@cleocode/core 2026.9.8 → 2026.9.9

package/dist/memory/graph-auto-populate.d.ts.map

@@ -1 +1 @@
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package/dist/memory/graph-auto-populate.js

@@ -7,7 +7,7 @@
  * storePattern, storeLearning, and task completion).
  *
  * Design constraints:
- * - All writes are BEST-EFFORT — never block or fail the primary operation.
+ * - Legacy writes are best-effort; scoped projections propagate failures.
  * - All writes are gated on brain.autoCapture via isAutoCaptureEnabled.
  * - Uses INSERT OR REPLACE (onConflictDoUpdate) for upsert semantics.
  * - Edge inserts are idempotent via the composite PK (fromId, toId, edgeType).
@@ -16,7 +16,11 @@
  * @epic T523
  */
 import { createHash } from 'node:crypto';
+import { resolveCleoConfig } from '../config/registry.js';
 import { getLogger } from '../logger.js';
+import { generateProjectHash } from '../nexus/hash.js';
+import { worktreeScope } from '../paths.js';
+import { assertOperationWriteFence } from '../store/background-jobs.js';
 import { getBrainDb } from '../store/memory-sqlite.js';
 import { brainPageEdges, brainPageNodes } from '../store/schema/memory-schema.js';
 // Structured (pino) logger — writes directly to stderr, NOT through `console.*`.
@@ -43,6 +47,40 @@ async function shouldAutoPopulateGraph(projectRoot) {
         return false;
     }
 }
+/** Read the captured project's policy without silently treating read failures as disabled. */
+async function scopedGraphEnabled(context) {
+    context.assertActive();
+    const config = await resolveCleoConfig({
+        scope: 'merged',
+        projectRoot: context.identity.projectRoot,
+    });
+    context.assertActive();
+    const brain = config['brain'];
+    if (brain === undefined)
+        return true;
+    if (typeof brain !== 'object' || brain === null || Array.isArray(brain)) {
+        throw new Error('Invalid brain configuration for graph projection');
+    }
+    if (!('autoCapture' in brain) || brain.autoCapture === undefined)
+        return true;
+    if (typeof brain.autoCapture !== 'boolean') {
+        throw new Error('Invalid brain.autoCapture configuration for graph projection');
+    }
+    return brain.autoCapture;
+}
+/** Check cancellation and policy for strict callers; retain legacy best-effort behavior. */
+async function graphWriteEnabled(projectRoot, context) {
+    if (!context)
+        return shouldAutoPopulateGraph(projectRoot);
+    context.assertActive();
+    if (projectRoot !== context.identity.projectRoot) {
+        throw new Error('Graph projection root differs from captured operation scope');
+    }
+    if (!(await scopedGraphEnabled(context))) {
+        throw new Error('Graph projection policy disabled during execution');
+    }
+    return true;
+}
 // ---------------------------------------------------------------------------
 // Public API
 // ---------------------------------------------------------------------------
@@ -58,7 +96,7 @@ async function shouldAutoPopulateGraph(projectRoot) {
  * content; their hash will be null so duplicates are not rejected.
  *
  * This function is gated on brain.autoCapture. If the gate is disabled or any
- * error occurs, it returns silently without throwing.
+ * error occurs, legacy calls return silently. Context-aware calls throw failures.
  *
  * @param projectRoot - Absolute path to the project root directory.
  * @param nodeId - Stable composite ID in the form '<type>:<source-id>'.
@@ -67,49 +105,77 @@ async function shouldAutoPopulateGraph(projectRoot) {
  * @param qualityScore - 0.0 (noise) to 1.0 (canonical).
  * @param content - Canonical text used to derive the content hash.
  * @param metadata - Optional type-specific metadata blob.
+ * @param context - Captured scope; when supplied, failures throw and writes check cancellation.
  *
+ * @remarks Scoped calls pin storage routing and refuse to join an unowned transaction.
+ * @example
+ * ```ts
+ * await upsertGraphNode(root, 'task:T123', 'task', 'Task', 0.7, '');
+ * ```
  * @task T537
  */
-export async function upsertGraphNode(projectRoot, nodeId, nodeType, label, qualityScore, content, metadata) {
-    try {
-        if (!(await shouldAutoPopulateGraph(projectRoot)))
-            return;
-        const db = await getBrainDb(projectRoot);
-        const now = new Date().toISOString().replace('T', ' ').slice(0, 19);
