@cleocode/core 2026.9.7 → 2026.9.9

package/dist/memory/brain-backfill.js.map

@@ -1 +1 @@
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package/dist/memory/brain-doctor.d.ts

@@ -27,6 +27,8 @@
  * @see T1147 W7 for the mutator sweep that acts on these findings
  * @see T1148 W8 M7 gate — `cleo memory doctor --assert-clean` must exit 0 before Sentient v1
  */
+import type { KnowledgeDiagnostic } from '@cleocode/contracts';
+import { getBrainNativeDb } from '../store/memory-sqlite.js';
 /** A single detected noise entry. */
 export interface BrainNoiseEntry {
     /** Noise pattern identifier. */
@@ -76,6 +78,12 @@ export interface BrainDoctorResult {
      * This is the condition checked by `cleo memory doctor --assert-clean`.
      */
     isClean: boolean;
+    /** Structural scan completeness, independent of extraction and semantic authority. */
+    structure?: KnowledgeDiagnostic;
+    /** Semantic reconciliation is not performed by this structural scanner. */
+    semantics?: KnowledgeDiagnostic;
+    /** Extraction health is reported separately and does not establish semantic correctness. */
+    extraction?: KnowledgeDiagnostic;
     /** ISO 8601 timestamp when the scan completed. */
     scannedAt: string;
     /**
@@ -101,6 +109,18 @@ export interface ProvenanceDistribution {
     /** Count with provenance_chain set (derived rows). */
     derivedCount: number;
 }
+/**
+ * Count all graph edges with a missing endpoint while retaining a bounded sample.
+ * @param db - Canonical native brain handle for the explicitly selected project.
+ * @returns An exact orphan-edge finding, or null when both endpoints exist for every edge.
+ * @remarks A single statement keeps the total and sample consistent. Query failures propagate;
+ * this read-only assessment neither removes history nor invents missing records.
+ * @example
+ * ```ts
+ * const finding = scanBrainGraphOrphans(nativeDb);
+ * ```
+ */
+export declare function scanBrainGraphOrphans(db: NonNullable<ReturnType<typeof getBrainNativeDb>>): BrainNoiseEntry | null;
 /**
  * Run a read-only noise scan over `.cleo/brain.db` and return a structured
  * findings report.
@@ -124,6 +144,7 @@ export interface ProvenanceDistribution {
  * ```
  *
  * @task T1262
+ * @remarks Structural failures remain explicit; semantic authority is not inferred from structural cleanliness.
  */
 export declare function scanBrainNoise(projectRoot: string): Promise<BrainDoctorResult>;
 //# sourceMappingURL=brain-doctor.d.ts.map

package/dist/memory/brain-doctor.d.ts.map

@@ -1 +1 @@
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package/dist/memory/brain-doctor.js

@@ -53,6 +53,53 @@ function sampleIds(rows) {
 // ============================================================================
 // Public API
 // ============================================================================
+/**
+ * Count all graph edges with a missing endpoint while retaining a bounded sample.
+ * @param db - Canonical native brain handle for the explicitly selected project.
+ * @returns An exact orphan-edge finding, or null when both endpoints exist for every edge.
+ * @remarks A single statement keeps the total and sample consistent. Query failures propagate;
+ * this read-only assessment neither removes history nor invents missing records.
+ * @example
+ * ```ts
+ * const finding = scanBrainGraphOrphans(nativeDb);
+ * ```
+ */
+export function scanBrainGraphOrphans(db) {
+    const rows = db
+        .prepare(`
+    SELECT e.from_id || '->' || e.to_id AS id, COUNT(*) OVER () AS total
+    FROM main.brain_page_edges e
+    LEFT JOIN main.brain_page_nodes src ON src.id = e.from_id
+    LEFT JOIN main.brain_page_nodes dst ON dst.id = e.to_id
+    LEFT JOIN main.tasks_tasks task_source
+      ON e.edge_type = 'task_touches_symbol' AND e.from_id = 'task:' || task_source.id
+    LEFT JOIN main.nexus_nodes code_target
+      ON e.edge_type IN ('code_reference', 'task_touches_symbol', 'mentions', 'documents', 'conduit_mentions_symbol') AND code_target.id = e.to_id
+    LEFT JOIN main.nexus_nodes code_source
+      ON e.edge_type = 'modified_by' AND code_source.id = e.from_id
+    WHERE (src.id IS NULL AND task_source.id IS NULL AND code_source.id IS NULL)
+       OR (dst.id IS NULL AND code_target.id IS NULL)
+    ORDER BY e.from_id, e.to_id
+    LIMIT 5
+  `)
+        .all();
+    if (rows.length === 0)
+        return null;
+    const count = rows[0]?.total;
+    if (typeof count !== 'number')
+        throw new Error('Invalid graph orphan count');
+    const samples = rows.map((row) => {
+        if (typeof row.id !== 'string')
+            throw new Error('Invalid graph orphan identifier');
+        return row.id;
+    });
+    return {
+        pattern: 'orphan-edge',
+        count,
+        sampleIds: samples,
