@cleocode/core 2026.9.20 → 2026.9.22

package/dist/system/skill-fixtures.js

@@ -0,0 +1,331 @@
+/**
+ * Test-fixture sweep for the real skills root — finds and quarantines skill
+ * directories that caamp unit tests wrote into `<cleoHome>/skills` before the
+ * test sandbox covered the skills root (T12645).
+ *
+ * Measured 2026-09-28 on macOS: 53 of the 70 entries were fixtures —
+ * `<prefix>-<uuid>` dirs from `skills-installer.test.ts` /
+ * `skills-installer-recordrow.test.ts`, plus `real-skill`, `skill-alpha` and
+ * `skill-beta`. Every one surfaced in skill listings and harness installs.
+ *
+ * Matching is deliberately narrow. An entry is a fixture only when BOTH hold:
+ * - its name is `<slug>-<uuid>` or one of {@link SKILL_FIXTURE_EXACT_NAMES};
+ * - its content is exactly what those tests write: a `SKILL.md` whose
+ *   description is `Test skill <name>` or `Deep nested skill`, plus only
+ *   small regular files and directories (no links).
+ * A name match whose content does not fit is reported `unclassified` and left
+ * in place. Hidden/underscore entries (`.audit-log`, `_archive`, …), manifest
+ * skills and bundled skill names are never candidates.
+ *
+ * Repair MOVES each fixture into
+ * `<cleoHome>/audit/skill-fixture-quarantine/<receiptId>/<name>` — nothing
+ * is deleted — and appends intent/completed receipts to
+ * `<cleoHome>/audit/skill-fixtures.jsonl`, each naming both paths and the
+ * sha256 of every file moved. Across filesystems (EXDEV) the move is a copy,
+ * re-hashed against that inventory before the source is removed.
+ * {@link restoreSkillFixtures} moves a run's entries back.
+ *
+ * @task T12645
+ */
+import { createHash, randomUUID } from 'node:crypto';
+import { appendFileSync, cpSync, existsSync, lstatSync, mkdirSync, readdirSync, readFileSync, renameSync, rmSync, } from 'node:fs';
+import { basename, join, relative } from 'node:path';
+import { getCleoHome } from '../paths.js';
+import { listCanonicalSkillNames, parseFrontmatter } from '../skills/discovery.js';
+import { resolveBundledSkillsDir, resolveSkillsRoot } from '../skills/skill-root.js';
+/** Repair command printed in remedies. */
+export const SKILL_FIXTURES_REPAIR_COMMAND = 'cleo doctor skill-fixtures --repair';
+/** `<slug>-<uuid>` — every randomized caamp installer fixture name. */
+export const SKILL_FIXTURE_UUID_NAME = /^[a-z0-9][a-z0-9._-]*-[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$/;
+/** Fixed fixture names written by `skills-installer.test.ts`. */
+export const SKILL_FIXTURE_EXACT_NAMES = [
+    'real-skill',
+    'skill-alpha',
+    'skill-beta',
+];
+/** The only SKILL.md descriptions those tests write. */
+const FIXTURE_DESCRIPTION = /^(Test skill \S+|Deep nested skill)$/;
+/** Fixture files are one-liners; anything bigger is not ours to judge. */
+const MAX_FIXTURE_FILE_BYTES = 1024;
+/** Fixtures hold at most a handful of entries. */
+const MAX_FIXTURE_ENTRIES = 16;
+/** Stable comparison key for a file inventory. */
+function inventoryKey(files) {
+    return JSON.stringify([...files].sort((a, b) => a.path.localeCompare(b.path)));
+}
+/**
+ * Move `from` to `to`. A plain rename when possible; when rename fails with
+ * EXDEV (quarantine on another filesystem), copy, re-hash the copy against
+ * `expected`, and only then remove the source. A copy that does not verify is
+ * removed and the source stays in place.
+ */
+function moveVerified(from, to, expected, rename) {
+    try {
+        rename(from, to);
+        return { from, to, method: 'rename', sourceRemoved: true, sourceError: null };
+    }
+    catch (err) {
+        if (err.code !== 'EXDEV')
+            throw err;
+    }
+    try {
+        cpSync(from, to, { recursive: true, errorOnExist: true, force: false });
+    }
+    catch (err) {
+        // A partial copy is ours to remove; the source was never touched.
+        rmSync(to, { recursive: true, force: true });
+        throw new Error(`copy of ${from} to ${to} failed (${err.message}); partial copy removed, source left in place`);
+    }
+    const copied = classifySkillFixture(basename(to), to).files;
+    if (inventoryKey(copied) !== inventoryKey(expected)) {
+        rmSync(to, { recursive: true, force: true });
+        throw new Error(`copy of ${from} to ${to} did not match the recorded sha256 inventory; source left in place`);
+    }
+    try {
+        rmSync(from, { recursive: true });
+    }
+    catch (err) {
+        return { from, to, method: 'copy', sourceRemoved: false, sourceError: err.message };
+    }
+    return { from, to, method: 'copy', sourceRemoved: true, sourceError: null };
+}
+/** Manifest skill names plus every skill directory bundled in `@cleocode/skills`. */
