@cleocode/core 2026.8.8 → 2026.9.1

package/dist/tasks/tool-semaphore.js

@@ -41,12 +41,13 @@
  * @task T12091
  * @adr ADR-061
  */
-import { existsSync, mkdirSync, writeFileSync } from 'node:fs';
-import { availableParallelism, totalmem } from 'node:os';
+import { existsSync, mkdirSync, readFileSync, rmSync, writeFileSync } from 'node:fs';
+import { availableParallelism, hostname, totalmem } from 'node:os';
 import { join } from 'node:path';
 import lockfile from 'proper-lockfile';
 import { getCleoHome } from '../paths.js';
 import { ResourceMonitor } from '../resources/monitor.js';
+import { isHeavyTool } from './heavy-tool-env.js';
 // ---------------------------------------------------------------------------
 // Concurrency-limit defaults + override resolution
 // ---------------------------------------------------------------------------
@@ -153,7 +154,12 @@ export function resolveMaxConcurrent(canonical, cpuCount, totalRamGib) {
  * and single-threaded, so they keep their static budget.
  */
 function isPressureSensitive(canonical) {
-    return canonical === 'test' || canonical === 'build';
+    // Delegates rather than repeating the literal. This was the third
+    // independent definition of "heavy"; all three agreed by coincidence, and a
+    // fifth heavy tool would have needed three coordinated edits — with a missed
+    // one producing a SILENT asymmetry (a tool granted the long deadline and the
+    // worker caps but not a semaphore slot, or the reverse).
+    return isHeavyTool(canonical);
 }
 /**
  * Scale a static slot budget down under memory pressure (T12001 · choke-point
@@ -212,6 +218,159 @@ function hasConcurrencyOverride(canonical) {
 export function semaphoreDir(canonical) {
     return join(getCleoHome(), 'locks', `tool-${canonical}`);
 }
+/**
+ * Path of the sidecar holder record for a slot.
+ *
+ * Deliberately a SIBLING of the lock rather than a file inside it:
+ * `proper-lockfile` removes its lock directory with `rmdir`, which fails if we
+ * have put anything inside it.
+ *
+ * @internal
+ * @task T12113 (gh#1222)
+ */
+function holderPath(slotPath) {
+    return `${slotPath}.holder.json`;
+}
+/**
+ * Record who holds a slot. Best-effort: a failure here must never fail an
+ * acquire that has already succeeded, because the slot IS held at that point
+ * and throwing would leak it.
+ *
+ * @internal
+ * @task T12113 (gh#1222)
+ */
+function writeHolder(slotPath, canonical) {
+    const holder = {
+        pid: process.pid,
+        host: hostname(),
+        acquiredAt: new Date().toISOString(),
+        canonical,
+        slot: slotPath,
+    };
+    try {
+        writeFileSync(holderPath(slotPath), JSON.stringify(holder), 'utf-8');
+    }
+    catch {
+        /* best-effort — never fail an acquire that succeeded */
+    }
+}
+/**
+ * Read a slot's holder record. Returns `null` when absent or unparseable —
+ * both mean "we cannot say who holds this", which is treated as alive.
+ *
+ * @internal
+ * @task T12113 (gh#1222)
+ */
+export function readHolder(slotPath) {
+    try {
+        const parsed = JSON.parse(readFileSync(holderPath(slotPath), 'utf-8'));
+        if (typeof parsed.pid !== 'number' || typeof parsed.host !== 'string')
+            return null;
+        return parsed;
+    }
+    catch {
+        return null;
+    }
+}
+/**
+ * Is a slot's recorded holder still running?
+ *
+ * Fails SAFE: an unknown holder, a holder on another host, or any error is
+ * reported as ALIVE. Reaping a live holder's slot would let two heavy suites
+ * run against one bound — the exact oversubscription the semaphore exists to
+ * prevent — so uncertainty must never authorise a reap.
+ *
+ * @param holder - Holder record, or `null` when none could be read.
+ * @returns `true` when the slot must be treated as legitimately held.
