@cleocode/core 2026.10.12 → 2026.10.13

package/dist/tools/fs.js.map

@@ -1 +1 @@
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package/dist/worktree/list.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"list.d.ts","sourceRoot":"","sources":["../../src/worktree/list.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAsCG;AAMH,OAAO,KAAK,EACV,YAAY,EACZ,iBAAiB,EACjB,mBAAmB,EAGnB,sBAAsB,EACvB,MAAM,qBAAqB,CAAC;AAc7B;;;;GAIG;AACH,UAAU,cAAc;IACtB,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,CAAC;IACf,MAAM,EAAE,OAAO,CAAC;CACjB;AAED;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAsB,aAAa,CACjC,IAAI,GAAE,iBAAsB,GAC3B,OAAO,CAAC,YAAY,CAAC,mBAAmB,CAAC,CAAC,CAwL5C;AAeD;;;;;;;;;;;GAWG;AACH,wBAAgB,kBAAkB,CAAC,WAAW,EAAE,MAAM,GAAG,cAAc,EAAE,CAqDxE;AAED;;;;;;GAMG;AACH,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAG9D;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,wBAAwB,CAAC,MAAM,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAc3F;AAED;;;;;;;;;;;;GAYG;AACH,wBAAgB,oBAAoB,CAClC,MAAM,EAAE,MAAM,EACd,WAAW,EAAE,MAAM,EACnB,UAAU,GAAE,MAA4B,GACvC,OAAO,CAWT;AAED;;;;;;;;;;;;;GAaG;AACH,wBAAgB,cAAc,CAAC,KAAK,EAAE;IACpC,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,QAAQ,EAAE,OAAO,CAAC;IAClB,QAAQ,EAAE,OAAO,CAAC;IAClB,QAAQ,EAAE,OAAO,CAAC;IAClB,OAAO,EAAE,OAAO,CAAC;CAClB,GAAG,sBAAsB,CAOzB;AAED;;;;;;;;;;;;GAYG;AACH,wBAAsB,sBAAsB,CAC1C,OAAO,EAAE,MAAM,EAAE,EACjB,WAAW,EAAE,MAAM,GAClB,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,CA+B9B;AAED;;;;;;;;GAQG;AACH,wBAAgB,eAAe,CAAC,YAAY,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAUnE;AA0CD;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,mBAAmB,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAYtE;AAED;;;;;;;;;;;;;;;GAeG;AACH,wBAAgB,gBAAgB,CAAC,KAAK,EAAE;IACtC,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,GAAG,IAAI,CAAC;IAC5B,mBAAmB,EAAE,MAAM,GAAG,IAAI,CAAC;IACnC,iBAAiB,EAAE,MAAM,GAAG,SAAS,CAAC;CACvC,GAAG,MAAM,CA2BT;AAED;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,0BAA0B,CAAC,WAAW,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAoB7E;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,iBAAiB,CAAC,YAAY,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,GAAG,IAAI,GAAG,OAAO,CAQ3F"}

package/dist/worktree/list.js

@@ -71,6 +71,8 @@ export async function listWorktrees(opts = {}) {
     const staleDays = opts.staleDays ?? DEFAULT_STALE_DAYS;
     const staleThresholdMs = staleDays * 24 * 60 * 60 * 1000;
     const nowMs = Date.now();
+    // Lazy: keeps @cleocode/worktree out of this module's static graph (T13696).
+    const { readKeepMarker } = await import('@cleocode/worktree');
     let porcelainEntries;
     try {
         porcelainEntries = enumerateWorktrees(projectRoot);
@@ -174,6 +176,7 @@ export async function listWorktrees(opts = {}) {
             owningTaskStatus,
             statusCategory,
             source,
+            ...keptField(entry.path, readKeepMarker),
         };
     });
     // --- T9804: Append sentinel-only entries (not in git porcelain output) ---
@@ -216,6 +219,7 @@ export async function listWorktrees(opts = {}) {
             owningTaskStatus,
             statusCategory,
             source: sentinel.source,
+            ...keptField(sentinel.path, readKeepMarker),
         });
     }
     const filtered = opts.statusFilter && opts.statusFilter.length > 0
@@ -223,6 +227,11 @@ export async function listWorktrees(opts = {}) {
         : worktrees;
     return engineSuccess({ worktrees: filtered });
 }
+/** `{ kept }` when a disposal kept this worktree (its keep marker), else `{}` (T13701). */
+function keptField(path, readKeepMarker) {
+    const kept = readKeepMarker(path);
+    return kept ? { kept } : {};
+}
 // ---------------------------------------------------------------------------
 // Internal helpers — exported for tests only.
 // ---------------------------------------------------------------------------