+        description: `${count} brain graph edges have a missing source or target node; inspect backed records before reconstructing derived nodes. Preserve unresolved historical edges.`,
+    };
+}
 /**
  * Run a read-only noise scan over `.cleo/brain.db` and return a structured
  * findings report.
@@ -76,45 +123,42 @@ function sampleIds(rows) {
  * ```
  *
  * @task T1262
+ * @remarks Structural failures remain explicit; semantic authority is not inferred from structural cleanliness.
  */
 export async function scanBrainNoise(projectRoot) {
     // Initialize brain.db connection (required before getBrainNativeDb() is callable)
     await getBrainDb(projectRoot);
     const db = getBrainNativeDb(projectRoot);
     const findings = [];
-    if (!db) {
-        // brain.db not available — return clean scan (cannot detect noise without DB)
-        return {
-            totalScanned: 0,
-            findings: [],
-            isClean: true,
-            scannedAt: new Date().toISOString(),
-        };
-    }
+    const errors = [];
+    if (!db)
+        throw new Error('BRAIN database unavailable: structural health was not assessed');
     try {
         // ── 1. Total scanned (union of all typed tables) ────────────────────────
         const tables = ['brain_observations', 'brain_decisions', 'brain_patterns', 'brain_learnings'];
         let totalScanned = 0;
         for (const table of tables) {
             try {
-                const row = db.prepare(`SELECT COUNT(*) as c FROM ${table}`).get();
+                const row = db.prepare(`SELECT COUNT(*) as c FROM main.${table}`).get();
                 totalScanned += row?.c ?? 0;
             }
-            catch {
+            catch (error) {
+                errors.push(error instanceof Error ? error.message : String(error));
                 // Table may not exist in all installations — skip silently.
             }
         }
         // ── 2. missing-type ─────────────────────────────────────────────────────
         {
             const rows = [];
-            for (const table of tables) {
+            for (const table of tables.filter((table) => table !== 'brain_learnings')) {
                 try {
                     const res = db
-                        .prepare(`SELECT id FROM ${table} WHERE type IS NULL OR type = '' LIMIT 20`)
+                        .prepare(`SELECT id FROM main.${table} WHERE type IS NULL OR type = '' LIMIT 20`)
                         .all();
                     rows.push(...res);
                 }
-                catch {
+                catch (error) {
+                    errors.push(error instanceof Error ? error.message : String(error));
                     // skip
                 }
             }
@@ -133,11 +177,12 @@ export async function scanBrainNoise(projectRoot) {
             for (const table of tables) {
                 try {
                     const res = db
-                        .prepare(`SELECT id FROM ${table} WHERE provenance IS NULL LIMIT 20`)
+                        .prepare(`SELECT id FROM main.${table} WHERE provenance_class IS NULL LIMIT 20`)
                         .all();
                     rows.push(...res);
                 }
-                catch {
+                catch (error) {
+                    errors.push(error instanceof Error ? error.message : String(error));
                     // skip — provenance column may not exist in all schema versions
                 }
             }
@@ -153,14 +198,15 @@ export async function scanBrainNoise(projectRoot) {
         // ── 4. low-confidence ────────────────────────────────────────────────────
         {
             const rows = [];
-            for (const table of tables) {
+            for (const table of ['brain_learnings']) {
                 try {
                     const res = db
-                        .prepare(`SELECT id FROM ${table} WHERE confidence IS NOT NULL AND confidence < ? LIMIT 20`)
+                        .prepare(`SELECT id FROM main.${table} WHERE confidence IS NOT NULL AND confidence < ? LIMIT 20`)
                         .all(LOW_CONFIDENCE_THRESHOLD);
                     rows.push(...res);
                 }
-                catch {
+                catch (error) {
+                    errors.push(error instanceof Error ? error.message : String(error));
                     // skip — confidence column may not exist
                 }
             }
@@ -182,14 +228,15 @@ export async function scanBrainNoise(projectRoot) {
             for (const table of tables) {
                 try {
                     const res = db
-                        .prepare(`SELECT id FROM ${table}
+                        .prepare(`SELECT id FROM main.${table}
                WHERE verified = 0
-                 AND created_at < ?