+ *
+ * @task T12113 (gh#1222)
+ */
+export function isHolderAlive(holder) {
+    if (!holder)
+        return true; // unknown — assume alive
+    if (holder.host !== hostname())
+        return true; // pid is not ours to judge
+    try {
+        process.kill(holder.pid, 0); // signal 0 = existence check, sends nothing
+        return true;
+    }
+    catch (err) {
+        // EPERM means the process exists but belongs to another user.
+        return err.code === 'EPERM';
+    }
+}
+/**
+ * Release a slot whose recorded holder is gone.
+ *
+ * Removes `proper-lockfile`'s lock directory directly — the same thing its own
+ * stale recovery does, but decided by process liveness instead of by a 10
+ * minute mtime timeout.
+ *
+ * @param slotPath - Slot lock file path.
+ * @returns `true` when an orphaned slot was actually reaped.
+ *
+ * @task T12113 (gh#1222)
+ */
+export function reapSlotIfOrphaned(slotPath) {
+    const holder = readHolder(slotPath);
+    if (isHolderAlive(holder))
+        return false;
+    try {
+        rmSync(`${slotPath}.lock`, { recursive: true, force: true });
+        rmSync(holderPath(slotPath), { force: true });
+        return true;
+    }
+    catch {
+        return false;
+    }
+}
+/**
+ * Enumerate every slot of a canonical tool with its holder and liveness.
+ *
+ * Backs the operator-facing lock inspection surface requested in gh#1222 —
+ * "who is holding this, and is it even alive?" — which previously required
+ * reading `~/.local/share/cleo/locks/` by hand.
+ *
+ * @param canonical - Canonical tool name.
+ * @returns One row per existing slot file.
+ *
+ * @task T12113 (gh#1222)
+ */
+export function listSlotHolders(canonical) {
+    const dir = semaphoreDir(canonical);
+    if (!existsSync(dir))
+        return [];
+    const rows = [];
+    for (let i = 0;; i++) {
+        const slotPath = join(dir, `slot-${i}.lock`);
+        if (!existsSync(slotPath))
+            break;
+        const holder = readHolder(slotPath);
+        rows.push({
+            slot: slotPath,
+            held: existsSync(`${slotPath}.lock`),
+            holder,
+            alive: isHolderAlive(holder),
+        });
+    }
+    return rows;
+}
+/**
+ * Reap every orphaned slot of a canonical tool.
+ *
+ * @param canonical - Canonical tool name.
+ * @returns Paths of the slots actually reaped.
+ *
+ * @task T12113 (gh#1222)
+ */
+export function reapOrphanedSlots(canonical) {
+    const reaped = [];
+    for (const row of listSlotHolders(canonical)) {
+        if (row.held && !row.alive && reapSlotIfOrphaned(row.slot))
+            reaped.push(row.slot);
+    }
+    return reaped;
+}
 function ensureSlotFiles(dir, count) {
     if (!existsSync(dir)) {
         mkdirSync(dir, { recursive: true });
@@ -301,12 +460,29 @@ export async function acquireGlobalSlot(canonical, opts = {}) {
             const path = slots[idx];
             if (!path)
                 continue;
+            let acquired = null;
             try {
-                const release = await lockfile.lock(path, {
-                    retries: 0,
-                    stale: staleMs,
-                    realpath: false,
-                });
+                acquired = await lockfile.lock(path, { retries: 0, stale: staleMs, realpath: false });
+            }
+            catch {
+                // gh#1222: the slot is held — but by whom? proper-lockfile decides
+                // staleness from mtime, so a process that died without releasing
+                // holds the slot for the full staleMs (10 min) and is
+                // indistinguishable from a legitimately slow suite. Ask the holder
+                // record instead: a dead pid on this host is orphaned NOW. Fails
+                // safe — an unknown or remote holder is treated as alive.
