@cleocode/core 2026.10.9 → 2026.10.10-canary.2

package/dist/build-provenance.json

@@ -1,6 +1,6 @@
 {
   "schema": 1,
-  "gitHead": "5c901fb18ef61e04598780b6113adb238c59d5be",
-  "builtAt": "2026-10-12T01:10:43.880Z",
+  "gitHead": "007ff2ef022d32aa632532fd8447c6703ccb0777",
+  "builtAt": "2026-10-12T09:30:27.030Z",
   "linkedWorktree": null
 }

package/dist/decide/sites/registry.d.ts

@@ -137,6 +137,32 @@ export declare const DECIDE_BENCH_DECISION_SITE: {
     readonly task: "T12495";
     readonly note: "Benchmark verb: replays the duplicate, observation-type and contradiction questions; answers are scored, never acted on.";
 };
+/**
+ * `docs.triage` — batch keep/update/supersede/archive verdicts over draft docs
+ * (T13446). Proposals only: the site never mutates a doc; `--record` persists
+ * each verdict as a `proposed` D#### decision for owner review.
+ */
+export declare const DOC_TRIAGE_DECISION_SITE: {
+    readonly id: "docs.triage";
+    readonly title: "CleoDocs draft triage (keep/update/supersede/archive)";
+    readonly files: readonly ["packages/core/src/docs/triage.ts"];
+    readonly questionType: "choice";
+    readonly primaryRung: "system-one";
+    readonly ladder: readonly ["generative"];
+    readonly fallback: "rule";
+    readonly floors: {
+        readonly '*': 0.6;
+    };
+    readonly ownerEscalation: "below-floor";
+    readonly modeKey: "decide.sites.docTriage";
+    readonly generativeKey: "decide.generativeFallback.docTriage";
+    readonly defaultMode: "shadow";
+    readonly llmSystemKey: "consolidation";
+    readonly writePath: false;
+    readonly sends: readonly ["memory-text"];
+    readonly task: "T13446";
+    readonly note: "Batch job over `cleo docs triage`; rule fallback is age/topics/link heuristics. Shadow until go-live evidence exists.";
+};
 /**
  * Every registered decision site. The System One sites come first, then the
  * generative and agent-rung sites.

package/dist/decide/sites/registry.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"registry.d.ts","sourceRoot":"","sources":["../../../src/decide/sites/registry.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AAEH,OAAO,KAAK,EAAE,sBAAsB,EAAE,MAAM,qBAAqB,CAAC;AAElE,uFAAuF;AACvF,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;;;;;;;;CAkBM,CAAC;AAE5C,8FAA8F;AAC9F,eAAO,MAAM,oCAAoC;;;;;;;;;;;;;;;;;;;CAoBN,CAAC;AAE5C,yEAAyE;AACzE,eAAO,MAAM,8BAA8B;;;;;;;;;;;;;;;;;;CAgBA,CAAC;AAE5C,uFAAuF;AACvF,eAAO,MAAM,4BAA4B;;;;;;;;;;;;;;;;;;CAmBE,CAAC;AAE5C,wEAAwE;AACxE,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;;CAcM,CAAC;AAE5C;;;;;;GAMG;AACH,eAAO,MAAM,0BAA0B;;;;;;;;;;;;;;CAcI,CAAC;AAkP5C;;;GAGG;AACH,eAAO,MAAM,cAAc,EAAE,SAAS,sBAAsB,EAQ3D,CAAC;AAEF;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,EAAE,EAAE,MAAM,GAAG,sBAAsB,GAAG,SAAS,CAE9E"}
+{"version":3,"file":"registry.d.ts","sourceRoot":"","sources":["../../../src/decide/sites/registry.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AAEH,OAAO,KAAK,EAAE,sBAAsB,EAAE,MAAM,qBAAqB,CAAC;AAElE,uFAAuF;AACvF,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;;;;;;;;CAkBM,CAAC;AAE5C,8FAA8F;AAC9F,eAAO,MAAM,oCAAoC;;;;;;;;;;;;;;;;;;;CAoBN,CAAC;AAE5C,yEAAyE;AACzE,eAAO,MAAM,8BAA8B;;;;;;;;;;;;;;;;;;CAgBA,CAAC;AAE5C,uFAAuF;AACvF,eAAO,MAAM,4BAA4B;;;;;;;;;;;;;;;;;;CAmBE,CAAC;AAE5C,wEAAwE;AACxE,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;;CAcM,CAAC;AAE5C;;;;;;GAMG;AACH,eAAO,MAAM,0BAA0B;;;;;;;;;;;;;;CAcI,CAAC;AAE5C;;;;GAIG;AACH,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;;;;;;;;CAkBM,CAAC;AAkP5C;;;GAGG;AACH,eAAO,MAAM,cAAc,EAAE,SAAS,sBAAsB,EAS3D,CAAC;AAEF;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,EAAE,EAAE,MAAM,GAAG,sBAAsB,GAAG,SAAS,CAE9E"}

package/dist/decide/sites/registry.js

@@ -134,6 +134,30 @@ export const DECIDE_BENCH_DECISION_SITE = {
     task: 'T12495',
     note: 'Benchmark verb: replays the duplicate, observation-type and contradiction questions; answers are scored, never acted on.',
 };
+/**
+ * `docs.triage` — batch keep/update/supersede/archive verdicts over draft docs
+ * (T13446). Proposals only: the site never mutates a doc; `--record` persists
+ * each verdict as a `proposed` D#### decision for owner review.