+                 AND ${table === 'brain_patterns' ? 'extracted_at' : 'created_at'} < ? AND citation_count = 0
                LIMIT 20`)
                         .all(staleIso);
                     rows.push(...res);
                 }
-                catch {
+                catch (error) {
+                    errors.push(error instanceof Error ? error.message : String(error));
                     // skip — schema may differ
                 }
             }
@@ -208,16 +255,17 @@ export async function scanBrainNoise(projectRoot) {
             for (const table of tables) {
                 try {
                     const res = db
-                        .prepare(`SELECT id FROM ${table}
-               WHERE content IN (
-                 SELECT content FROM ${table}
-                 WHERE content IS NOT NULL
-                 GROUP BY content HAVING COUNT(*) > 1
+                        .prepare(`SELECT id FROM main.${table}
+               WHERE content_hash IN (
+                 SELECT content_hash FROM main.${table}
+                 WHERE content_hash IS NOT NULL
+                 GROUP BY content_hash HAVING COUNT(*) > 1
                ) LIMIT 20`)
                         .all();
                     rows.push(...res);
                 }
-                catch {
+                catch (error) {
+                    errors.push(error instanceof Error ? error.message : String(error));
                     // skip — content column may not exist in all tables
                 }
             }
@@ -231,23 +279,12 @@ export async function scanBrainNoise(projectRoot) {
             }
         }
         try {
-            const rows = db
-                .prepare(`SELECT e.id FROM brain_edges e
-             LEFT JOIN brain_nodes src ON src.id = e.source_id
-             LEFT JOIN brain_nodes tgt ON tgt.id = e.target_id
-             WHERE src.id IS NULL OR tgt.id IS NULL
-             LIMIT 20`)
-                .all();
-            if (rows.length > 0) {
-                findings.push({
-                    pattern: 'orphan-edge',
-                    count: rows.length,
-                    sampleIds: sampleIds(rows),
-                    description: 'Brain graph edges pointing to non-existent nodes — referential integrity violation.',
-                });
-            }
+            const orphanFinding = scanBrainGraphOrphans(db);
+            if (orphanFinding)
+                findings.push(orphanFinding);
         }
-        catch {
+        catch (error) {
+            errors.push(error instanceof Error ? error.message : String(error));
             // brain_edges / brain_nodes may not exist
         }
         // ── 7. Auto-extract pipeline health (T1903) ──────────────────────────────
@@ -257,20 +294,41 @@ export async function scanBrainNoise(projectRoot) {
         return {
             totalScanned,
             findings,
-            isClean: findings.length === 0,
+            isClean: findings.length === 0 && errors.length === 0,
+            structure: {
+                status: errors.length ? 'failed' : findings.length ? 'findings' : 'clean',
+                reasons: [...errors, ...findings.map((finding) => finding.description)],
+                evidence: [],
+            },
+            semantics: {
+                status: 'unavailable',
+                reasons: [
+                    'Structural scans do not establish semantic authority; inspect explicit conflicts and sourced replacements.',
+                ],
+                evidence: [],
+            },
+            extraction: {
+                status: !autoExtractHealth
+                    ? 'unavailable'
+                    : autoExtractHealth.healthy
+                        ? 'clean'
+                        : 'findings',
+                reasons: !autoExtractHealth
+                    ? ['Extraction metrics could not be assessed.']
+                    : autoExtractHealth.healthy
+                        ? []
+                        : [
+                            'Extraction production is below the expected ratio; this does not mean the structural scan failed.',
+                        ],
+                evidence: [],
+            },
             scannedAt: new Date().toISOString(),
             autoExtractHealth,
             provenanceDistribution,
         };
     }
-    catch {
-        // Return a minimal clean result on unexpected errors rather than crashing.
-        return {
-            totalScanned: 0,
-            findings: [],
-            isClean: true,
-            scannedAt: new Date().toISOString(),
-        };
+    catch (error) {
+        throw new Error('BRAIN structural assessment failed', { cause: error });
     }
 }
 // ============================================================================

