ *
+ * Safety invariants (T11996):
+ * - Fail-closed: if `activeTaskIds` is empty AND worktrees exist, skip pruning
+ *   entirely and return `skippedFailClosed: true`. This prevents mass-deletion
+ *   when the task store is unavailable or freshly initialised.
+ * - Dirty guard: worktrees with uncommitted changes are quarantined (packed
+ *   into `.tar.gz` in `<worktreesRoot>/../quarantine/worktrees/`) instead of
+ *   deleted. The original directory is left on disk.
+ * - Unpushed guard: worktrees whose branch has commits not reachable from any
+ *   remote ref are quarantined, not deleted.
+ * - A worktree that is both dirty AND has unpushed commits is quarantined once.
  *
  * @param options - See `PruneOrphanWorktreesOptions`.
  * @returns Cleanup result.
  *
  * @task T9043
+ * @task T11996
  */
 export declare function pruneOrphanWorktrees(options: PruneOrphanWorktreesOptions): CleanupResult;
 /**

package/dist/gc/cleanup.d.ts.map

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package/dist/gc/cleanup.js

@@ -22,7 +22,8 @@
  *
  * @task T9043
  */
-import { existsSync, readdirSync, rmSync, statSync } from 'node:fs';
+import { execFileSync } from 'node:child_process';
+import { appendFileSync, existsSync, mkdirSync, readdirSync, rmSync, statSync } from 'node:fs';
 import { tmpdir } from 'node:os';
 import { join } from 'node:path';
 // ---------------------------------------------------------------------------
@@ -114,30 +115,200 @@ function formatAge(ms) {
 // ---------------------------------------------------------------------------
 // Public API — worktree pruning
 // ---------------------------------------------------------------------------
+/**
+ * Check whether a worktree has uncommitted changes (dirty state).
+ *
+ * Runs `git status --porcelain` inside the worktree. A non-empty output means
+ * there are staged or unstaged changes (including untracked files via `-uall`).
+ * Returns `false` when git is unavailable or the directory is not a valid git
+ * worktree — treat as clean so we never block cleanup due to a git error.
+ *
+ * @param worktreePath - Absolute path to the worktree directory.
+ * @returns `true` when uncommitted changes are present; `false` otherwise.
+ *
+ * @task T11996
+ * @internal
+ */
+function isWorktreeDirty(worktreePath) {
+    try {
+        const out = execFileSync('git', ['-C', worktreePath, 'status', '--porcelain', '-uall'], {
+            encoding: 'utf-8',
+            stdio: ['pipe', 'pipe', 'pipe'],
+            timeout: 10_000,
+        });
+        return out.trim().length > 0;
+    }
+    catch {
+        return false;
+    }
+}
+/**
+ * Check whether a worktree has commits that have not been pushed to any remote.
+ *
+ * Two cases are detected:
+ * (a) Branches with a configured upstream: commits ahead of `@{upstream}`.
+ * (b) Branches with NO upstream (never pushed): any commits on the branch that
+ *     are not reachable from any remote-tracking ref.
+ * (c) Detached HEAD: commits not reachable from any remote-tracking ref.
+ *
+ * Returns `false` when git is unavailable or the worktree has no commits.
+ *
+ * @param worktreePath - Absolute path to the worktree directory.
+ * @returns `true` when unpushed commits exist; `false` otherwise.