+                if (reapSlotIfOrphaned(path)) {
+                    try {
+                        acquired = await lockfile.lock(path, { retries: 0, stale: staleMs, realpath: false });
+                    }
+                    catch {
+                        acquired = null; // someone else won the race for the reaped slot
+                    }
+                }
+            }
+            if (acquired) {
+                const release = acquired;
+                writeHolder(path, canonical);
                 let released = false;
                 return async () => {
                     if (released)
@@ -320,19 +496,32 @@ export async function acquireGlobalSlot(canonical, opts = {}) {
                         // (e.g. via stale recovery). Swallow — the post-condition
                         // is "slot is free", which is true either way.
                     }
+                    try {
+                        rmSync(`${path}.holder.json`, { force: true });
+                    }
+                    catch {
+                        /* best-effort — a stale holder record is only ever advisory */
+                    }
                 };
             }
-            catch {
-                // slot busy; try next
-            }
         }
         // All slots busy — sleep and retry.
         await sleep(pollMs);
     }
+    // gh#1222: name the holders. "Everything is busy" with no way to see WHO is
+    // what made an orphaned slot look like a broken semaphore.
+    const holders = listSlotHolders(canonical)
+        .filter((r) => r.held)
+        .map((r) => {
+        const h = r.holder;
+        if (!h)
+            return `${r.slot}: holder unknown`;
+        return `${r.slot}: pid ${h.pid} on ${h.host} since ${h.acquiredAt}${r.alive ? '' : ' (DEAD)'}`;
+    });
     throw new Error(`Timed out after ${timeoutMs}ms waiting for a free '${canonical}' tool slot ` +
-        `(max ${max} concurrent). Override with CLEO_TOOL_CONCURRENCY_${canonical
-            .toUpperCase()
-            .replace(/-/g, '_')}=<n>.`);
+        `(max ${max} concurrent).` +
+        (holders.length > 0 ? ` Current holders — ${holders.join('; ')}.` : '') +
+        ` Override with CLEO_TOOL_CONCURRENCY_${canonical.toUpperCase().replace(/-/g, '_')}=<n>.`);
 }
 function sleep(ms) {
     return new Promise((r) => setTimeout(r, ms));

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package/dist/validation/doctor/checks.d.ts

@@ -55,6 +55,70 @@ export declare function checkCoreFilesNotIgnored(projectRoot?: string): CheckRes
  * @task T5160
  */
 export declare function checkSqliteNotTracked(projectRoot?: string): CheckResult;
+/**
+ * Warn when a stash stack is shared by several worktrees.
+ *
+ * ## The failure this exists to stop (T12161)
+ *
+ * The stash is a property of the repository, not of the working tree. Every
+ * worktree sharing a `.git` sees the same stack, so `git stash pop` — which
+ * takes `stash@{0}` when given no argument — pops whatever another session
+ * pushed most recently, into YOUR tree, on YOUR branch.
+ *
+ * Measured 2026-09-12 in this repo: an agent ran `git stash push` on an
+ * untracked file (a no-op, so nothing was pushed), then `git stash pop`, and
+ * silently received an unrelated entry from a 26-deep stack belonging to
+ * another session's branch work. It modified a generated manifest the agent
+ * had never touched. It was caught before commit by a diff review, not by any
+ * tooling.
+ *
+ * The stack here is not transient: entries date back months, across branches
+ * that are long merged. A single-worktree repo has none of this exposure,
+ * which is why the check stays silent there rather than nagging every user
+ * about a normal stash.
+ *
+ * @param projectRoot - repository to inspect; defaults to the resolved root.
+ * @returns a warning naming the depth and the top entry, or a pass.
+ *
+ * @task T12161
+ */
+export declare function checkSharedWorktreeStashes(projectRoot?: string): CheckResult;
+/**
+ * Warn when a repo-LOCAL identity override is absent from recent history.
+ *
+ * ## The failure this exists to stop (T12161)
+ *
+ * `user.name` and `user.email` set at `--local` scope live in `.git/config`,
+ * which every worktree shares. One session setting a throwaway identity — for
+ * a measurement, a probe, a bisect — silently re-authors every commit made by
+ * every other session in every other worktree until someone notices.
+ *
+ * Measured 2026-09-12 in this repo: `user.name` was left as `compose probe
+ * <probe@local>` after a merge-composition experiment, and three commits from
+ * a different session on a different branch were authored under it. Nothing
+ * warned; it was found by reading `git log` for an unrelated reason.
