@cleocode/core 2026.8.1 → 2026.8.3

package/dist/nexus/analyze-orchestrator.d.ts.map

@@ -1 +1 @@
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package/dist/nexus/analyze-orchestrator.js

@@ -61,6 +61,34 @@ export async function runNexusAnalysis(params) {
         catch {
             // table may be empty — ignore
         }
+        // T12074: clear the FTS shadow explicitly.
+        //
+        // `nexus_symbols_fts` is kept in sync by AFTER INSERT/DELETE/UPDATE
+        // triggers on `nexus_nodes`, keyed on `rowid`. When the shadow drifts —
+        // rows whose base row vanished by a path that did not fire the delete
+        // trigger — those orphaned rowids survive the clear above and then COLLIDE
+        // with the rebuild's `INSERT INTO nexus_symbols_fts(rowid, …)`, because
+        // the insert supplies an explicit rowid.
+        //
+        // The failure mode is severe and silent about its cause: the reindex has
+        // already emptied `nexus_nodes`/`nexus_relations`, so the collision leaves
+        // the project with a DESTROYED index and an `E_PIPELINE_FAILED` whose
+        // message is a bare "Failed query: insert into nexus_nodes" plus 8,500
+        // bound parameters. Observed on this repo 2026-08-06: a graph of 24,482
+        // nodes / 39,163 relations reduced to 500 / 0 by a single `cleo nexus
+        // analyze`, with 70 orphaned shadow rows as the only cause.
+        //
+        // That matters doubly because `analyze` is the repair command the agent
+        // protocol — and the stale-index error added in T12068 — tell agents to
+        // run. A repair path that can destroy the thing it repairs is worse than
+        // no repair path.
+        try {
+            const { sql } = await import('drizzle-orm');
+            db.run(sql `DELETE FROM nexus_symbols_fts`);
+        }
+        catch {
+            // FTS shadow is optional (older schemas lack it) — ignore
+        }
     }
     const result = await runPipeline(repoPath, projectId, db, tables, onProgress, {
         incremental,

package/dist/nexus/analyze-orchestrator.js.map

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package/dist/nexus/context.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"context.d.ts","sourceRoot":"","sources":["../../src/nexus/context.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAIH,OAAO,EAAE,KAAK,YAAY,EAA8B,MAAM,qBAAqB,CAAC;AAIpF,mDAAmD;AACnD,MAAM,WAAW,kBAAkB;IACjC,6BAA6B;IAC7B,MAAM,EAAE,MAAM,CAAC;IACf,4BAA4B;IAC5B,SAAS,EAAE,MAAM,CAAC;IAClB,0BAA0B;IAC1B,OAAO,EAAE,MAAM,CAAC;IAChB,oCAAoC;IACpC,MAAM,EAAE,MAAM,EAAE,CAAC;CAClB;AAED,oDAAoD;AACpD,MAAM,WAAW,oBAAoB;IACnC,gDAAgD;IAChD,YAAY,EAAE,MAAM,CAAC;IACrB,qCAAqC;IACrC,MAAM,EAAE,OAAO,CAAC;IAChB,kCAAkC;IAClC,IAAI,EAAE,MAAM,CAAC;IACb,8CAA8C;IAC9C,IAAI,EAAE,MAAM,CAAC;IACb,mCAAmC;IACnC,QAAQ,EAAE,OAAO,CAAC;CACnB;AAED,mCAAmC;AACnC,MAAM,WAAW,mBAAmB;IAClC,uBAAuB;IACvB,SAAS,EAAE,OAAO,CAAC;IACnB,oCAAoC;IACpC,KAAK,EAAE,OAAO,CAAC;IACf,0CAA0C;IAC1C,IAAI,EAAE,MAAM,CAAC;IACb,8CAA8C;IAC9C,IAAI,EAAE,OAAO,CAAC;CACf;AAED,iDAAiD;AACjD,MAAM,WAAW,gBAAgB;IAC/B,eAAe;IACf,MAAM,EAAE,MAAM,CAAC;IACf,mBAAmB;IACnB,IAAI,EAAE,OAAO,CAAC;IACd,iBAAiB;IACjB,IAAI,EAAE,OAAO,CAAC;IACd,0BAA0B;IAC1B,QAAQ,EAAE,OAAO,CAAC;IAClB,4BAA4B;IAC5B,SAAS,EAAE,OAAO,CAAC;IACnB,0BAA0B;IAC1B,OAAO,EAAE,OAAO,CAAC;IACjB,sCAAsC;IACtC,UAAU,EAAE,OAAO,CAAC;IACpB,yCAAyC;IACzC,UAAU,EAAE,OAAO,CAAC;IACpB,qCAAqC;IACrC,SAAS,EAAE;QAAE,EAAE,EAAE,MAAM,GAAG,IAAI,CAAC;QAAC,KAAK,EAAE,OAAO,CAAA;KAAE,GAAG,IAAI,CAAC;IACxD,4CAA4C;IAC5C,OAAO,EAAE,oBAAoB,EAAE,CAAC;IAChC,4CAA4C;IAC5C,OAAO,EAAE,oBAAoB,EAAE,CAAC;IAChC,qCAAqC;IACrC,SAAS,EAAE,mBAAmB,EAAE,CAAC;IACjC,gEAAgE;IAChE,MAAM,CAAC,EAAE,kBAAkB,CAAC;CAC7B;AAED,4CAA4C;AAC5C,MAAM,WAAW,mBAAmB;IAClC,8DAA8D;IAC9D,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,oDAAoD;IACpD,WAAW,CAAC,EAAE,OAAO,CAAC;CACvB;AAED,oDAAoD;AACpD,MAAM,WAAW,kBAAkB;IACjC,6BAA6B;IAC7B,KAAK,EAAE,MAAM,CAAC;IACd,kBAAkB;IAClB,SAAS,EAAE,MAAM,CAAC;IAClB,kCAAkC;IAClC,UAAU,EAAE,MAAM,CAAC;IACnB,0CAA0C;IAC1C,OAAO,EAAE,gBAAgB,EAAE,CAAC;CAC7B;AAED;;;;;;;;;;;;;;;;;;GAkBG;AACH,wBAAsB,gBAAgB,CACpC,UAAU,EAAE,MAAM,EAClB,SAAS,EAAE,MAAM,EACjB,QAAQ,EAAE,MAAM,EAChB,IAAI,GAAE,mBAAwB,GAC7B,OAAO,CAAC,kBAAkB,CAAC,CA4L7B;AAGD,wBAAsB,YAAY,CAChC,UAAU,EAAE,MAAM,EAClB,SAAS,EAAE,MAAM,EACjB,QAAQ,EAAE,MAAM,EAChB,KAAK,EAAE,MAAM,EACb,WAAW,EAAE,OAAO,GACnB,OAAO,CAAC,YAAY,CAAC,OAAO,CAAC,CAAC,CAUhC"}