+ *
+ * @task T11996
+ * @internal
+ */
+function hasUnpushedCommits(worktreePath) {
+    // Case (a): branch has a tracking upstream — check ahead count
+    try {
+        const aheadStr = execFileSync('git', ['-C', worktreePath, 'rev-list', '--count', '@{upstream}..HEAD'], {
+            encoding: 'utf-8',
+            stdio: ['pipe', 'pipe', 'pipe'],
+            timeout: 10_000,
+        }).trim();
+        const aheadCount = Number.parseInt(aheadStr, 10);
+        if (!Number.isNaN(aheadCount) && aheadCount > 0)
+            return true;
+        // Upstream exists and no unpushed commits
+        return false;
+    }
+    catch {
+        // No upstream configured — fall through to case (b)/(c)
+    }
+    // Case (b)/(c): no upstream — check if HEAD is reachable from any remote ref
+    try {
+        // List all remote-tracking refs
+        const remoteRefsOut = execFileSync('git', ['-C', worktreePath, 'for-each-ref', '--format=%(refname)', 'refs/remotes/'], {
+            encoding: 'utf-8',
+            stdio: ['pipe', 'pipe', 'pipe'],
+            timeout: 10_000,
+        }).trim();
+        const remoteRefs = remoteRefsOut.split('\n').filter(Boolean);
+        if (remoteRefs.length === 0) {
+            // No remotes at all — any commit is effectively "unpushed"
+            try {
+                const headOut = execFileSync('git', ['-C', worktreePath, 'rev-parse', 'HEAD'], {
+                    encoding: 'utf-8',
+                    stdio: ['pipe', 'pipe', 'pipe'],
+                    timeout: 5_000,
+                }).trim();
+                return headOut.length > 0;
+            }
+            catch {
+                return false;
+            }
+        }
+        // Check whether HEAD is reachable from the union of all remote refs
+        const args = ['-C', worktreePath, 'rev-list', '--count', 'HEAD', '--not', ...remoteRefs];
+        const countOut = execFileSync('git', args, {
+            encoding: 'utf-8',
+            stdio: ['pipe', 'pipe', 'pipe'],
+            timeout: 15_000,
+        }).trim();
+        const count = Number.parseInt(countOut, 10);
+        return !Number.isNaN(count) && count > 0;
+    }
+    catch {
+        return false;
+    }
+}
+/**
+ * Quarantine a dirty or unpushed worktree by packing it into a `.tar.gz`
+ * archive under `<worktreesRoot>/../quarantine/worktrees/`. The original
+ * directory is left intact.
+ *
+ * Writes an audit JSONL entry to `<worktreesRoot>/../quarantine/audit.jsonl`.
+ *
+ * @param worktreePath - Absolute path to the worktree directory to archive.
+ * @param taskId - Task ID for the entry name.
+ * @param quarantineDir - Absolute path to the quarantine root directory.
+ * @param reason - Human-readable reason (e.g. `'dirty'`, `'unpushed'`).
+ * @returns Absolute path to the created archive, or `null` on failure.
+ *
+ * @task T11996
+ * @internal
+ */
+function quarantineWorktreeDir(worktreePath, taskId, quarantineDir, reason) {
+    try {
+        mkdirSync(quarantineDir, { recursive: true });
+        const ts = new Date().toISOString().replace(/[:.]/g, '-');
+        const archiveName = `${taskId}-${ts}.tar.gz`;
+        const archivePath = join(quarantineDir, archiveName);
+        // Use tar with --exclude to capture untracked AND ignored files.
+        // We deliberately do NOT exclude anything here: the quarantine must be a
+        // complete snapshot including .env, build artifacts, etc. (T11996 AC).
+        execFileSync('tar', [
+            '-czf',
+            archivePath,
+            // Dereference symlinks so the archive is self-contained.
+            '--dereference',
+            // Use the parent directory as CWD so the archive root is `<taskId>/`.
+            '-C',
+            join(worktreePath, '..'),
+            taskId,
+        ], {
+            stdio: ['pipe', 'pipe', 'pipe'],
+            timeout: 120_000,
+        });
+        // Write audit entry
+        const auditPath = join(quarantineDir, 'audit.jsonl');
+        const entry = JSON.stringify({
+            ts: new Date().toISOString(),
+            action: 'quarantine',
+            worktreePath,
+            taskId,
+            archivePath,
+            reason,
+            agentId: process.env['CLEO_AGENT_ID'] ?? 'cleo',
+        });
+        appendFileSync(auditPath, `${entry}\n`, { encoding: 'utf-8' });
+        return archivePath;
+    }
+    catch {
+        return null;
+    }
+}
 /**
  * Prune orphaned agent worktree directories.
  *
  * Scans `worktreesRoot` (or `worktreesRoot/<projectHash>`) for directories
- * whose names are NOT in `activeTaskIds` and removes them. Uses `rmSync`
- * directly because the worktrees at this point are only filesystem artefacts
- * — the agent has already merged its work via `completeAgentWorktreeViaMerge`.
- * Git worktree de-registration is attempted with `git worktree prune` at the
- * level of the caller (cleo gc or cleo doctor does not need a git root here;
- * individual worktrees have their own `.git` file redirects which become stale
- * and are cleaned up by `git worktree prune` in the primary repo).
+ * whose names are NOT in `activeTaskIds` and removes them.
+ *
+ * Safety invariants (T11996):
+ * - Fail-closed: if `activeTaskIds` is empty AND worktrees exist, skip pruning
+ *   entirely and return `skippedFailClosed: true`. This prevents mass-deletion
+ *   when the task store is unavailable or freshly initialised.
+ * - Dirty guard: worktrees with uncommitted changes are quarantined (packed
+ *   into `.tar.gz` in `<worktreesRoot>/../quarantine/worktrees/`) instead of
+ *   deleted. The original directory is left on disk.