package/dist/worktree/list.js.map

@@ -1 +1 @@
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package/dist/worktree/prune.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"prune.d.ts","sourceRoot":"","sources":["../../src/worktree/prune.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;GAsBG;AAGH,OAAO,KAAK,EACV,YAAY,EAEZ,0BAA0B,EAC1B,4BAA4B,EAC5B,YAAY,EACb,MAAM,qBAAqB,CAAC;AAM7B;;;;;;;;;;;;;;;;;;;;;;;;;;GA0BG;AACH,wBAAsB,8BAA8B,CAClD,IAAI,EAAE,0BAA0B,GAC/B,OAAO,CAAC,YAAY,CAAC,4BAA4B,CAAC,CAAC,CA8GrD;AAMD;;;GAGG;AACH,wBAAgB,eAAe,CAAC,EAAE,EAAE,YAAY,GAAG,MAAM,CAiBxD;AAED;;;;;;;;;;;;;;;;;;GAkBG;AACH,wBAAgB,sBAAsB,CACpC,EAAE,EAAE,YAAY,EAChB,WAAW,EAAE,MAAM,GAClB;IAAE,OAAO,EAAE,IAAI,CAAC;IAAC,aAAa,EAAE,OAAO,CAAA;CAAE,GAAG;IAAE,OAAO,EAAE,KAAK,CAAC;IAAC,KAAK,EAAE,MAAM,CAAA;CAAE,CAwC/E"}
+{"version":3,"file":"prune.d.ts","sourceRoot":"","sources":["../../src/worktree/prune.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;GAsBG;AAGH,OAAO,KAAK,EACV,YAAY,EAGZ,0BAA0B,EAC1B,4BAA4B,EAC5B,YAAY,EACb,MAAM,qBAAqB,CAAC;AAY7B;;;;;;;;;;;;;;;;;;;;;;;;;;GA0BG;AACH,wBAAsB,8BAA8B,CAClD,IAAI,EAAE,0BAA0B,GAC/B,OAAO,CAAC,YAAY,CAAC,4BAA4B,CAAC,CAAC,CAsJrD;AAsBD;;;GAGG;AACH,wBAAgB,eAAe,CAAC,EAAE,EAAE,YAAY,GAAG,MAAM,CAiBxD;AAED;;;;;;;;;;;;;;;;;;GAkBG;AACH,wBAAgB,sBAAsB,CACpC,EAAE,EAAE,YAAY,EAChB,WAAW,EAAE,MAAM,GAClB;IAAE,OAAO,EAAE,IAAI,CAAC;IAAC,aAAa,EAAE,OAAO,CAAA;CAAE,GAAG;IAAE,OAAO,EAAE,KAAK,CAAC;IAAC,KAAK,EAAE,MAAM,CAAA;CAAE,CAwC/E"}