-        // Only compute a content hash for non-trivial content (external reference
-        // nodes like task/session/epic may have empty content).
-        const trimmed = content.trim().toLowerCase();
-        const contentHash = trimmed
-            ? createHash('sha256').update(trimmed).digest('hex').substring(0, 16)
-            : null;
-        await db
-            .insert(brainPageNodes)
-            .values({
-            id: nodeId,
-            nodeType,
-            label: label.substring(0, 200),
-            qualityScore,
-            contentHash,
-            metadataJson: metadata ? JSON.stringify(metadata) : null,
-            lastActivityAt: now,
-            createdAt: now,
-            updatedAt: now,
-        })
-            .onConflictDoUpdate({
-            target: brainPageNodes.id,
-            set: {
+export async function upsertGraphNode(projectRoot, nodeId, nodeType, label, qualityScore, content, metadata, context) {
+    const write = async () => {
+        try {
+            if (!(await graphWriteEnabled(projectRoot, context)))
+                return;
+            context?.assertActive();
+            const db = await getBrainDb(projectRoot);
+            context?.assertActive();
+            const now = new Date().toISOString().replace('T', ' ').slice(0, 19);
+            // Only compute a content hash for non-trivial content (external reference
+            // nodes like task/session/epic may have empty content).
+            const trimmed = content.trim().toLowerCase();
+            const contentHash = trimmed
+                ? createHash('sha256').update(trimmed).digest('hex').substring(0, 16)
+                : null;
+            const query = db
+                .insert(brainPageNodes)
+                .values({
+                id: nodeId,
+                nodeType,
                 label: label.substring(0, 200),
                 qualityScore,
+                contentHash,
+                metadataJson: metadata ? JSON.stringify(metadata) : null,
                 lastActivityAt: now,
+                createdAt: now,
                 updatedAt: now,
-                metadataJson: metadata ? JSON.stringify(metadata) : null,
-            },
-        });
-    }
-    catch (err) {
-        // Log but never surface — this is a best-effort side effect.
-        log.warn({ err }, 'upsertGraphNode failed');
-    }
+            })
+                .onConflictDoUpdate({
+                target: brainPageNodes.id,
+                set: {
+                    label: label.substring(0, 200),
+                    qualityScore,
+                    lastActivityAt: now,
+                    updatedAt: now,
+                    metadataJson: metadata ? JSON.stringify(metadata) : null,
+                },
+            });
+            if (context) {
+                db.transaction((tx) => {
+                    assertOperationWriteFence(tx, context);
+                    query.run();
+                });
+            }
+            else {
+                query.run();
+            }
+        }
+        catch (err) {
+            if (context)
+                throw err;
+            // Log but never surface — this is a best-effort side effect.
+            log.warn({ err }, 'upsertGraphNode failed');
+        }
+    };
+    return context
+        ? worktreeScope.run({
+            worktreeRoot: context.identity.projectRoot,
+            projectHash: generateProjectHash(context.identity.projectRoot),
+            execution: context,
+        }, write)
+        : write();
 }
 /**
  * Add a directed, typed edge between two graph nodes (idempotent).
@@ -119,7 +185,7 @@ export async function upsertGraphNode(projectRoot, nodeId, nodeType, label, qual
  * multiple times with the same arguments.
  *
  * This function is gated on brain.autoCapture. If the gate is disabled or any
- * error occurs, it returns silently without throwing.
+ * error occurs, legacy calls return silently. Context-aware calls throw failures.
  *
  * @param projectRoot - Absolute path to the project root directory.
  * @param fromId - Source node ID (brain_page_nodes.id).
@@ -127,30 +193,58 @@ export async function upsertGraphNode(projectRoot, nodeId, nodeType, label, qual
  * @param edgeType - Typed relationship from BRAIN_EDGE_TYPES.
  * @param weight - Edge confidence/weight (0.0–1.0). Defaults to 1.0.
  * @param provenance - Human-readable note on why this edge was emitted.