+function defaultProtectedNames() {
+    const names = new Set(listCanonicalSkillNames());
+    const bundled = resolveBundledSkillsDir();
+    if (bundled !== null)
+        for (const name of readdirSync(bundled))
+            names.add(name);
+    return [...names];
+}
+/**
+ * Classify one fixture-named entry by content.
+ *
+ * @param name - Entry name.
+ * @param entryPath - Absolute entry path.
+ * @returns The classified entry.
+ */
+export function classifySkillFixture(name, entryPath) {
+    const entry = {
+        name,
+        path: entryPath,
+        state: 'unclassified',
+        reason: null,
+        files: [],
+    };
+    const stat = lstatSync(entryPath);
+    if (!stat.isDirectory()) {
+        entry.reason = stat.isSymbolicLink() ? 'is a symlink' : 'is not a directory';
+        return entry;
+    }
+    const pending = [entryPath];
+    let seen = 0;
+    while (pending.length > 0) {
+        const dir = pending.pop();
+        for (const child of readdirSync(dir)) {
+            const childPath = join(dir, child);
+            const childStat = lstatSync(childPath);
+            if (++seen > MAX_FIXTURE_ENTRIES) {
+                entry.reason = `more than ${MAX_FIXTURE_ENTRIES} entries`;
+                return entry;
+            }
+            if (childStat.isDirectory()) {
+                pending.push(childPath);
+            }
+            else if (!childStat.isFile()) {
+                entry.reason = `${relative(entryPath, childPath)} is not a regular file`;
+                return entry;
+            }
+            else if (childStat.size > MAX_FIXTURE_FILE_BYTES) {
+                entry.reason = `${relative(entryPath, childPath)} is larger than ${MAX_FIXTURE_FILE_BYTES} bytes`;
+                return entry;
+            }
+            else {
+                const content = readFileSync(childPath);
+                entry.files.push({
+                    path: relative(entryPath, childPath),
+                    bytes: childStat.size,
+                    sha256: createHash('sha256').update(content).digest('hex'),
+                });
+            }
+        }
+    }
+    const skillMd = join(entryPath, 'SKILL.md');
+    if (!existsSync(skillMd)) {
+        entry.reason = 'no SKILL.md';
+        return entry;
+    }
+    const { description } = parseFrontmatter(readFileSync(skillMd, 'utf-8'));
+    if (!FIXTURE_DESCRIPTION.test(String(description ?? '').trim())) {
+        entry.reason = `SKILL.md description is not a test fixture's: ${JSON.stringify(description)}`;
+        return entry;
+    }
+    entry.state = 'fixture';
+    return entry;
+}
+/**
+ * Audit a skills root for caamp test fixtures.
+ *
+ * @param opts - Injection points (tests).
+ * @returns Every fixture-named entry, classified, with the remedy.
+ * @task T12645
+ */
+export function auditSkillFixtures(opts = {}) {
+    const skillsRoot = opts.skillsRoot ?? resolveSkillsRoot();
+    const protectedNames = new Set(opts.protectedNames ?? defaultProtectedNames());
+    const entries = [];
+    const names = existsSync(skillsRoot) ? readdirSync(skillsRoot).sort() : [];
+    for (const name of names) {
+        if (name.startsWith('.') || name.startsWith('_') || protectedNames.has(name))
+            continue;
+        if (!SKILL_FIXTURE_UUID_NAME.test(name) && !SKILL_FIXTURE_EXACT_NAMES.includes(name))
+            continue;
+        entries.push(classifySkillFixture(name, join(skillsRoot, name)));
+    }
+    const fixture = entries.filter((e) => e.state === 'fixture').length;
+    return {
+        skillsRoot,
+        entries,
+        counts: { fixture, unclassified: entries.length - fixture },
+        healthy: fixture === 0,
+        remedy: fixture === 0 ? null : SKILL_FIXTURES_REPAIR_COMMAND,
+    };
+}
+/**
+ * Move every fixture found by {@link auditSkillFixtures} into a per-run
+ * quarantine directory, with intent and outcome receipts. Each entry is
+ * re-classified immediately before its move; one that changed is skipped.
+ *
+ * @param opts - `dryRun` plans without writing; plus injection points.
+ * @returns The post-repair audit and the receipt.
+ * @task T12645
+ */
+export function repairSkillFixtures(opts = {}) {
+    const dryRun = opts.dryRun === true;
+    const before = auditSkillFixtures(opts);
+    const auditDir = opts.auditDir ?? join(getCleoHome(), 'audit');
+    const receiptId = randomUUID();
+    const quarantineDir = join(auditDir, 'skill-fixture-quarantine', receiptId);
+    const fixtures = before.entries.filter((e) => e.state === 'fixture');
+    const receipt = {
+        receiptId,
+        at: new Date().toISOString(),
+        dryRun,
+        phase: 'planned',
+        quarantineDir,