+ *
+ * ## Why this reads `--local` and not the effective identity
+ *
+ * `git config user.email` returns the MERGED value — local, then global, then
+ * system. Reading that would flag a first-time contributor whose perfectly
+ * correct global identity simply has no commits here yet, which is noise. A
+ * repo-local override is different in kind: it is a deliberate act scoped to
+ * this repository, it is the only kind that one session can impose on another
+ * through the shared `.git`, and when it authored none of recent history the
+ * overwhelmingly likely explanation is that somebody else set it for something
+ * else. So the remedy is to REMOVE the override and fall back to the
+ * committer's own global identity — not to set another value.
+ *
+ * Gated on a shared `.git` for the same reason as the stash check: a local
+ * identity in a single-worktree repo affects only the person who set it.
+ *
+ * @param projectRoot - repository to inspect; defaults to the resolved root.
+ * @returns a warning naming the override, or a pass.
+ *
+ * @task T12161
+ */
+export declare function checkSharedGitIdentity(projectRoot?: string): CheckResult;
 /**
  * Check if any legacy output directories still exist.
  * Delegates detection to the migration/agent-outputs utility.

package/dist/validation/doctor/checks.d.ts.map

@@ -1 +1 @@
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package/dist/validation/doctor/checks.js

@@ -11,6 +11,7 @@ import { execFileSync } from 'node:child_process';
 import { accessSync, constants, existsSync, readdirSync, readFileSync, statSync } from 'node:fs';
 import { homedir } from 'node:os';
 import { join } from 'node:path';
+import { listRegisteredWorktrees } from '@cleocode/worktree';
 import { CORE_PROTECTED_FILES } from '../../constants.js';
 import { detectLegacyAgentOutputs } from '../../migration/agent-outputs.js';
 import { getAgentsHome, getCleoHome, getCleoTemplatesTildePath, getProjectRoot, } from '../../paths.js';
@@ -594,6 +595,251 @@ export function checkSqliteNotTracked(projectRoot) {
     }
 }
 // ============================================================================
+// Check: Shared-worktree git hazards (T12161)
+// ============================================================================
+/**
+ * Worktrees that share this repository's single `.git` directory.
+ *
+ * Returns 1 for an ordinary checkout. Anything above 1 means several working
+ * trees — in this project, usually several concurrent agent sessions — are
+ * backed by ONE object store, ONE config file and ONE stash stack.
+ *
+ * @param root - repository path to inspect.
+ * @returns worktree count, or `null` when git could not answer.
+ */
+function sharedWorktreeCount(root) {
+    // Routed through `@cleocode/worktree` rather than a raw `git worktree list`
+    // per D010 / T9984 — the registry is that package's surface, and it already
+    // owns porcelain parsing. `listRegisteredWorktrees` never throws: an
+    // unreadable registry yields `[]`. A real repository always has at least one
+    // registered worktree, so an empty list means "could not determine", which is
+    // `null` here and NOT "zero worktrees" — the difference decides whether the
+    // caller warns or stays silent.
+    const registered = listRegisteredWorktrees(root);
+    return registered.length > 0 ? registered.length : null;
+}
+/**
+ * Warn when a stash stack is shared by several worktrees.
+ *
+ * ## The failure this exists to stop (T12161)
+ *
+ * The stash is a property of the repository, not of the working tree. Every
+ * worktree sharing a `.git` sees the same stack, so `git stash pop` — which
+ * takes `stash@{0}` when given no argument — pops whatever another session
+ * pushed most recently, into YOUR tree, on YOUR branch.
+ *
+ * Measured 2026-09-12 in this repo: an agent ran `git stash push` on an
+ * untracked file (a no-op, so nothing was pushed), then `git stash pop`, and
+ * silently received an unrelated entry from a 26-deep stack belonging to
+ * another session's branch work. It modified a generated manifest the agent
+ * had never touched. It was caught before commit by a diff review, not by any
+ * tooling.