+ */
+export const DOC_TRIAGE_DECISION_SITE = {
+    id: 'docs.triage',
+    title: 'CleoDocs draft triage (keep/update/supersede/archive)',
+    files: ['packages/core/src/docs/triage.ts'],
+    questionType: 'choice',
+    primaryRung: 'system-one',
+    ladder: ['generative'],
+    fallback: 'rule',
+    floors: { '*': 0.6 },
+    ownerEscalation: 'below-floor',
+    modeKey: 'decide.sites.docTriage',
+    generativeKey: 'decide.generativeFallback.docTriage',
+    defaultMode: 'shadow',
+    llmSystemKey: 'consolidation',
+    writePath: false,
+    sends: ['memory-text'],
+    task: 'T13446',
+    note: 'Batch job over `cleo docs triage`; rule fallback is age/topics/link heuristics. Shadow until go-live evidence exists.',
+};
 /**
  * Generative and agent-rung sites that predate the ladder: registered so every
  * model call site is listed (spec §3.3). All `on`; none uses System One.
@@ -384,6 +408,7 @@ export const DECISION_SITES = [
     OWNER_DECISION_DECISION_SITE,
     DECIDE_ASK_DECISION_SITE,
     DECIDE_BENCH_DECISION_SITE,
+    DOC_TRIAGE_DECISION_SITE,
     ...GENERATIVE_SITES,
 ];
 /**

package/dist/decide/sites/registry.js.map

@@ -1 +1 @@
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+{"version":3,"file":"registry.js","sourceRoot":"","sources":["../../../src/decide/sites/registry.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AAIH,uFAAuF;AACvF,MAAM,CAAC,MAAM,wBAAwB,GAAG;IACtC,EAAE,EAAE,2BAA2B;IAC/B,KAAK,EAAE,iCAAiC;IACxC,KAAK,EAAE,CAAC,+CAA+C,CAAC;IACxD,YAAY,EAAE,MAAM;IACpB,WAAW,EAAE,YAAY;IACzB,MAAM,EAAE,CAAC,YAAY,CAAC;IACtB,QAAQ,EAAE,MAAM;IAChB,MAAM,EAAE,EAAE,GAAG,EAAE,GAAG,EAAE;IACpB,eAAe,EAAE,OAAO;IACxB,OAAO,EAAE,iCAAiC;IAC1C,aAAa,EAAE,8CAA8C;IAC7D,WAAW,EAAE,QAAQ;IACrB,YAAY,EAAE,eAAe;IAC7B,SAAS,EAAE,IAAI;IACf,KAAK,EAAE,CAAC,WAAW,CAAC;IACpB,IAAI,EAAE,QAAQ;IACd,IAAI,EAAE,qFAAqF;CAClD,CAAC;AAE5C,8FAA8F;AAC9F,MAAM,CAAC,MAAM,oCAAoC,GAAG;IAClD,EAAE,EAAE,+BAA+B;IACnC,KAAK,EAAE,uCAAuC;IAC9C,KAAK,EAAE;QACL,oDAAoD;QACpD,uCAAuC;KACxC;IACD,YAAY,EAAE,QAAQ;IACtB,WAAW,EAAE,YAAY;IACzB,MAAM,EAAE,CAAC,YAAY,CAAC;IACtB,QAAQ,EAAE,MAAM;IAChB,MAAM,EAAE,EAAE,GAAG,EAAE,GAAG,EAAE;IACpB,eAAe,EAAE,OAAO;IACxB,OAAO,EAAE,oCAAoC;IAC7C,aAAa,EAAE,iDAAiD;IAChE,WAAW,EAAE,QAAQ;IACrB,SAAS,EAAE,IAAI;IACf,KAAK,EAAE,CAAC,aAAa,CAAC;IACtB,IAAI,EAAE,QAAQ;IACd,IAAI,EAAE,gEAAgE;CAC7B,CAAC;AAE5C,yEAAyE;AACzE,MAAM,CAAC,MAAM,8BAA8B,GAAG;IAC5C,EAAE,EAAE,yBAAyB;IAC7B,KAAK,EAAE,iCAAiC;IACxC,KAAK,EAAE,CAAC,uDAAuD,CAAC;IAChE,YAAY,EAAE,QAAQ;IACtB,WAAW,EAAE,YAAY;IACzB,MAAM,EAAE,EAAE;IACV,QAAQ,EAAE,MAAM;IAChB,MAAM,EAAE,EAAE,GAAG,EAAE,GAAG,EAAE;IACpB,eAAe,EAAE,OAAO;IACxB,OAAO,EAAE,8BAA8B;IACvC,WAAW,EAAE,QAAQ;IACrB,SAAS,EAAE,IAAI;IACf,KAAK,EAAE,CAAC,aAAa,CAAC;IACtB,IAAI,EAAE,QAAQ;IACd,IAAI,EAAE,iEAAiE;CAC9B,CAAC;AAE5C,uFAAuF;AACvF,MAAM,CAAC,MAAM,4BAA4B,GAAG;IAC1C,EAAE,EAAE,8BAA8B;IAClC,KAAK,EAAE,gCAAgC;IACvC,KAAK,EAAE;QACL,6DAA6D;QAC7D,uDAAuD;KACxD;IACD,YAAY,EAAE,MAAM;IACpB,WAAW,EAAE,MAAM;IACnB,MAAM,EAAE,CAAC,YAAY,CAAC;IACtB,QAAQ,EAAE,MAAM;IAChB,MAAM,EAAE,EAAE,GAAG,EAAE,GAAG,EAAE;IACpB,eAAe,EAAE,eAAe;IAChC,OAAO,EAAE,4BAA4B;IACrC,WAAW,EAAE,QAAQ;IACrB,SAAS,EAAE,IAAI;IACf,KAAK,EAAE,CAAC,WAAW,CAAC;IACpB,IAAI,EAAE,QAAQ;IACd,IAAI,EAAE,gEAAgE;CAC7B,CAAC;AAE5C,wEAAwE;AACxE,MAAM,CAAC,MAAM,wBAAwB,GAAG;IACtC,EAAE,EAAE,gBAAgB;IACpB,KAAK,EAAE,kCAAkC;IACzC,KAAK,EAAE,CAAC,wCAAwC,CAAC;IACjD,YAAY,EAAE,MAAM;IACpB,WAAW,EAAE,YAAY;IACzB,MAAM,EAAE,EAAE;IACV,QAAQ,EAAE,MAAM;IAChB,eAAe,EAAE,OAAO;IACxB,WAAW,EAAE,IAAI;IACjB,SAAS,EAAE,KAAK;IAChB,KAAK,EAAE,CAAC,eAAe,CAAC;IACxB,IAAI,EAAE,QAAQ;IACd,IAAI,EAAE,yEAAyE;CACtC,CAAC;AAE5C;;;;;;GAMG;AACH,MAAM,CAAC,MAAM,0BAA0B,GAAG;IACxC,EAAE,EAAE,kBAAkB;IACtB,KAAK,EAAE,wCAAwC;IAC/C,KAAK,EAAE,CAAC,0CAA0C,CAAC;IACnD,YAAY,EAAE,QAAQ;IACtB,WAAW,EAAE,YAAY;IACzB,MAAM,EAAE,EAAE;IACV,QAAQ,EAAE,MAAM;IAChB,eAAe,EAAE,OAAO;IACxB,WAAW,EAAE,IAAI;IACjB,SAAS,EAAE,KAAK;IAChB,KAAK,EAAE,CAAC,WAAW,EAAE,aAAa,CAAC;IACnC,IAAI,EAAE,QAAQ;IACd,IAAI,EAAE,0HAA0H;CACvF,CAAC;AAE5C;;;;GAIG;AACH,MAAM,CAAC,MAAM,wBAAwB,GAAG;IACtC,EAAE,EAAE,aAAa;IACjB,KAAK,EAAE,uDAAuD;IAC9D,KAAK,EAAE,CAAC,kCAAkC,CAAC;IAC3C,YAAY,EAAE,QAAQ;IACtB,WAAW,EAAE,YAAY;IACzB,MAAM,EAAE,CAAC,YAAY,CAAC;IACtB,QAAQ,EAAE,MAAM;IAChB,MAAM,EAAE,EAAE,GAAG,EAAE,GAAG,EAAE;IACpB,eAAe,EAAE,aAAa;IAC9B,OAAO,EAAE,wBAAwB;IACjC,aAAa,EAAE,qCAAqC;IACpD,WAAW,EAAE,QAAQ;IACrB,YAAY,EAAE,eAAe;IAC7B,SAAS,EAAE,KAAK;IAChB,KAAK,EAAE,CAAC,aAAa,CAAC;IACtB,IAAI,EAAE,QAAQ;IACd,IAAI,EAAE,uHAAuH;CACpF,CAAC;AAE5C;;;GAGG;AACH,MAAM,gBAAgB,GAAG;IACvB;QACE,EAAE,EAAE,mBAAmB;QACvB,KAAK,EAAE,mBAAmB;QAC1B,KAAK,EAAE,CAAC,sCAAsC,CAAC;QAC/C,YAAY,EAAE,MAAM;QACpB,WAAW,EAAE,YAAY;QACzB,MAAM,EAAE,EAAE;QACV,QAAQ,EAAE,MAAM;QAChB,eAAe,EAAE,OAAO;QACxB,WAAW,EAAE,IAAI;QACjB,YAAY,EAAE,YAAY;QAC1B,SAAS,EAAE,KAAK;QAChB,KAAK,EAAE,CAAC,aAAa,CAAC;QACtB,IAAI,EAAE,QAAQ;KACf;IACD;QACE,EAAE,EAAE,mBAAmB;QACvB,KAAK,EAAE,kCAAkC;QACzC,KAAK,EAAE;YACL,4CAA4C;YAC5C,kDAAkD;YAClD,kDAAkD;SACnD;QACD,YAAY,EAAE,MAAM;QACpB,WAAW,EAAE,YAAY;QACzB,MAAM,EAAE,EAAE;QACV,QAAQ,EAAE,MAAM;QAChB,eAAe,EAAE,OAAO;QACxB,WAAW,EAAE,IAAI;QACjB,YAAY,EAAE,YAAY;QAC1B,SAAS,EAAE,KAAK;QAChB,KAAK,EAAE,CAAC,aAAa,CAAC;QACtB,IAAI,EAAE,QAAQ;KACf;IACD;QACE,EAAE,EAAE,6BAA6B;QACjC,KAAK,EAAE,uCAAuC;QAC9C,KAAK,EAAE,CAAC,iDAAiD,CAAC;QAC1D,YAAY,EAAE,MAAM;QACpB,WAAW,EAAE,YAAY;QACzB,MAAM,EAAE,EAAE;QACV,QAAQ,EAAE,MAAM;QAChB,eAAe,EAAE,OAAO;QACxB,WAAW,EAAE,IAAI;QACjB,SAAS,EAAE,KAAK;QAChB,KAAK,EAAE,CAAC,aAAa,CAAC;QACtB,IAAI,EAAE,QAAQ;QACd,IAAI,EAAE,8EAA8E;KACrF;IACD;QACE,EAAE,EAAE,sBAAsB;QAC1B,KAAK,EAAE,qCAAqC;QAC5C,KAAK,EAAE;YACL,iDAAiD;YACjD,2CAA2C;SAC5C;QACD,YAAY,EAAE,MAAM;QACpB,WAAW,EAAE,YAAY;QACzB,MAAM,EAAE,EAAE;QACV,QAAQ,EAAE,MAAM;QAChB,eAAe,EAAE,OAAO;QACxB,WAAW,EAAE,IAAI;QACjB,YAAY,EAAE,eAAe;QAC7B,SAAS,EAAE,KAAK;QAChB,KAAK,EAAE,CAAC,aAAa,CAAC;QACtB,IAAI,EAAE,QAAQ;KACf;IACD;QACE,EAAE,EAAE,4BAA4B;QAChC,KAAK,EAAE,sBAAsB;QAC7B,KAAK,EAAE,CAAC,gDAAgD,CAAC;QACzD,YAAY,EAAE,MAAM;QACpB,WAAW,EAAE,YAAY;QACzB,MAAM,EAAE,EAAE;QACV,QAAQ,EAAE,MAAM;QAChB,eAAe,EAAE,OAAO;QACxB,WAAW,EAAE,IAAI;QACjB,SAAS,EAAE,KAAK;QAChB,KAAK,EAAE,CAAC,aAAa,CAAC;QACtB,IAAI,EAAE,QAAQ;KACf;IACD;QACE,EAAE,EAAE,oBAAoB;QACxB,KAAK,EAAE,oBAAoB;QAC3B,KAAK,EAAE,CAAC,yCAAyC,CAAC;QAClD,YAAY,EAAE,MAAM;QACpB,WAAW,EAAE,YAAY;QACzB,MAAM,EAAE,EAAE;QACV,QAAQ,EAAE,MAAM;QAChB,eAAe,EAAE,OAAO;QACxB,WAAW,EAAE,IAAI;QACjB,SAAS,EAAE,KAAK;QAChB,KAAK,EAAE,CAAC,aAAa,CAAC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package/dist/docs/doctor.d.ts

@@ -6,11 +6,18 @@
  * invoked with `apply: true`, performs the repairs that are safe to run
  * in-place:
  *
- *   - `dangling-pointers`   — `local-file` rows whose path is gone from disk
- *                             or lives inside a worktree/tmp directory. Repair
- *                             archives the row (`lifecycle_status = 'archived'`)
- *                             when the file is gone; existing files are left
- *                             alone (content capture is T13360's scope).
+ *   - `dangling-pointers`   — rows whose recorded local `path` is gone from
+ *                             disk or lives inside a worktree/tmp directory.