+        planned: fixtures.map((e) => ({
+            from: e.path,
+            to: join(quarantineDir, e.name),
+            files: e.files,
+        })),
+        moved: [],
+        skipped: before.entries
+            .filter((e) => e.state === 'unclassified')
+            .map((e) => ({ path: e.path, reason: e.reason ?? 'unclassified' })),
+        error: null,
+        receiptLog: null,
+    };
+    if (dryRun || fixtures.length === 0)
+        return { audit: before, receipt };
+    mkdirSync(quarantineDir, { recursive: true });
+    receipt.receiptLog = join(auditDir, 'skill-fixtures.jsonl');
+    const log = (phase) => {
+        receipt.phase = phase;
+        appendFileSync(receipt.receiptLog, `${JSON.stringify(receipt)}\n`, 'utf8');
+    };
+    log('intent');
+    try {
+        for (const entry of fixtures) {
+            const now = classifySkillFixture(entry.name, entry.path);
+            if (now.state !== 'fixture' || inventoryKey(now.files) !== inventoryKey(entry.files)) {
+                receipt.skipped.push({ path: entry.path, reason: 'changed since audit; left in place' });
+                continue;
+            }
+            receipt.moved.push(moveVerified(entry.path, join(quarantineDir, entry.name), entry.files, opts.rename ?? renameSync));
+        }
+    }
+    catch (err) {
+        receipt.error = err instanceof Error ? err.message : String(err);
+        log('failed');
+        throw err;
+    }
+    log('completed');
+    return { audit: auditSkillFixtures(opts), receipt };
+}
+/**
+ * Undo one {@link repairSkillFixtures} run: move every entry its receipt
+ * records as moved back from quarantine to its original path. An entry whose
+ * original path is occupied, whose quarantine copy is gone, or whose files no
+ * longer match the recorded sha256 inventory is skipped and reported. Appends
+ * a `restored` line to the same JSONL log.
+ *
+ * @param receiptId - The repair receipt id (also the quarantine dir name).
+ * @param opts - `dryRun` plans without moving; `auditDir` / `rename` injection.
+ * @returns The restore receipt.
+ * @throws When the log has no finished run with that id, or it was already restored.
+ * @task T12645
+ */
+export function restoreSkillFixtures(receiptId, opts = {}) {
+    const auditDir = opts.auditDir ?? join(getCleoHome(), 'audit');
+    const receiptLog = join(auditDir, 'skill-fixtures.jsonl');
+    const lines = existsSync(receiptLog)
+        ? readFileSync(receiptLog, 'utf8')
+            .split('\n')
+            .filter((line) => line.trim().length > 0)
+            .map((line) => JSON.parse(line))
+            .filter((line) => line.receiptId === receiptId)
+        : [];
+    if (lines.some((line) => line.phase === 'restored')) {
+        throw new Error(`skill-fixture receipt ${receiptId} was already restored`);
+    }
+    const run = [...lines]
+        .reverse()
+        .find((line) => line.phase === 'completed' || line.phase === 'failed');
+    if (run === undefined) {
+        throw new Error(`no completed or failed skill-fixture repair ${receiptId} in ${receiptLog}`);
+    }
+    const dryRun = opts.dryRun === true;
+    const receipt = {
+        receiptId,
+        at: new Date().toISOString(),
+        dryRun,
+        phase: 'restore-planned',
+        restored: [],
+        skipped: [],
+        receiptLog: null,
+    };
+    for (const move of run.moved) {
+        const files = run.planned.find((p) => p.from === move.from)?.files ?? [];
+        if (!existsSync(move.to)) {
+            receipt.skipped.push({ path: move.to, reason: 'quarantine copy is missing' });
+        }
+        else if (existsSync(move.from)) {
+            receipt.skipped.push({ path: move.from, reason: 'original path is occupied' });
+        }
+        else if (inventoryKey(classifySkillFixture(basename(move.to), move.to).files) !== inventoryKey(files)) {
+            receipt.skipped.push({
+                path: move.to,
+                reason: 'quarantined files no longer match the receipt',
+            });
+        }
+        else if (dryRun) {
+            receipt.restored.push({
+                from: move.to,
+                to: move.from,
+                method: 'rename',
+                sourceRemoved: true,
+                sourceError: null,
+            });
+        }
+        else {
+            receipt.restored.push(moveVerified(move.to, move.from, files, opts.rename ?? renameSync));
+        }
+    }
+    if (!dryRun) {
+        receipt.phase = 'restored';
+        receipt.receiptLog = receiptLog;
+        appendFileSync(receiptLog, `${JSON.stringify(receipt)}\n`, 'utf8');
+    }
+    return receipt;
+}
+//# sourceMappingURL=skill-fixtures.js.map