+ *
+ * The stack here is not transient: entries date back months, across branches
+ * that are long merged. A single-worktree repo has none of this exposure,
+ * which is why the check stays silent there rather than nagging every user
+ * about a normal stash.
+ *
+ * @param projectRoot - repository to inspect; defaults to the resolved root.
+ * @returns a warning naming the depth and the top entry, or a pass.
+ *
+ * @task T12161
+ */
+export function checkSharedWorktreeStashes(projectRoot) {
+    const root = getProjectRoot(projectRoot);
+    const id = 'shared_worktree_stashes';
+    if (!existsSync(join(root, '.git'))) {
+        return {
+            id,
+            category: 'configuration',
+            status: 'info',
+            message: 'Not a git repository (skipping shared-stash check)',
+            details: { isGitRepo: false },
+            fix: null,
+        };
+    }
+    const worktrees = sharedWorktreeCount(root);
+    let entries;
+    try {
+        entries = execFileSync('git', ['stash', 'list', '--pretty=%H %gd %gs'], {
+            cwd: root,
+            encoding: 'utf-8',
+            stdio: ['ignore', 'pipe', 'ignore'],
+        })
+            .split('\n')
+            .filter((l) => l.trim().length > 0);
+    }
+    catch {
+        return {
+            id,
+            category: 'configuration',
+            status: 'info',
+            message: 'Could not read the stash list (skipping shared-stash check)',
+            details: { worktrees },
+            fix: null,
+        };
+    }
+    // A stash in a single-worktree repo is ordinary and private. The hazard is
+    // specifically that another tree can pop it out from under you.
+    if (entries.length === 0 || worktrees === null || worktrees < 2) {
+        return {
+            id,
+            category: 'configuration',
+            status: 'passed',
+            message: entries.length === 0
+                ? 'Stash stack is empty'
+                : `${entries.length} stash entr${entries.length === 1 ? 'y' : 'ies'}, single worktree — not shared`,
+            details: { stashCount: entries.length, worktrees },
+            fix: null,
+        };
+    }
+    return {
+        id,
+        category: 'configuration',
+        status: 'warning',
+        message: `${entries.length} stash entries are shared by ${worktrees} worktrees — ` +
+            "a bare `git stash pop` here takes another session's work, not yours",
+        details: {
+            stashCount: entries.length,
+            worktrees,
+            // SHA first, deliberately. `stash@{n}` is a POSITION, not an identity:
+            // dropping any entry renumbers every one below it, so an index cited in a
+            // report can name a different stash by the time anyone reads it. Observed
+            // 2026-09-12: one stash referred to as `stash@{2}` and then `stash@{1}`
+            // inside a single session. The SHA is stable and `git stash show <sha>`
+            // accepts it.
+            topEntry: entries[0] ?? null,
+        },
+        fix: 'Never use a bare `git stash pop` in this repo. Run `git stash list`, identify your own entry, and apply it explicitly with `git stash apply stash@{N}`.',
+    };
+}
+/**
+ * Warn when a repo-LOCAL identity override is absent from recent history.
+ *
+ * ## The failure this exists to stop (T12161)
+ *
+ * `user.name` and `user.email` set at `--local` scope live in `.git/config`,
+ * which every worktree shares. One session setting a throwaway identity — for
+ * a measurement, a probe, a bisect — silently re-authors every commit made by
+ * every other session in every other worktree until someone notices.
+ *
+ * Measured 2026-09-12 in this repo: `user.name` was left as `compose probe
+ * <probe@local>` after a merge-composition experiment, and three commits from
+ * a different session on a different branch were authored under it. Nothing
+ * warned; it was found by reading `git log` for an unrelated reason.
+ *
+ * ## Why this reads `--local` and not the effective identity
+ *
+ * `git config user.email` returns the MERGED value — local, then global, then
+ * system. Reading that would flag a first-time contributor whose perfectly
+ * correct global identity simply has no commits here yet, which is noise. A
+ * repo-local override is different in kind: it is a deliberate act scoped to
+ * this repository, it is the only kind that one session can impose on another
+ * through the shared `.git`, and when it authored none of recent history the
+ * overwhelmingly likely explanation is that somebody else set it for something
+ * else. So the remedy is to REMOVE the override and fall back to the
+ * committer's own global identity — not to set another value.