+ *                             Rows already `lifecycle_status = 'archived'`
+ *                             are excluded (T13562). Repair for a missing
+ *                             `local-file` target archives the row; a
+ *                             `blob`-kind payload carrying a stale legacy
+ *                             `path` whose content still resolves in the
+ *                             content-addressed blob store is re-pointed
+ *                             instead — the stale `path` field is cleared
+ *                             (`clear-stale-path`, T13562) since the bytes
+ *                             are alive. Existing files are left alone
+ *                             (content capture is T13360's scope).
  *   - `doc-version-skew`    — slugged rows whose `docVersion` trails the
  *                             revision count in `.cleo/audit/docs-versioning.jsonl`
  *                             (the T13351 bug left historical rows at 1). Repair
@@ -173,6 +180,9 @@ export type RunDocsDoctorResult = {
  * Apply: the backup gate runs first, then repairs execute in dependency
  * order (doc-version-skew, empty-provenance, dangling-pointers, and finally
  * the wikilinks rebuild, which re-derives from the freshly repaired columns).
+ * On apply the report's diagnostics are re-scanned AFTER the repairs so the
+ * envelope reflects POST-repair state and the summary counts match it
+ * (T13560); a dry run reports the pre-repair state unchanged.
  *
  * @param projectRoot - Absolute path to the CLEO project root.
  * @param opts - Apply flag, stale-draft threshold, backup receipt.

package/dist/docs/doctor.d.ts.map

@@ -1 +1 @@
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package/dist/docs/doctor.js

@@ -6,11 +6,18 @@
  * invoked with `apply: true`, performs the repairs that are safe to run
  * in-place:
  *
- *   - `dangling-pointers`   — `local-file` rows whose path is gone from disk
- *                             or lives inside a worktree/tmp directory. Repair
- *                             archives the row (`lifecycle_status = 'archived'`)
- *                             when the file is gone; existing files are left
- *                             alone (content capture is T13360's scope).
+ *   - `dangling-pointers`   — rows whose recorded local `path` is gone from
+ *                             disk or lives inside a worktree/tmp directory.
+ *                             Rows already `lifecycle_status = 'archived'`
+ *                             are excluded (T13562). Repair for a missing
+ *                             `local-file` target archives the row; a
+ *                             `blob`-kind payload carrying a stale legacy
+ *                             `path` whose content still resolves in the
+ *                             content-addressed blob store is re-pointed
+ *                             instead — the stale `path` field is cleared
+ *                             (`clear-stale-path`, T13562) since the bytes
+ *                             are alive. Existing files are left alone
+ *                             (content capture is T13360's scope).
  *   - `doc-version-skew`    — slugged rows whose `docVersion` trails the
  *                             revision count in `.cleo/audit/docs-versioning.jsonl`
  *                             (the T13351 bug left historical rows at 1). Repair
@@ -47,11 +54,13 @@ import { tmpdir } from 'node:os';
 import { isAbsolute, join, resolve, sep } from 'node:path';
 import { getCleoWorktreesRoot } from '@cleocode/paths';
 import { eq } from 'drizzle-orm';
+import { resolveCleoDir } from '../paths.js';
 import { createAttachmentStore } from '../store/attachment-store.js';
+import { blobContentExists } from '../store/blob-keep.js';
 import { docsWikilinks } from '../store/schema/attachments.js';
 import { getDb } from '../store/sqlite.js';
 import { docsAttachments } from '../store/tasks-schema.js';
-import { deriveDocLinks, isScannableTextMime, linksJsonOrNull } from './derive-links.js';
+import { deriveDocLinks, isScannableTextMime, linksJsonOrNull, } from './derive-links.js';
 import { DOCS_VERSIONING_AUDIT_FILE } from './docs-update.js';
 import { deriveWikilinkEdges, rebuildDocsWikilinks } from './wikilinks.js';
 /**
@@ -112,6 +121,30 @@ function asLocalFile(payload) {
             : {}),
     };
 }
+/**
+ * Narrow a parsed payload to the legacy `blob`-with-`path` shape. The current
+ * contract never writes `path` on a blob payload, so any hit is legacy data.
+ * @internal
+ */
+function asBlobWithPath(payload) {
+    if (payload['kind'] !== 'blob')
+        return null;
+    const path = payload['path'];
+    if (typeof path !== 'string' || path.length === 0)
+        return null;
+    return { kind: 'blob', path };
+}
+/**
+ * True when the row's content is retrievable from the content-addressed blob
+ * store right now (primary file or a live keep-link). Read-only — safe in a
+ * dry-run planning pass.
+ * @internal
+ */
+function blobRowContentAlive(row, payload, projectRoot) {
+    const mimeRaw = payload['mime'];
+    const mime = typeof mimeRaw === 'string' ? mimeRaw : 'application/octet-stream';
+    return blobContentExists(resolveCleoDir(projectRoot), row.sha256, mime);
+}
 /**
  * True when `absPath` points inside a worktree or temp directory:
  * the canonical CLEO worktrees root, a `.claude/worktrees/` agent spawn, or
@@ -244,54 +277,53 @@ async function fetchRowContent(row, payload, projectRoot) {
     }
 }
 /**
- * Run the docs store health check.