package/dist/worktree/prune.js

@@ -23,7 +23,8 @@
  */
 import { existsSync } from 'node:fs';
 import { engineError, engineSuccess } from '@cleocode/contracts/engine-result.js';
-import { gitSilent, napiDestroyWorktree } from '@cleocode/worktree';
+import { describeDisposalBlockers, gitSilent, guardWorktreeDisposal, napiDestroyWorktree, } from '@cleocode/worktree';
+import { taskEvidenceAtoms } from '../tasks/evidence-paths.js';
 import { appendWorktreeAuditEntry, resolveWorktreeAuditActor } from './audit.js';
 import { isPrimaryWorktree, listWorktrees, resolvePrimaryWorktreePath } from './list.js';
 /**
@@ -74,6 +75,42 @@ export async function pruneOrphanedWorktreesByStatus(opts) {
     let prunedCount = 0;
     for (const wt of candidates) {
         const reason = reasonForStatus(wt);
+        // T13700: the same guard as complete/cancel — dependents, evidence and the keep marker.
+        const kept = guardWorktreeDisposal(wt.path, {
+            taskId: wt.taskId,
+            reason,
+            projectRoot: opts.projectRoot,
+            evidence: await loadTaskEvidence(opts.projectRoot, wt.taskId),
+            dryRun,
+        });
+        if (kept !== null) {
+            const error = describeDisposalBlockers(wt.path, kept);
+            outcomes.push({
+                path: wt.path,
+                branch: wt.branch,
+                taskId: wt.taskId,
+                reason,
+                pruned: false,
+                branchDeleted: false,
+                error,
+                kept,
+            });
+            if (!dryRun) {
+                appendWorktreeAuditEntry(opts.projectRoot, 
+                // @sync-invariant none:local-only a worktree on this machine's disk, recorded in its local audit log; never replicated
+                {
+                    actor,
+                    action: 'prune',
+                    target: wt.path,
+                    ...(wt.branch ? { branch: wt.branch } : {}),
+                    ...(wt.taskId ? { taskId: wt.taskId } : {}),
+                    reason: `${reason}+kept`,
+                    success: false,
+                    error,
+                }, opts.auditLogPath);
+            }
+            continue;
+        }
         if (dryRun) {
             outcomes.push({
                 path: wt.path,
@@ -141,6 +178,20 @@ export async function pruneOrphanedWorktreesByStatus(opts) {
 // ---------------------------------------------------------------------------
 // Internal helpers — exported for tests only.
 // ---------------------------------------------------------------------------
+/** The owning task's recorded evidence, or `[]` when there is no task or the store is unreadable. */
+async function loadTaskEvidence(projectRoot, taskId) {
+    if (taskId === null)
+        return [];
+    try {
+        const { getTaskAccessor } = await import('../store/data-accessor.js');
+        const task = await (await getTaskAccessor(projectRoot)).loadSingleTask(taskId);
+        return task ? taskEvidenceAtoms(task) : [];
+    }
+    catch {
+        // Without the store the marker and dependents scan still guard the disposal.
+        return [];
+    }
+}
 /**
  * Map a {@link WorktreeInfo} entry's `statusCategory` to a short human-readable
  * reason string used in audit logs + envelope outcomes.

package/dist/worktree/prune.js.map

@@ -1 +1 @@
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package/migrations/drizzle-cleo-project/20261013000000_t13360-migrated-doc-import/migration.sql

@@ -0,0 +1,61 @@
+-- T13360 (saga T13339, epic T13340) — honest migration of legacy docs into
+-- the re-keyed store (spec `cleodocs-rearch-design` §5, D11165).
+--
+-- What this file does:
+--
+--   1. `conduit_attachment_versions` gains an `origin` column (nullable).
+--      NULL means the version was written natively by this build; the string
+--      'migrated' marks a row imported from the legacy docs store by the
+--      T13360 data migration (spec §5: "every imported history row is labeled
+--      origin: migrated"). ADD COLUMN only — no rebuild: the key columns
+--      (id, uid, attachment_uid, version_number) are untouched, so the
+--      FK-parent rebuild caveat does not apply.
+--
+--   2. Creates `conduit_doc_migration_ledger`, the AUDITABLE record for the
+--      data migration (spec §5: the dangling-pointer docs are "content-
+--      captured or marked dangling — never silently imported"; AC3). One row
+--      per migrated doc slug, keyed by the slug itself; the `uid` column is
+--      declared last (the row-identity heal appends a missing uid column at
+--      the end, T13359 precedent) and its UNIQUE index is deliberately NOT
+--      created here — `ensureRowIdentitySchema` owns `uq_<table>_uid` for
+--      every declared table at every open. `status` is frozen at the DDL
+--      layer to ('captured','dangling').
+--
+--      The table is SYNCING (portable-project, table-classification) with a
+--      NATURAL row identity over (slug) in ROW_IDENTITY: both devices derive
+--      one uid per slug, a re-run on either device coalesces onto the same
+--      row, and the append-only accessor (never UPDATE, never DELETE) makes
+--      every row an immutable audit receipt of what the migration did.
+--
+--   3. No DML runs here (the data import is the harness-run `cleo docs
+--      migrate`), so nothing is non-deterministic (gate 36 rule 5); the
+--      `datetime('now')` occurrences below are DDL column defaults, which are
+--      exempt. No trigger is created (the owned-trigger clause rule does not
+--      apply), no statement deletes from or re-keys an FK parent (rule 6),
+--      and no `_sync_cap_` name appears (only `store/sync/machinery.ts` owns
+--      those, gate 36 rule 2).
+--
+-- @task T13360
+-- @epic T13340
+-- @saga T13339
+
+ALTER TABLE `conduit_attachment_versions` ADD COLUMN `origin` text;
+--> statement-breakpoint
+
+CREATE TABLE IF NOT EXISTS `conduit_doc_migration_ledger` (
+	`slug` text NOT NULL,
+	`doc_uid` text,
+	`status` text DEFAULT 'captured' NOT NULL,
+	`reason` text NOT NULL DEFAULT '',
+	`legacy_path` text,
+	`legacy_sha256` text,
+	`versions_imported` integer DEFAULT 0 NOT NULL,
+	`migrated_at` text DEFAULT (datetime('now')) NOT NULL,
+	`uid` text,
+	CONSTRAINT `conduit_doc_migration_ledger_pk` PRIMARY KEY(`slug`),
+	CHECK ("status" IN ('captured', 'dangling')),
+	CHECK ("migrated_at" IS NULL OR "migrated_at" GLOB '[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9]*')
+);
+--> statement-breakpoint
+
+CREATE INDEX IF NOT EXISTS `idx_conduit_doc_migration_ledger_doc_uid` ON `conduit_doc_migration_ledger` (`doc_uid`);