+ *
+ * Gated on a shared `.git` for the same reason as the stash check: a local
+ * identity in a single-worktree repo affects only the person who set it.
+ *
+ * @param projectRoot - repository to inspect; defaults to the resolved root.
+ * @returns a warning naming the override, or a pass.
+ *
+ * @task T12161
+ */
+export function checkSharedGitIdentity(projectRoot) {
+    const root = getProjectRoot(projectRoot);
+    const id = 'shared_git_identity';
+    if (!existsSync(join(root, '.git'))) {
+        return {
+            id,
+            category: 'configuration',
+            status: 'info',
+            message: 'Not a git repository (skipping shared-identity check)',
+            details: { isGitRepo: false },
+            fix: null,
+        };
+    }
+    const worktrees = sharedWorktreeCount(root);
+    if (worktrees === null || worktrees < 2) {
+        return {
+            id,
+            category: 'configuration',
+            status: 'passed',
+            message: 'Single worktree — git identity is not shared',
+            details: { worktrees },
+            fix: null,
+        };
+    }
+    const gitValue = (args) => {
+        try {
+            const out = execFileSync('git', [...args], {
+                cwd: root,
+                encoding: 'utf-8',
+                stdio: ['ignore', 'pipe', 'ignore'],
+            }).trim();
+            return out.length > 0 ? out : null;
+        }
+        catch {
+            return null;
+        }
+    };
+    const localEmail = gitValue(['config', '--local', 'user.email']);
+    // No repo-local override: whatever identity is in play came from the
+    // committer's own global config and is none of this check's business.
+    if (localEmail === null) {
+        return {
+            id,
+            category: 'configuration',
+            status: 'passed',
+            message: 'No repo-local git identity override — each session uses its own global identity',
+            details: { worktrees, localOverride: null },
+            fix: null,
+        };
+    }
+    const authors = (gitValue(['log', '-50', '--format=%ae']) ?? '')
+        .split('\n')
+        .filter((l) => l.trim().length > 0);
+    // No history to compare against proves nothing either way.
+    if (authors.length === 0) {
+        return {
+            id,
+            category: 'configuration',
+            status: 'passed',
+            message: 'No commit history to compare the local git identity against',
+            details: { worktrees, localOverride: localEmail },
+            fix: null,
+        };
+    }
+    if (authors.includes(localEmail)) {
+        return {
+            id,
+            category: 'configuration',
+            status: 'passed',
+            message: `Repo-local git identity (${localEmail}) appears in recent history`,
+            details: { worktrees, localOverride: localEmail, sampled: authors.length },
+            fix: null,
+        };
+    }
+    const mostRecent = authors[0] ?? '(unknown)';
+    return {
+        id,
+        category: 'configuration',
+        status: 'warning',
+        message: `Repo-local git identity "${localEmail}" authored none of the last ${authors.length} ` +
+            `commits, and this .git is shared by ${worktrees} worktrees — every session ` +
+            'committing right now is attributed to it',
+        details: {
+            worktrees,
+            localOverride: localEmail,
+            sampled: authors.length,
+            mostRecentHistoricalAuthor: mostRecent,
+        },
+        fix: 'If this override is left over from another session, remove it so each session uses its own identity: git config --local --unset user.email && git config --local --unset user.name',
+    };
+}
+// ============================================================================
 // Check: Legacy agent-outputs path
 // ============================================================================
 /**
@@ -1439,6 +1685,9 @@ export function runAllGlobalChecks(cleoHome, projectRoot) {
         checkNoLocalSchemas(projectRoot),
         // Orphan worktrees audit (T9043)
         auditOrphanWorktrees(),
+        // Shared-worktree git hazards (T12161)
+        checkSharedWorktreeStashes(projectRoot),
+        checkSharedGitIdentity(projectRoot),
     ];
 }
 // ============================================================================