+ * Scan the store and compute diagnostics + repair inputs in one pass.
  *
- * Dry run (default): every diagnostic is reported and every repair is
- * listed as a plan item with `applied: false` — nothing is written.
- * Apply: the backup gate runs first, then repairs execute in dependency
- * order (doc-version-skew, empty-provenance, dangling-pointers, and finally
- * the wikilinks rebuild, which re-derives from the freshly repaired columns).
+ * The function is pure with respect to the database — it is called twice on
+ * an apply run (before repairs, to build the plan; after repairs, so the
+ * report's diagnostics reflect POST-repair state, T13560).
  *
- * @param projectRoot - Absolute path to the CLEO project root.
- * @param opts - Apply flag, stale-draft threshold, backup receipt.
- * @returns The structured report, or a backup-gate refusal.
- * @task T13447
+ * @internal
  */
-// @sync-invariant docs.lifecycle.transitions the only lifecycle write is draft→archived for dangling rows, a legal matrix transition
-export async function runDocsDoctor(projectRoot, opts = {}) {
-    const apply = opts.apply === true;
-    const olderThanDays = opts.olderThanDays ?? DOCS_DOCTOR_DEFAULT_OLDER_THAN_DAYS;
-    if (apply) {
-        const refusal = checkBackupReceipt(opts.backupReceiptPath);
-        if (refusal)
-            return { ok: false, error: refusal };
-    }
-    const db = await getDb(projectRoot);
+async function scanStore(projectRoot, db, olderThanDays) {
     const rows = await db.select().from(docsAttachments).all();
     const payloadById = new Map();
     for (const row of rows)
         payloadById.set(row.id, parseAttachmentJson(row.attachmentJson));
-    const repairs = [];
     // ── dangling-pointers ──────────────────────────────────────────────────────
     const danglingItems = [];
     let danglingCount = 0;
     const archivable = [];
+    const clearable = [];
     for (const row of rows) {
+        // Archived rows already had their repair — counting them again would make
+        // the post-apply count unchanged (T13562a).
+        if (row.lifecycleStatus === 'archived')
+            continue;
         const payload = payloadById.get(row.id) ?? null;
         const localFile = payload === null ? null : asLocalFile(payload);
-        if (!localFile)
+        const blobWithPath = payload === null ? null : asBlobWithPath(payload);
+        const pointer = localFile ?? blobWithPath;
+        if (!pointer)
             continue;
-        const absPath = isAbsolute(localFile.path)
-            ? localFile.path
-            : resolve(projectRoot, localFile.path);
+        const absPath = isAbsolute(pointer.path) ? pointer.path : resolve(projectRoot, pointer.path);
         const exists = existsSync(absPath);
         const ephemeral = isWorktreeOrTmpPath(absPath);
         if (exists && ephemeral === null)
             continue;
         danglingCount += 1;
         const reason = !exists ? 'missing' : (ephemeral ?? 'missing');
-        if (!exists)
+        if (localFile && !exists) {
             archivable.push({ row, path: absPath });
+        }
+        else if (blobWithPath &&
+            !exists &&
+            payload !== null &&
+            blobRowContentAlive(row, payload, projectRoot)) {
+            // The blob bytes are retrievable by sha256 — re-point the metadata at
+            // the content-addressed store by clearing the stale path (T13562b).