package/migrations/drizzle-cleo-project/20261014000000_t13362-docs-publications-ledger/migration.sql

@@ -0,0 +1,45 @@
+-- T13362 (saga T13339, epic T13340) — retire the legacy docs-publications.json
+-- sidecar: the publication ledger moves into the project `cleo.db` as store
+-- rows, and the pre-commit drift hook / CI docs-drift gate read the table.
+--
+-- What this file does:
+--
+--   1. Creates `docs_publications`, the SYNCING (portable-project,
+--      table-classification) publication ledger. One row per published
+--      (owner, blob, path) triple; `cleo docs publish` upserts on that
+--      natural key and the drift surfaces (`cleo docs status`, the
+--      pre-commit hook, the attachment janitor's publication-sha protection)
+--      read it back. Identity is NATURAL over (owner_id, blob_name,
+--      published_path) in ROW_IDENTITY: both devices derive one uid per
+--      triple and a re-publish on either device coalesces on apply.
+--
+--      The `uid` column is declared last (the row-identity heal appends a
+--      missing uid column at the end, T13359 precedent) and its UNIQUE index
+--      is deliberately NOT created here — `ensureRowIdentitySchema` owns
+--      `uq_<table>_uid` for every declared table at every open.
+--
+--   2. No DML runs here (the legacy `.cleo/docs-publications.json` entries are
+--      seeded lazily by the read shim on first access, idempotently), so
+--      nothing is non-deterministic (gate 36 rule 5); the `datetime('now')`
+--      occurrences in OTHER folders are irrelevant — this file has no column
+--      defaults at all. No trigger is created (the owned-trigger clause rule
+--      does not apply), no statement deletes from or re-keys an FK parent
+--      (rule 6), and no `_sync_cap_` name appears (rule 2).
+--
+-- @task T13362
+-- @epic T13340
+-- @saga T13339
+
+CREATE TABLE IF NOT EXISTS `docs_publications` (
+	`owner_id` text NOT NULL,
+	`blob_name` text NOT NULL,
+	`published_path` text NOT NULL,
+	`last_blob_sha` text NOT NULL,
+	`published_at` text NOT NULL,
+	`uid` text,
+	CONSTRAINT `docs_publications_pk` PRIMARY KEY(`owner_id`, `blob_name`, `published_path`),
+	CHECK ("published_at" IS NULL OR "published_at" GLOB '[0-9][0-9][0-9][0-9]-[0-9][0-9]-[0-9][0-9]*')
+);
+--> statement-breakpoint
+
+CREATE INDEX IF NOT EXISTS `idx_docs_publications_published_path` ON `docs_publications` (`published_path`);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cleocode/core",
-  "version": "2026.10.12",
+  "version": "2026.10.13",
   "description": "CLEO core business logic kernel — tasks, sessions, memory, orchestration, lifecycle, with bundled SQLite store",
   "type": "module",
   "main": "./dist/index.js",
@@ -496,16 +496,16 @@
     "write-file-atomic": "^7.0.1",
     "yaml": "^2.8.3",
     "zod": "^4.3.6",
-    "@cleocode/adapters": "2026.10.12",
-    "@cleocode/agents": "2026.10.12",
-    "@cleocode/caamp": "2026.10.12",
-    "@cleocode/contracts": "2026.10.12",
-    "@cleocode/git-shim": "2026.10.12",
-    "@cleocode/lafs": "2026.10.12",
-    "@cleocode/nexus": "2026.10.12",
-    "@cleocode/paths": "2026.10.12",
-    "@cleocode/skills": "2026.10.12",
-    "@cleocode/worktree": "2026.10.12"
+    "@cleocode/adapters": "2026.10.13",
+    "@cleocode/agents": "2026.10.13",
+    "@cleocode/caamp": "2026.10.13",
+    "@cleocode/contracts": "2026.10.13",
+    "@cleocode/git-shim": "2026.10.13",
+    "@cleocode/nexus": "2026.10.13",
+    "@cleocode/paths": "2026.10.13",
+    "@cleocode/worktree": "2026.10.13",
+    "@cleocode/skills": "2026.10.13",
+    "@cleocode/lafs": "2026.10.13"
   },
   "engines": {
     "node": ">=24.16.0"
@@ -531,7 +531,7 @@
     "@types/proper-lockfile": "^4.1.4",
     "@types/tar": "^6.1.13",
     "@types/write-file-atomic": "^4.0.3",
-    "@cleocode/utils": "2026.10.12"
+    "@cleocode/utils": "2026.10.13"
   },
   "repository": {
     "type": "git",
@@ -540,7 +540,7 @@
   },
   "optionalDependencies": {
     "llmtxt": "^2026.5.15",
-    "@cleocode/studio": "^2026.10.12"
+    "@cleocode/studio": "^2026.10.13"
   },
   "scripts": {
     "build": "tsc && node scripts/copy-selfimprove-fixtures.mjs && node scripts/write-build-provenance.mjs",