+ * - Unpushed guard: worktrees whose branch has commits not reachable from any
+ *   remote ref are quarantined, not deleted.
+ * - A worktree that is both dirty AND has unpushed commits is quarantined once.
  *
  * @param options - See `PruneOrphanWorktreesOptions`.
  * @returns Cleanup result.
  *
  * @task T9043
+ * @task T11996
  */
 export function pruneOrphanWorktrees(options) {
     const { worktreesRoot, projectHash, activeTaskIds, dryRun = false } = options;
     const removed = [];
+    const quarantined = [];
     const errors = [];
     let skipped = 0;
+    let skippedFailClosed = false;
     if (!existsSync(worktreesRoot)) {
-        return { removed: 0, removedPaths: [], skipped, errors, dryRun };
+        return {
+            removed: 0,
+            removedPaths: [],
+            quarantined: 0,
+            quarantinedPaths: [],
+            skipped,
+            errors,
+            dryRun,
+        };
     }
     // Determine which per-project directories to scan.
     let projectDirs;
@@ -151,7 +322,15 @@ export function pruneOrphanWorktrees(options) {
             entries = readdirSync(worktreesRoot);
         }
         catch {
-            return { removed: 0, removedPaths: [], skipped, errors, dryRun };
+            return {
+                removed: 0,
+                removedPaths: [],
+                quarantined: 0,
+                quarantinedPaths: [],
+                skipped: 0,
+                errors,
+                dryRun,
+            };
         }
         projectDirs = entries
             .map((e) => join(worktreesRoot, e))
@@ -172,6 +351,41 @@ export function pruneOrphanWorktrees(options) {
         catch {
             continue;
         }
+        // T11996 Fail-closed: if preserve set is empty AND worktrees exist, skip
+        // this project entirely to prevent mass-deletion when the task store is
+        // unreadable or the DB is freshly initialised. Write an audit warning.
+        const existingWorktrees = taskEntries.filter((e) => {
+            try {
+                return statSync(join(projectDir, e)).isDirectory();
+            }
+            catch {
+                return false;
+            }
+        });
+        if (activeTaskIds.size === 0 && existingWorktrees.length > 0) {
+            // Write a structured audit warning to the quarantine audit log so the
+            // operator can investigate. ZERO desktop output per binding amendment 6.
+            try {
+                const quarantineDir = join(worktreesRoot, '..', 'quarantine', 'worktrees');
+                mkdirSync(quarantineDir, { recursive: true });
+                const auditPath = join(quarantineDir, '..', 'audit.jsonl');
+                const entry = JSON.stringify({
+                    ts: new Date().toISOString(),
+                    action: 'prune-skip-fail-closed',
+                    projectDir,
+                    existingWorktreeCount: existingWorktrees.length,
+                    reason: 'preserve set empty while worktrees exist — skipping to prevent mass-deletion (T11996 fail-closed)',
+                    agentId: process.env['CLEO_AGENT_ID'] ?? 'cleo',
+                });
+                appendFileSync(auditPath, `${entry}\n`, { encoding: 'utf-8' });
+            }
+            catch {
+                // audit is best-effort
+            }
+            skipped += existingWorktrees.length;
+            skippedFailClosed = true;
+            continue;
+        }
         for (const taskId of taskEntries) {
             if (activeTaskIds.has(taskId)) {
                 skipped++;
@@ -188,24 +402,59 @@ export function pruneOrphanWorktrees(options) {
                 skipped++;
                 continue;
             }
-            if (dryRun) {
-                removed.push(worktreePath);
+            // T11996: Check dirty/unpushed state before any destructive action.
+            // Evaluate dirty first; only run unpushed check if clean (short-circuit).