package/dist/memory/brain-doctor.js.map

@@ -1 +1 @@
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@@ -1 +1 @@
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+{"version":3,"file":"brain-links.d.ts","sourceRoot":"","sources":["../../src/memory/brain-links.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAOH,OAAO,KAAK,EACV,gBAAgB,EAChB,kBAAkB,EAClB,gBAAgB,EAChB,gBAAgB,EAChB,kBAAkB,EAClB,eAAe,EAChB,MAAM,kCAAkC,CAAC;AAC1C,OAAO,EAAE,KAAK,EAAE,MAAM,oBAAoB,CAAC;AAE3C,KAAK,UAAU,GAAG,CAAC,OAAO,kBAAkB,CAAC,CAAC,MAAM,CAAC,CAAC;AACtD,KAAK,QAAQ,GAAG,CAAC,OAAO,gBAAgB,CAAC,CAAC,MAAM,CAAC,CAAC;AA4DlD,oCAAoC;AACpC,MAAM,WAAW,aAAa;IAC5B,UAAU,EAAE,UAAU,CAAC;IACvB,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,EAAE,QAAQ,CAAC;CACpB;AAED;;;;;;;;;;;GAWG;AACH,wBAAsB,gBAAgB,CACpC,WAAW,EAAE,MAAM,EACnB,UAAU,EAAE,UAAU,EACtB,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,MAAM,EACd,QAAQ,EAAE,QAAQ,EAClB,eAAe,CAAC,EAAE,OAAO,CAAC,UAAU,CAAC,OAAO,KAAK,CAAC,CAAC,GAClD,OAAO,CAAC,kBAAkB,CAAC,CAgC7B;AAED;;;;;;;;;;;;;;GAcG;AACH,wBAAsB,4BAA4B,CAChD,WAAW,EAAE,MAAM,EACnB,UAAU,EAAE,UAAU,EACtB,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,MAAM,EACd,QAAQ,EAAE,QAAQ,GACjB,OAAO,CAAC,kBAAkB,CAAC,CAK7B;AAED;;;;GAIG;AACH,wBAAsB,oBAAoB,CACxC,WAAW,EAAE,MAAM,EACnB,UAAU,EAAE,UAAU,EACtB,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,MAAM,EACd,QAAQ,EAAE,QAAQ,GACjB,OAAO,CAAC,IAAI,CAAC,CAGf;AAED;;;;GAIG;AACH,wBAAsB,YAAY,CAChC,WAAW,EAAE,MAAM,EACnB,MAAM,EAAE,MAAM,GACb,OAAO,CAAC,kBAAkB,EAAE,CAAC,CAG/B;AAED;;;;GAIG;AACH,wBAAsB,cAAc,CAClC,WAAW,EAAE,MAAM,EACnB,UAAU,EAAE,UAAU,EACtB,QAAQ,EAAE,MAAM,GACf,OAAO,CAAC,kBAAkB,EAAE,CAAC,CAG/B;AAED;;;;GAIG;AACH,wBAAsB,QAAQ,CAC5B,WAAW,EAAE,MAAM,EACnB,KAAK,EAAE,aAAa,EAAE,GACrB,OAAO,CAAC;IAAE,OAAO,EAAE,MAAM,CAAC;IAAC,OAAO,EAAE,MAAM,CAAA;CAAE,CAAC,CAkC/C;AAED;;;;;GAKG;AACH,wBAAsB,kBAAkB,CACtC,WAAW,EAAE,MAAM,EACnB,MAAM,EAAE,MAAM,GACb,OAAO,CAAC,gBAAgB,EAAE,CAAC,CAa7B;AAED;;;;;GAKG;AACH,wBAAsB,iBAAiB,CACrC,WAAW,EAAE,MAAM,EACnB,MAAM,EAAE,MAAM,GACb,OAAO,CAAC,eAAe,EAAE,CAAC,CAa5B;AAED;;;;;GAKG;AACH,wBAAsB,kBAAkB,CACtC,WAAW,EAAE,MAAM,EACnB,MAAM,EAAE,MAAM,GACb,OAAO,CAAC,gBAAgB,EAAE,CAAC,CAa7B"}