+ * @param context - Captured scope; when supplied, failures throw and writes check cancellation.
  *
+ * @remarks Scoped calls pin storage routing and refuse to join an unowned transaction.
+ * @example
+ * ```ts
+ * await addGraphEdge(root, 'task:T123', 'llmtxt:hash', 'embeds');
+ * ```
  * @task T537
  */
-export async function addGraphEdge(projectRoot, fromId, toId, edgeType, weight = 1.0, provenance) {
-    try {
-        if (!(await shouldAutoPopulateGraph(projectRoot)))
-            return;
-        const db = await getBrainDb(projectRoot);
-        const now = new Date().toISOString().replace('T', ' ').slice(0, 19);
-        await db
-            .insert(brainPageEdges)
-            .values({
-            fromId,
-            toId,
-            edgeType,
-            weight,
-            provenance: provenance ?? null,
-            createdAt: now,
-        })
-            .onConflictDoNothing();
-    }
-    catch (err) {
-        log.warn({ err }, 'addGraphEdge failed');
-    }
+export async function addGraphEdge(projectRoot, fromId, toId, edgeType, weight = 1.0, provenance, context) {
+    const write = async () => {
+        try {
+            if (!(await graphWriteEnabled(projectRoot, context)))
+                return;
+            context?.assertActive();
+            const db = await getBrainDb(projectRoot);
+            context?.assertActive();
+            const now = new Date().toISOString().replace('T', ' ').slice(0, 19);
+            const query = db
+                .insert(brainPageEdges)
+                .values({
+                fromId,
+                toId,
+                edgeType,
+                weight,
+                provenance: provenance ?? null,
+                createdAt: now,
+            })
+                .onConflictDoNothing();
+            if (context) {
+                db.transaction((tx) => {
+                    assertOperationWriteFence(tx, context);
+                    query.run();
+                });
+            }
+            else {
+                query.run();
+            }
+        }
+        catch (err) {
+            if (context)
+                throw err;
+            log.warn({ err }, 'addGraphEdge failed');
+        }
+    };
+    return context
+        ? worktreeScope.run({
+            worktreeRoot: context.identity.projectRoot,
+            projectHash: generateProjectHash(context.identity.projectRoot),
+            execution: context,
+        }, write)
+        : write();
 }
 // ---------------------------------------------------------------------------
 // T945 Stage A — universal semantic graph hooks
@@ -237,6 +331,34 @@ export async function ensureLlmtxtNode(projectRoot, sha256, ownerId, label) {
         log.warn({ err }, 'ensureLlmtxtNode failed');
     }
 }
+/**
+ * Project a canonical document into the graph with captured scope and visible failures.
+ *
+ * @remarks Each synchronous write checks the same absolute deadline. This does not preempt
+ * SQLite or promise atomicity across the node and edge; a failed edge leaves an
+ * idempotently resumable partial projection. Canonical document bytes are untouched.
+ *
+ * @param context - Caller-owned immutable identity, deadline and cancellation.
+ * @param sha256 - Canonical document content hash.
+ * @param ownerId - Qualified graph owner identity.
+ * @param label - Document display label.
+ * @returns Completed or explicitly disabled graph projection in the captured project.
+ * @throws Error - Configuration, storage, cancellation or deadline failure.
+ * @example
+ * ```ts
+ * const result = await ensureLlmtxtNodeScoped(context, sha256, 'task:T123', 'Design');
+ * ```
+ */
+export async function ensureLlmtxtNodeScoped(context, sha256, ownerId, label) {
+    const identity = context.identity;
+    const result = { projectId: identity.projectId, projectRoot: identity.projectRoot };
+    if (!(await scopedGraphEnabled(context)))
+        return { ...result, status: 'disabled' };
+    const nodeId = `llmtxt:${sha256}`;
+    await upsertGraphNode(identity.projectRoot, nodeId, 'llmtxt', label, 0.8, sha256, { sha256 }, context);
+    await addGraphEdge(identity.projectRoot, ownerId, nodeId, 'embeds', 1, 'auto:docs-add', context);
+    return { ...result, status: 'completed' };
+}
 /**
  * Upsert a `msg:<id>` graph node for a CONDUIT message and, when the message
  * body references one or more `T###` task IDs, emit `discusses` edges from