package/templates/CLEO-INJECTION.md

@@ -1,6 +1,6 @@
 # CLEO Protocol
 
-Version: 2.24.11 | CLI-only dispatch | `cleo <command> [args]`
+Version: 2.24.13 | CLI-only dispatch | `cleo <command> [args]`
 
 <!-- CLEO-INJECTION:section=session-start -->
 ## Universal protocol

package/templates/CLEO-REFERENCE.md

@@ -1,6 +1,6 @@
 # CLEO Protocol — on-demand reference
 
-Version: 2.24.11 | Companion to the always-loaded `CLEO-INJECTION.md` core
+Version: 2.24.13 | Companion to the always-loaded `CLEO-INJECTION.md` core
 
 Not injected into agent context. Print one section with `cleo briefing inject --section <name>`; tier-2 spawn prompts embed this whole file. Section names are the `CLEO-INJECTION:section` markers below.
 
@@ -301,7 +301,7 @@ All overrides append a line to `.cleo/audit/force-bypass.jsonl`. Use sparingly.
 
 ### Test evidence without churn (T12957)
 
-The evidence run is the one run. Start with `cleo done <id> --plan`, which picks affected → ci → full and shows each tool's cache state. When the PR has merged and the project sets `evidence.ciSatisfies`, record `testsPassed`/`qaPassed` with `ci:<pr>` and run nothing locally. Otherwise, when `testing.affectedCommand` is configured, use `tool:test-affected` (packages the diff touches plus dependents); a full `tool:test` is then only for changes to root config, which affected planning refuses. Without it, use a targeted `test-run:<json>` of the test files you changed, or `tool:test`. While iterating, run only the failing or changed test files; never run the suite by hand and then again through `tool:test`. On macOS heavy `test`/`build` runs take one machine-wide slot by default (`CLEO_TOOL_CONCURRENCY_TEST=<n>` raises it).
+The evidence run is the one run. Start with `cleo done <id> --plan`, which picks affected → ci and shows each tool's cache state; it never plans a whole-suite `tool:test` it would have to run (owner decision 2026-10-12, T13647) and refuses with `test-run-needed` instead, naming the scoped evidence to record. When the PR has merged and the project sets `evidence.ciSatisfies`, record `testsPassed`/`qaPassed` with `ci:<pr>` and run nothing locally. Otherwise, when `testing.affectedCommand` is configured, use `tool:test-affected` (packages the diff touches plus dependents); a full `tool:test` is then only for changes to root config, which affected planning refuses. Without it, use a targeted `test-run:<json>` of the test files you changed, or `tool:test`. After the merge, a scoped run carries to the merge commit only when the change's files are byte-identical; otherwise a targeted `test-run:` recorded on a main HEAD that descends from the merge, on the current tree and covering the change's files, stands in whatever the merge commit's own CI concluded (owner decision 2026-10-13, T13673). While iterating, run only the failing or changed test files; never run the suite by hand and then again through `tool:test`. On macOS heavy `test`/`build` runs take one machine-wide slot by default (`CLEO_TOOL_CONCURRENCY_TEST=<n>` raises it).
 
 ### `pr:<number>` retroactive atom (T9764)