package/dist/nexus/context.js

@@ -10,6 +10,7 @@ import path from 'node:path';
 import { notInArray } from 'drizzle-orm';
 import { engineError, engineSuccess } from '../engine-result.js';
 import { getNexusDb, nexusSchema } from '../store/nexus-sqlite.js';
+import { buildSymbolMissError } from './symbol-miss.js';
 /**
  * Retrieve caller/callee context and process participation for a named symbol.
  *
@@ -53,9 +54,8 @@ export async function getSymbolContext(symbolName, projectId, repoPath, opts = {
     const rawMatchingNodes = projectSymbolNodes.filter((n) => n['name'] != null && String(n['name']).toLowerCase().includes(lowerSymbol));
     const matchingNodes = sortMatchingNodes(rawMatchingNodes, symbolName);
     if (matchingNodes.length === 0) {
-        const err = new Error(`No symbol found matching '${symbolName}' in project ${projectId}`);
-        err.code = 'E_NOT_FOUND';
-        throw err;
+        // T12068: distinguish "no such symbol" from "index predates the symbol".
+        throw buildSymbolMissError(symbolName, projectId, projectSymbolNodes);
     }
     // Fetch all relations for callers/callees/process edges (project-scoped DB).
     let allRelations = [];

package/dist/nexus/context.js.map

@@ -1 +1 @@
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package/dist/nexus/impact.d.ts.map

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package/dist/nexus/impact.js

@@ -10,6 +10,7 @@
 import { eq, notInArray } from 'drizzle-orm';
 import { engineError, engineSuccess } from '../engine-result.js';
 import { getNexusDb, getNexusNativeDb, nexusSchema } from '../store/nexus-sqlite.js';
+import { buildSymbolMissError } from './symbol-miss.js';
 /**
  * Analyse the blast radius for a named code symbol via BFS upstream traversal.
  *
@@ -53,9 +54,8 @@ export async function getSymbolImpact(symbolName, projectId, _repoPath, opts = {
     const rawMatchingNodes = projectSymbolNodes.filter((n) => n['name'] != null && String(n['name']).toLowerCase().includes(lowerSymbol));
     const matchingNodes = sortMatchingNodes(rawMatchingNodes, symbolName);
     if (matchingNodes.length === 0) {
-        const err = new Error(`No symbol found matching '${symbolName}' in project ${projectId}`);
-        err.code = 'E_NOT_FOUND';
-        throw err;
+        // T12068: distinguish "no such symbol" from "index predates the symbol".
+        throw buildSymbolMissError(symbolName, projectId, projectSymbolNodes);
     }
     // Fetch all relations (project-scoped DB — ADR-090 · T11648: no `project_id`
     // predicate). T11545: plasticity `weight` lives in the sibling

package/dist/nexus/impact.js.map

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package/dist/nexus/living-brain.js