+            clearable.push({ row, path: absPath, payload });
+        }
         if (danglingItems.length < DOCS_DOCTOR_MAX_DETAIL_ITEMS) {
             danglingItems.push({
                 attachmentId: row.id,
@@ -299,19 +331,10 @@ export async function runDocsDoctor(projectRoot, opts = {}) {
                 path: absPath,
                 exists,
                 reason,
+                ...(blobWithPath ? { kind: 'blob' } : {}),
             });
         }
     }
-    for (const { row, path } of archivable) {
-        repairs.push({
-            kind: 'dangling-pointers',
-            action: 'archive-dangling',
-            applied: apply,
-            attachmentId: row.id,
-            ...(row.slug !== null ? { slug: row.slug } : {}),
-            detail: `marked-dangling: local-file target missing (${path}) → lifecycle_status = 'archived'`,
-        });
-    }
     // ── doc-version-skew ───────────────────────────────────────────────────────
     const revisionCounts = readAuditRevisionCounts(projectRoot);
     const skewItems = [];
@@ -334,16 +357,6 @@ export async function runDocsDoctor(projectRoot, opts = {}) {
             });
         }
     }
-    for (const { row, expected } of skewed) {
-        repairs.push({
-            kind: 'doc-version-skew',
-            action: 'set-doc-version',
-            applied: apply,
-            attachmentId: row.id,
-            ...(row.slug !== null ? { slug: row.slug } : {}),
-            detail: `audit-note: docVersion ${row.docVersion} → ${expected} (audit log revisions + 1)`,
-        });
-    }
     // ── empty-provenance ───────────────────────────────────────────────────────
     const provItems = [];
     let provCount = 0;
@@ -362,25 +375,11 @@ export async function runDocsDoctor(projectRoot, opts = {}) {
             ? labelsRaw.filter((l) => typeof l === 'string')
             : undefined;
         provCount += 1;
-        backfillable.push({ row, content, labels });
+        backfillable.push({ row, content, labels, derived: deriveDocLinks(content, labels) });
         if (provItems.length < DOCS_DOCTOR_MAX_DETAIL_ITEMS) {
             provItems.push({ attachmentId: row.id, slug: row.slug });
         }
     }
-    for (const { row, content, labels } of backfillable) {
-        const derived = deriveDocLinks(content, labels);
-        const derivedCount = derived.topics.length + derived.relatedTasks.length;
-        repairs.push({
-            kind: 'empty-provenance',
-            action: 'backfill-provenance',
-            applied: apply && derivedCount > 0,
-            attachmentId: row.id,
-            ...(row.slug !== null ? { slug: row.slug } : {}),
-            detail: derivedCount > 0
-                ? `derived topics=[${derived.topics.join(',')}] related_tasks=[${derived.relatedTasks.join(',')}]`
-                : 'no derivable topics or task mentions — columns stay NULL',
-        });
-    }
     // ── wikilinks-drift ────────────────────────────────────────────────────────
     const slugById = new Map();
     for (const row of rows) {
@@ -409,14 +408,10 @@ export async function runDocsDoctor(projectRoot, opts = {}) {
     const driftItems = missingEdges
         .slice(0, DOCS_DOCTOR_MAX_DETAIL_ITEMS)
         .map((e) => ({ fromSlug: e.fromSlug, toSlug: e.toSlug, relation: e.relation }));
-    if (missingEdges.length > 0) {
-        repairs.push({
-            kind: 'wikilinks-drift',
-            action: 'rebuild-wikilinks',
-            applied: apply,
-            detail: `${missingEdges.length} expected edge(s) absent from docs_wikilinks → full re-derivation`,
-        });
-    }
+    // A backfill changes the topics/related_tasks columns, so the derived edge
+    // set changes even when the pre-repair drift is zero — the rebuild must be
+    // planned whenever a backfill will actually write columns (T13561).
+    const backfillChangesLinks = backfillable.some((b) => b.derived.topics.length + b.derived.relatedTasks.length > 0);
     // ── legacy-store-present ───────────────────────────────────────────────────
     const legacyCandidates = [
         {
@@ -485,17 +480,108 @@ export async function runDocsDoctor(projectRoot, opts = {}) {
             truncated: staleRows.length > staleItems.length,
         },
     ];
+    return {
+        diagnostics,
+        dangling: { archivable, clearable },
+        skewed,
+        backfillable,
+        missingEdges,
+        needsWikilinksRebuild: missingEdges.length > 0 || backfillChangesLinks,
+    };
+}
+/**
+ * Run the docs store health check.
+ *
+ * Dry run (default): every diagnostic is reported and every repair is
+ * listed as a plan item with `applied: false` — nothing is written.
+ * Apply: the backup gate runs first, then repairs execute in dependency
+ * order (doc-version-skew, empty-provenance, dangling-pointers, and finally
+ * the wikilinks rebuild, which re-derives from the freshly repaired columns).
+ * On apply the report's diagnostics are re-scanned AFTER the repairs so the
+ * envelope reflects POST-repair state and the summary counts match it
+ * (T13560); a dry run reports the pre-repair state unchanged.
+ *
+ * @param projectRoot - Absolute path to the CLEO project root.
+ * @param opts - Apply flag, stale-draft threshold, backup receipt.
+ * @returns The structured report, or a backup-gate refusal.