package/dist/memory/brain-links.js

@@ -7,11 +7,37 @@
  * @task T5156
  * @epic T5149
  */
+import { statSync } from 'node:fs';
+import { captureProjectScope, worktreeScope } from '../project-scope.js';
 import { taskExistsInTasksDb, taskExistsInTasksDbFresh } from '../store/cross-db-cleanup.js';
-import { getBrainAccessor } from '../store/memory-accessor.js';
+import { BrainDataAccessor, getBrainAccessor } from '../store/memory-accessor.js';
+import { peekProjectDomain } from '../store/ports/domain-binding.js';
 import { getDb } from '../store/sqlite.js';
-async function createMemoryTaskLink(projectRoot, memoryType, memoryId, taskId, linkType) {
-    const accessor = await getBrainAccessor(projectRoot);
+/** Authenticate the already-bound consolidated handle without reopening a moved path. */
+function retainedLinkAccessor(projectRoot, tasksDb) {
+    const scope = captureProjectScope(projectRoot, worktreeScope.getStore());
+    const binding = worktreeScope.run(scope, () => peekProjectDomain('tasks', scope.worktreeRoot));
+    if (!binding || binding.db !== tasksDb || !binding.store.isOpen || !binding.native.isOpen) {
+        throw new Error('Retained task handle is closed or does not belong to this project binding');
+    }
+    const identity = binding.store.identity;
+    if (identity.scope !== 'project' || !identity.fileDevice || !identity.fileInode) {
+        throw new Error('Retained task handle has no authenticated consolidated file identity');
+    }
+    const current = statSync(identity.dbPath, { bigint: true, throwIfNoEntry: false });
+    if (current &&
+        (String(current.dev) !== identity.fileDevice || String(current.ino) !== identity.fileInode)) {
+        throw new Error('Retained task handle refers to a replaced database generation');
+    }
+    const table = binding.native
+        .prepare("SELECT name FROM main.sqlite_schema WHERE type = 'table' AND name = 'brain_memory_links'")
+        .get();
+    if (!table)
+        throw new Error('Retained consolidated database lacks required brain_memory_links schema');
+    return new BrainDataAccessor(tasksDb);
+}
+async function createMemoryTaskLink(projectRoot, memoryType, memoryId, taskId, linkType, retained) {
+    const accessor = retained ?? (await getBrainAccessor(projectRoot));
     const existingLinks = await accessor.getLinksForMemory(memoryType, memoryId);
     const duplicate = existingLinks.find((l) => l.taskId === taskId && l.linkType === linkType);
     if (duplicate)
@@ -41,6 +67,7 @@ export async function linkMemoryToTask(projectRoot, memoryType, memoryId, taskId
     if (!memoryId || !taskId) {
         throw new Error('memoryId and taskId are required');
     }
+    const retained = tasksDbOverride ? retainedLinkAccessor(projectRoot, tasksDbOverride) : undefined;
     // Write-guard: reject stale task IDs before creating cross-db reference
     let taskExists;
     let tasksDb = null;
@@ -64,7 +91,7 @@ export async function linkMemoryToTask(projectRoot, memoryType, memoryId, taskId
     if (taskExists === false) {
         throw new Error(`Write-guard: task ${taskId} does not exist in tasks.db — refusing to create brain link`);
     }
-    return createMemoryTaskLink(projectRoot, memoryType, memoryId, taskId, linkType);
+    return createMemoryTaskLink(projectRoot, memoryType, memoryId, taskId, linkType, retained);
 }
 /**
  * Link memory to a task whose existence was validated before a multi-write batch.

package/dist/memory/brain-links.js.map

@@ -1 +1 @@
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package/dist/memory/brain-reasoning.d.ts.map

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