@@ -187,7 +187,7 @@ export async function getSymbolFullContext(symbolId, projectRoot) {
     // ---- BRAIN substrate ----
     try {
         await getBrainDb(projectRoot);
-        const brainNative = getBrainNativeDb();
+        const brainNative = getBrainNativeDb(projectRoot);
         if (brainNative) {
             // Query brain_page_edges for all edges connecting to this symbol
             // Covers: code_reference (memory→symbol), documents (decision→symbol),
@@ -266,7 +266,7 @@ export async function getSymbolFullContext(symbolId, projectRoot) {
     // ---- SENTIENT substrate ----
     try {
         await getBrainDb(projectRoot);
-        const brainNative = getBrainNativeDb();
+        const brainNative = getBrainNativeDb(projectRoot);
         if (brainNative) {
             // Query proposed tasks in tasks.db is not directly accessible here,
             // so we query the brain_page_nodes for sentient-tier2 nodes whose
@@ -370,7 +370,7 @@ export async function getTaskCodeImpact(taskId, projectRoot) {
         // Try to infer from task_touches_symbol edges
         try {
             await getBrainDb(projectRoot);
-            const brainNative = getBrainNativeDb();
+            const brainNative = getBrainNativeDb(projectRoot);
             await getNexusDb();
             const nexusNative = getNexusNativeDb();
             if (brainNative && nexusNative) {
@@ -489,7 +489,7 @@ export async function getTaskCodeImpact(taskId, projectRoot) {
     // ---- Brain observations with modified_by edges to task files ----
     try {
         await getBrainDb(projectRoot);
-        const brainNative = getBrainNativeDb();
+        const brainNative = getBrainNativeDb(projectRoot);
         await getNexusDb();
         const nexusNative = getNexusNativeDb();
         if (brainNative && nexusNative && result.files.length > 0) {
@@ -535,7 +535,7 @@ export async function getTaskCodeImpact(taskId, projectRoot) {
     // ---- Decisions from brain_memory_links ----
     try {
         await getBrainDb(projectRoot);
-        const brainNative = getBrainNativeDb();
+        const brainNative = getBrainNativeDb(projectRoot);
         if (brainNative) {
             const linkRows = typedAll(brainNative.prepare(`SELECT memory_id, memory_type, task_id, link_type
            FROM brain_memory_links
@@ -590,7 +590,7 @@ export async function getBrainEntryCodeAnchors(entryId, projectRoot) {
     ];
     try {
         await getBrainDb(projectRoot);
-        const brainNative = getBrainNativeDb();
+        const brainNative = getBrainNativeDb(projectRoot);
         await getNexusDb();
         const nexusNative = getNexusNativeDb();
         if (!brainNative || !nexusNative)
@@ -773,7 +773,7 @@ export async function reasonImpactOfChange(symbolId, projectRoot) {
     // ---- Brain risk notes via code_reference / documents / modified_by edges ----
     try {
         await getBrainDb(projectRoot);
-        const brainNative = getBrainNativeDb();
+        const brainNative = getBrainNativeDb(projectRoot);
         if (brainNative) {
             const riskEdgeTypes = [
                 EDGE_TYPES.CODE_REFERENCE,

package/dist/nexus/living-brain.js.map

@@ -1 +1 @@
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package/dist/nexus/symbol-miss.d.ts