package/dist/system/skill-fixtures.js.map

@@ -0,0 +1 @@
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package/dist/task-work/index.d.ts

@@ -6,6 +6,7 @@
  */
 import '../hooks/handlers/index.js';
 import type { KnowledgeCoverage } from '@cleocode/contracts';
+import { type StaleFocusPointer } from '../sessions/focus-state-store.js';
 import type { DataAccessor } from '../store/data-accessor.js';
 /** Result of getting current task. */
 export interface TaskCurrentResult {
@@ -13,6 +14,11 @@ export interface TaskCurrentResult {
     currentPhase: string | null;
     sessionNote: string | null;
     nextAction: string | null;
+    /**
+     * The focus pointer when it names a done, cancelled, archived or missing
+     * task. `currentTask` is then `null`: a finished task is never current (T12660).
+     */
+    staleFocus?: StaleFocusPointer;
 }
 /** Result of starting work on a task. */
 export interface TaskStartResult {

package/dist/task-work/index.d.ts.map

@@ -1 +1 @@
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package/dist/task-work/index.js

@@ -10,7 +10,7 @@ import { ExitCode } from '@cleocode/contracts';
 import { CleoError } from '../errors.js';
 import { assessKnowledgeCoverage } from '../nexus/knowledge.js';
 import { resolveOrCwd } from '../paths.js';
-import { readFocusState, writeFocusState } from '../sessions/focus-state-store.js';
+import { readFocusState, readLiveFocus, writeFocusState, } from '../sessions/focus-state-store.js';
 import { resolveSessionIdFromEnv } from '../sessions/session-id.js';
 import { trackBackgroundOp } from '../store/background-ops.js';
 import { getTaskAccessor } from '../store/data-accessor.js';
@@ -51,9 +51,12 @@ const PLANNING_STAGES = new Set([
  */
 export async function currentTask(cwd, accessor) {
     const acc = accessor ?? (await getTaskAccessor(cwd));
-    const focus = await readFocusState(acc, resolveFocusSessionId());
+    // T12660/T12684: the one validating focus reader — a pointer left behind by
+    // a completion (or the never-cleared legacy key) comes back stale.
+    const { state: focus, currentTask: live, staleFocus, } = await readLiveFocus(acc, resolveFocusSessionId());
     return {
-        currentTask: focus?.currentTask ?? null,
+        currentTask: live,
+        ...(staleFocus ? { staleFocus } : {}),
         currentPhase: focus?.currentPhase ?? null,
         sessionNote: focus?.sessionNote ?? null,
         nextAction: focus?.nextAction ?? null,

package/dist/task-work/index.js.map

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package/dist/tasks/add.d.ts.map

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package/dist/tasks/add.js

@@ -1064,13 +1064,15 @@ export async function addTask(options, cwd, accessor) {
         // row. The row is the product; duplicate detection is enrichment.
         const dupCheck = await checkDuplicatesBounded(options.title, options.description ?? '', dataAccessor, options.labels ?? [], cwd);
         if (dupCheck.shouldReject && !options.forceDuplicate) {
-            throw new CleoError(ExitCode.DUPLICATE_TASK_LIKELY, buildRejectMessage(dupCheck.candidates), {
+            throw new CleoError(ExitCode.DUPLICATE_TASK_LIKELY, buildRejectMessage(dupCheck.candidates, dupCheck.tier), {
                 fix: 'cleo add ... --force-duplicate',
                 details: {
                     field: 'title',
                     candidates: dupCheck.candidates,
                     maxScore: dupCheck.maxScore,
-                    threshold: 0.92,
+                    // A System One rejection is a probability >= 0.5, not a 0.92 similarity.
+                    threshold: dupCheck.tier === 'decision' ? 0.5 : 0.92,
+                    tier: dupCheck.tier,
                 },
             });
         }