+            const dirty = isWorktreeDirty(worktreePath);
+            const unpushed = dirty ? false : hasUnpushedCommits(worktreePath);
+            const shouldQuarantine = dirty || unpushed;
+            const quarantineReason = dirty ? 'dirty' : 'unpushed';
+            if (shouldQuarantine) {
+                if (dryRun) {
+                    quarantined.push(worktreePath);
+                }
+                else {
+                    const quarantineBase = join(worktreesRoot, '..', 'quarantine', 'worktrees');
+                    const archivePath = quarantineWorktreeDir(worktreePath, taskId, quarantineBase, quarantineReason);
+                    if (archivePath !== null) {
+                        quarantined.push(worktreePath);
+                    }
+                    else {
+                        errors.push({
+                            path: worktreePath,
+                            reason: 'quarantine tar failed — worktree preserved (T11996)',
+                        });
+                    }
+                }
             }
             else {
-                try {
-                    rmSync(worktreePath, { recursive: true, force: true });
+                if (dryRun) {
                     removed.push(worktreePath);
                 }
-                catch (err) {
-                    errors.push({
-                        path: worktreePath,
-                        reason: err instanceof Error ? err.message : String(err),
-                    });
+                else {
+                    try {
+                        rmSync(worktreePath, { recursive: true, force: true });
+                        removed.push(worktreePath);
+                    }
+                    catch (err) {
+                        errors.push({
+                            path: worktreePath,
+                            reason: err instanceof Error ? err.message : String(err),
+                        });
+                    }
                 }
             }
         }
     }
-    return { removed: removed.length, removedPaths: removed, skipped, errors, dryRun };
+    return {
+        removed: removed.length,
+        removedPaths: removed,
+        quarantined: quarantined.length,
+        quarantinedPaths: quarantined,
+        skipped,
+        errors,
+        dryRun,
+        ...(skippedFailClosed ? { skippedFailClosed: true } : {}),
+    };
 }
 // ---------------------------------------------------------------------------
 // Public API — temp dir pruning
@@ -234,7 +483,15 @@ export function pruneOrphanTempDirs(options = {}) {
         entries = readdirSync(tempDir, { withFileTypes: true });
     }
     catch {
-        return { removed: 0, removedPaths: [], skipped, errors, dryRun };
+        return {
+            removed: 0,
+            removedPaths: [],
+            quarantined: 0,
+            quarantinedPaths: [],
+            skipped,
+            errors,
+            dryRun,
+        };
     }
     for (const entry of entries) {
         if (!entry.isDirectory())
@@ -273,7 +530,15 @@ export function pruneOrphanTempDirs(options = {}) {
             }
         }
     }
-    return { removed: removed.length, removedPaths: removed, skipped, errors, dryRun };
+    return {
+        removed: removed.length,
+        removedPaths: removed,
+        quarantined: 0,
+        quarantinedPaths: [],
+        skipped,
+        errors,
+        dryRun,
+    };
 }
 // ---------------------------------------------------------------------------
 // Public API — audit (read-only, for cleo doctor)

package/dist/gc/cleanup.js.map

@@ -1 +1 @@
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package/dist/gc/janitor.d.ts

@@ -0,0 +1,149 @@
+/**
+ * CLEO Janitor — orphan process reaper + stale scope/lock/debris sweep.
+ *
+ * Composable engine that the GC subsystem and the `cleo janitor run` CLI verb
+ * call.  Every action is:
+ *   - Silent: no console output; one JSONL line per action appended to
+ *     `.cleo/audit/janitor.jsonl`, plus counts in the returned result.
+ *   - Idempotent: a fully-converged state produces zero actions on re-run.
+ *   - Dry-run capable: `dryRun: true` reports planned actions without mutating
+ *     anything.
+ *
+ * ## Categories
+ *
+ * | # | Category                 | Description                                          |
+ * |---|--------------------------|------------------------------------------------------|
+ * | 1 | `reaped`                 | Leaked MCP/agent helpers (registration-primary)      |
+ * | 2 | `scopesStopped`          | Cleo-owned systemd transient scopes that exited      |
+ * | 3 | `locksReclaimed`         | Sentient/GC lock files held by dead PIDs             |
+ * | 4 | `semaphoreSlotsCleared`  | Tool-semaphore slot dirs held past staleMs           |
+ * | 5 | `worktreesPruned`        | Orphan worktree directories                          |
+ * | 6 | `worktreesQuarantined`   | Dirty/unpushed worktrees quarantined                 |
+ * | 7 | `tmpRemoved`             | Stale CLEO temp directories                          |
+ * | 8 | `attachmentsRepaired`    | Attachment rows/files repaired                       |
+ * | 9 | `configsRepaired`        | Corrupt config files restored                        |
+ *
+ * ## Amendment compliance
+ *
+ * - **Amendment 1 (registration-primary)**: orphan detection uses cleo-owned
+ *   scope/pgid as PRIMARY discriminator; signature+age only for UNREGISTERED
+ *   processes when all stdio pipe peers are dead.
+ * - **Amendment 2 (regression)**: reparented double-fork of a LIVE session is
+ *   preserved; same of a DEAD session is reaped.
+ * - **Amendment 3 (scope reaping)**: restricted to units starting with
+ *   `cleo-` prefix inside `cleo.slice`.  Never touches `run-*.scope`.
+ * - **Amendment 4 (idempotency)**: TERM→KILL escalation spanning runs is
+ *   legitimate; a fully-converged state produces zero actions on second run.