@@ -0,0 +1,132 @@
+/**
+ * Actionable "symbol not in the index" errors for the NEXUS code-graph
+ * lookups (`cleo nexus impact` / `cleo nexus context`).
+ *
+ * ## Why this module exists (T12068)
+ *
+ * Both lookups used to throw a bare
+ *
+ * ```text
+ * No symbol found matching 'normalizeMarkers' in project L21udC9wcm9q…
+ * ```
+ *
+ * which is indistinguishable between the three causes an agent actually
+ * cares about:
+ *
+ *   1. the symbol genuinely does not exist (typo / wrong name),
+ *   2. the symbol exists but the index predates it — the common case, and
+ *   3. the project was never indexed at all.
+ *
+ * Cases 2 and 3 are *repairable in one command*; case 1 is not. Collapsing
+ * them into one opaque message means an agent that hits a stale index
+ * reasonably concludes the whole subsystem is broken and silently falls back
+ * to `grep` for the rest of the session — which is exactly what happened on
+ * 2026-08-05 against an index whose newest entry was 92 days old while the
+ * queried symbol had shipped that morning.
+ *
+ * The freshness signal is derived from node rows the caller has ALREADY
+ * materialised for its own matching pass, so building the richer message
+ * costs no extra query and nothing at all on the success path.
+ *
+ * @task T12068
+ */
+/**
+ * Structured detail attached to a symbol-miss error, so machine consumers
+ * can branch on freshness without re-parsing the message text.
+ */
+export interface SymbolMissDetails {
+    /** The symbol name that was searched for. */
+    readonly symbol: string;
+    /** Nexus project ID the lookup ran against. */
+    readonly projectId: string;
+    /** Number of symbol nodes present in the index. */
+    readonly indexedSymbolCount: number;
+    /** Most recent `indexed_at` across the index, or `null` when never indexed. */
+    readonly lastIndexedAt: string | null;
+    /**
+     * MEDIAN `indexed_at` across the index — the age of the index *body*
+     * rather than of its newest row. See {@link medianIndexedAt} for why the
+     * maximum is not a usable freshness signal.
+     */
+    readonly medianIndexedAt: string | null;
+    /** Whole days since {@link medianIndexedAt}, or `null` when never indexed. */
+    readonly indexAgeDays: number | null;
+    /** Coarse freshness classification, derived from {@link medianIndexedAt}. */
+    readonly freshness: 'fresh' | 'stale' | 'never-indexed';
+}
+/** An `E_NOT_FOUND` error carrying {@link SymbolMissDetails}. */
+export interface SymbolMissError extends Error {
+    code: 'E_NOT_FOUND';
+    details: SymbolMissDetails;
+}
+/**
+ * Newest `indexed_at` across a set of node rows.
+ *
+ * Timestamps are stored as lexicographically-ordered ISO-ish strings
+ * (`YYYY-MM-DD HH:MM:SS`), so a string comparison is a valid ordering and
+ * avoids parsing every row.
+ *
+ * @param nodes - node rows already loaded by the caller.
+ * @returns the maximum `indexed_at`, or `null` when no row carries one.
+ *
+ * @task T12068
+ */
+export declare function newestIndexedAt(nodes: ReadonlyArray<Record<string, unknown>>): string | null;
+/**
+ * MEDIAN `indexed_at` across a set of node rows.
+ *
+ * The **maximum** is not a usable freshness signal: an incremental run that
+ * re-indexes a handful of touched files stamps a few rows with today's date
+ * while the other 99% keep a months-old timestamp. Measured on this repo on
+ * 2026-08-06 the newest row was 0 days old and the index still could not
+ * resolve a symbol that had shipped the previous morning — because only 3 of
+ * 24,095 rows carried the recent stamp and 14,151 were from three months
+ * earlier.
+ *
+ * The median moves only once a real majority of the graph has been
+ * re-indexed, which is the property a freshness claim needs.
+ *
+ * @param nodes - node rows already loaded by the caller.
+ * @returns the median `indexed_at`, or `null` when no row carries one.
+ *
+ * @task T12068
+ */
+export declare function medianIndexedAt(nodes: ReadonlyArray<Record<string, unknown>>): string | null;
+/**
+ * Classify index freshness from a representative timestamp.
+ *
+ * Callers pass the MEDIAN (see {@link medianIndexedAt}), not the maximum.
+ *
+ * @param lastIndexedAt - representative `indexed_at`, or `null`.
+ * @param now - current time in epoch ms (injectable for tests).
+ * @returns freshness bucket and whole-day age (`null` age when never indexed).
+ *
+ * @task T12068
+ */
+export declare function classifyIndexFreshness(lastIndexedAt: string | null, now: number): {
+    freshness: SymbolMissDetails['freshness'];
+    indexAgeDays: number | null;
+};
+/**
+ * Build the `E_NOT_FOUND` error thrown when a symbol lookup matches nothing.
+ *
+ * The message always names the repair command when one would help, so an
+ * agent reading only the error text still knows what to do next.
+ *
+ * @param symbolName - the searched-for symbol.
+ * @param projectId  - nexus project ID the lookup ran against.
+ * @param nodes      - node rows the caller already loaded (used for freshness).
+ * @param now        - current time in epoch ms (injectable for tests).
+ * @returns an `Error` with `code = 'E_NOT_FOUND'` and {@link SymbolMissDetails}.
+ *
+ * @example
+ * ```ts
+ * if (matchingNodes.length === 0) {
+ *   throw buildSymbolMissError(symbolName, projectId, projectSymbolNodes);
+ * }
+ * ```
+ *
+ * @task T12068
+ */
+export declare function buildSymbolMissError(symbolName: string, projectId: string, nodes: ReadonlyArray<Record<string, unknown>>, now?: number): SymbolMissError;
+//# sourceMappingURL=symbol-miss.d.ts.map

package/dist/nexus/symbol-miss.d.ts.map

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