+ * @task T13447
+ */
+// @sync-invariant docs.lifecycle.transitions the only lifecycle write is draft→archived for dangling rows, a legal matrix transition
+export async function runDocsDoctor(projectRoot, opts = {}) {
+    const apply = opts.apply === true;
+    const olderThanDays = opts.olderThanDays ?? DOCS_DOCTOR_DEFAULT_OLDER_THAN_DAYS;
+    if (apply) {
+        const refusal = checkBackupReceipt(opts.backupReceiptPath);
+        if (refusal)
+            return { ok: false, error: refusal };
+    }
+    const db = await getDb(projectRoot);
+    const pre = await scanStore(projectRoot, db, olderThanDays);
+    const repairs = [];
+    for (const { row, path } of pre.dangling.archivable) {
+        repairs.push({
+            kind: 'dangling-pointers',
+            action: 'archive-dangling',
+            applied: apply,
+            attachmentId: row.id,
+            ...(row.slug !== null ? { slug: row.slug } : {}),
+            detail: `marked-dangling: local-file target missing (${path}) → lifecycle_status = 'archived'`,
+        });
+    }
+    for (const { row, path } of pre.dangling.clearable) {
+        repairs.push({
+            kind: 'dangling-pointers',
+            action: 'clear-stale-path',
+            applied: apply,
+            attachmentId: row.id,
+            ...(row.slug !== null ? { slug: row.slug } : {}),
+            detail: `cleared stale legacy path (${path}) — content alive in the blob store ` +
+                `(sha256 ${row.sha256.slice(0, 12)}…)`,
+        });
+    }
+    for (const { row, expected } of pre.skewed) {
+        repairs.push({
+            kind: 'doc-version-skew',
+            action: 'set-doc-version',
+            applied: apply,
+            attachmentId: row.id,
+            ...(row.slug !== null ? { slug: row.slug } : {}),
+            detail: `audit-note: docVersion ${row.docVersion} → ${expected} (audit log revisions + 1)`,
+        });
+    }
+    for (const { row, derived } of pre.backfillable) {
+        const derivedCount = derived.topics.length + derived.relatedTasks.length;
+        repairs.push({
+            kind: 'empty-provenance',
+            action: 'backfill-provenance',
+            applied: apply && derivedCount > 0,
+            attachmentId: row.id,
+            ...(row.slug !== null ? { slug: row.slug } : {}),
+            detail: derivedCount > 0
+                ? `derived topics=[${derived.topics.join(',')}] related_tasks=[${derived.relatedTasks.join(',')}]`
+                : 'no derivable topics or task mentions — columns stay NULL',
+        });
+    }
+    if (pre.needsWikilinksRebuild) {
+        repairs.push({
+            kind: 'wikilinks-drift',
+            action: 'rebuild-wikilinks',
+            applied: apply,
+            detail: pre.missingEdges.length > 0
+                ? `${pre.missingEdges.length} expected edge(s) absent from docs_wikilinks → full re-derivation`
+                : 'provenance backfill changes derived edges → full re-derivation',
+        });
+    }
     // ── Apply repairs (backup gate already passed) ─────────────────────────────
     if (apply) {
-        for (const { row, expected } of skewed) {
+        for (const { row, expected } of pre.skewed) {
             await db
                 .update(docsAttachments)
                 .set({ docVersion: expected })
                 .where(eq(docsAttachments.id, row.id))
                 .run();
         }
-        for (const { row, content, labels } of backfillable) {
-            const derived = deriveDocLinks(content, labels);
+        for (const { row, derived } of pre.backfillable) {
             if (derived.topics.length + derived.relatedTasks.length === 0)
                 continue;
             await db
@@ -507,20 +593,33 @@ export async function runDocsDoctor(projectRoot, opts = {}) {
                 .where(eq(docsAttachments.id, row.id))
                 .run();
         }
-        for (const { row } of archivable) {
+        for (const { row } of pre.dangling.archivable) {
             await db
                 .update(docsAttachments)
                 .set({ lifecycleStatus: 'archived' })
                 .where(eq(docsAttachments.id, row.id))
                 .run();
         }
-        if (missingEdges.length > 0) {
+        for (const { row, payload } of pre.dangling.clearable) {
+            const cleaned = { ...payload };
+            delete cleaned['path'];
+            await db
+                .update(docsAttachments)
+                .set({ attachmentJson: JSON.stringify(cleaned) })
+                .where(eq(docsAttachments.id, row.id))
+                .run();
+        }
+        if (pre.needsWikilinksRebuild) {
             await rebuildDocsWikilinks({ projectRoot });
         }
     }
-    const findings = diagnostics.reduce((sum, d) => sum + d.count, 0);
+    // T13560: on apply, re-scan so the envelope's diagnostics (and the summary
+    // computed from them) describe POST-repair state, consistent with a
+    // follow-up dry run. Dry runs keep the pre-repair scan.
+    const post = apply ? await scanStore(projectRoot, db, olderThanDays) : pre;
+    const findings = post.diagnostics.reduce((sum, d) => sum + d.count, 0);
     const summary = apply
-        ? `docs doctor applied ${repairs.filter((r) => r.applied).length} repair(s) across ${findings} finding(s)`
+        ? `docs doctor applied ${repairs.filter((r) => r.applied).length} repair(s); ${findings} finding(s) remain post-repair`
         : `docs doctor found ${findings} finding(s); ${repairs.length} repair(s) planned (dry-run — pass --apply to execute)`;
     return {
         ok: true,
@@ -528,7 +627,7 @@ export async function runDocsDoctor(projectRoot, opts = {}) {
             applied: apply,
             olderThanDays,
             backupReceiptPath: apply ? (opts.backupReceiptPath ?? null) : null,
-            diagnostics,
+            diagnostics: post.diagnostics,
             repairs,
             summary,
         },