+ * - **Amendment 5 (liveness probe)**: stale locks reclaimed only after
+ *   verifying the holder PID is dead — never on mtime alone.
+ * - **Amendment 6 (silence)**: every action → `.cleo/audit/janitor.jsonl`;
+ *   zero desktop notifications; zero console noise in non-verbose mode.
+ * - **Amendment 7 (tmp debris)**: reuses `gc/cleanup.ts` patterns directly.
+ *
+ * @module @cleocode/core/gc/janitor
+ * @task T11995
+ * @epic T11992
+ */
+/**
+ * Default minimum age (ms) of an unregistered process before reap eligibility.
+ * 10 minutes gives a freshly-spawned MCP server time to register.
+ */
+export declare const DEFAULT_GRACE_MS: number;
+/**
+ * Default SIGTERM→SIGKILL grace period (ms).
+ * Matches suite-reaper.ts value for consistency.
+ */
+export declare const SIGTERM_GRACE_MS = 3000;
+/**
+ * Default stale-ms for tool-semaphore slot lock directories.
+ * Matches tool-semaphore.ts default.
+ */
+export declare const DEFAULT_SEMAPHORE_STALE_MS = 600000;
+/** Per-category result counts returned by {@link runJanitor}. */
+export interface JanitorResult {
+    /** Orphan agent/MCP processes sent SIGTERM or SIGKILL. */
+    readonly reaped: number;
+    /** Cleo-owned transient scopes stopped + reset-failed. */
+    readonly scopesStopped: number;
+    /** Stale PID lock files reclaimed (sentient, gc). */
+    readonly locksReclaimed: number;
+    /** Stale tool-semaphore slot directories cleared. */
+    readonly semaphoreSlotsCleared: number;
+    /** Orphan worktree directories removed. */
+    readonly worktreesPruned: number;
+    /** Dirty/unpushed worktrees quarantined (not deleted). */
+    readonly worktreesQuarantined: number;
+    /** Stale CLEO tmp dirs removed. */
+    readonly tmpRemoved: number;
+    /** Attachment orphans marked or deleted. */
+    readonly attachmentsRepaired: number;
+    /** Corrupt config files restored from backup. */
+    readonly configsRepaired: number;
+    /** Total non-fatal errors encountered. */
+    readonly errors: number;
+    /** True when `dryRun: true` was set — no mutations were performed. */
+    readonly dryRun: boolean;
+}
+/** Options for {@link runJanitor}. */
+export interface JanitorOptions {
+    /**
+     * When true, report planned actions without performing any mutations.
+     * @default false
+     */
+    dryRun?: boolean;
+    /**
+     * Minimum age (ms) of an unregistered process before reap eligibility.
+     * @default DEFAULT_GRACE_MS (10 min)
+     */
+    gracePeriodMs?: number;
+    /**
+     * Absolute path to the project-level `.cleo/` directory.
+     * Defaults to `resolveCleoDir()` using the current working directory.
+     */
+    cleoDir?: string;
+    /**
+     * Root of the CLEO worktrees hierarchy.
+     * Defaults to `~/.local/share/cleo/worktrees/`.
+     */
+    worktreesRoot?: string;
+    /**
+     * Set of active (non-terminal) task IDs for the worktree prune guard.
+     * When `undefined`, worktree pruning is skipped entirely.
+     */
+    activeTaskIds?: Set<string>;
+    /**
+     * Selectively skip categories.  Omit or set `false` to run all.
+     */
+    skip?: {
+        processes?: boolean;
+        scopes?: boolean;
+        locks?: boolean;
+        semaphores?: boolean;
+        worktrees?: boolean;
+        tmp?: boolean;
+        attachments?: boolean;
+        config?: boolean;
+    };
+}
+/**
+ * Check whether a PID is alive via `kill(pid, 0)`.
+ * Returns `false` for ESRCH or any other error.
+ */
+export declare function isPidAlive(pid: number): boolean;
+/**
+ * Run the CLEO janitor sweep.
+ *
+ * Runs all enabled categories and returns a structured result with per-category
+ * counts.  Designed to be called from:
+ *   - `cleo janitor run [--dry-run]` (manual verb)
+ *   - GC subsystem sentient tick (daemon mode)
+ *   - Session start/end (daemon-off lazy mode)
+ *
+ * @param opts - Janitor options.
+ * @returns Structured result.
+ *
+ * @task T11995
+ * @epic T11992
+ */
+export declare function runJanitor(opts?: JanitorOptions): Promise<JanitorResult>;
+//# sourceMappingURL=janitor.d.ts.map

package/dist/gc/janitor.d.ts.map

@@ -0,0 +1 @@
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