package/dist/memory/graph-auto-populate.js.map

@@ -1 +1 @@
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package/dist/memory/graph-memory-bridge.d.ts

@@ -17,6 +17,7 @@
  * @task graph-memory-bridge
  * @epic T523
  */
+import type { DecisionCodeEvidenceLink } from '@cleocode/contracts';
 import { getNexusNativeDb } from '../store/nexus-sqlite.js';
 /** A single code-reference link created or found by the bridge. */
 export interface CodeReferenceLink {
@@ -54,6 +55,8 @@ export interface MemoriesForCodeResult {
         qualityScore: number;
         edgeWeight: number;
         matchStrategy: string;
+        /** Explicit verified source provenance when this is a sourced decision relation. */
+        provenance?: DecisionCodeEvidenceLink;
     }>;
 }
 /** Result from queryCodeForMemory. */
@@ -68,6 +71,8 @@ export interface CodeForMemoryResult {
         kind: string;
         edgeWeight: number;
         matchStrategy: string;
+        /** Explicit verified source provenance when this is a sourced decision relation. */
+        provenance?: DecisionCodeEvidenceLink;
     }>;
 }
 /**
@@ -98,7 +103,13 @@ export declare function linkMemoryToCode(projectRoot: string, memoryId: string,
  * @param filesModifiedJson - JSON array of file paths (may be null)
  * @param projectRoot - Absolute path to project root
  * @param nexusNative - Optional pre-loaded nexus database handle
- * @returns Count of edges written
+ * @returns Count of newly written edges; repeated calls preserve existing history.
+ * @remarks Only canonical file nodes are eligible. File evidence does not establish symbol-level changes;
+ * revision is explicitly unrecorded when the observation does not supply one.
+ * @example
+ * ```ts
+ * const written = await linkObservationToModifiedFiles(observationId, filePathsJson, projectRoot, undefined);
+ * ```
  */
 export declare function linkObservationToModifiedFiles(obsId: string, filesModifiedJson: string | null, projectRoot: string, nexusNative?: ReturnType<typeof getNexusNativeDb>): Promise<number>;
 /**
@@ -176,6 +187,8 @@ export declare function queryMemoriesForCode(projectRoot: string, symbol: string
 export declare function queryCodeForMemory(projectRoot: string, memoryId: string): Promise<CodeForMemoryResult>;
 /** A single code-memory link for display. */
 export interface CodeLinkEntry {
+    /** Explicit sourced relation metadata, when present. */
+    provenance?: DecisionCodeEvidenceLink;
     /** Brain memory node ID. */
     brainNodeId: string;
     /** Brain node type. */

package/dist/memory/graph-memory-bridge.d.ts.map

@@ -1 +1 @@
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package/dist/memory/graph-memory-bridge.js

@@ -26,6 +26,7 @@ import { brainPageEdges, brainPageNodes } from '../store/schema/memory-schema.js
 import { applyPerfPragmas } from '../store/sqlite-pragmas.js';
 import { typedAll } from '../store/typed-query.js';
 import { withWriterLease } from '../store/writer-lease.js';
+import { isCurrentDecisionCodeEvidence, linkDecisionToCodeEvidence, readDecisionCodeEvidence, } from './decision-cross-link.js';
 const _require = createRequire(import.meta.url);
 const { DatabaseSync } = _require('node:sqlite');
 // ---------------------------------------------------------------------------
@@ -143,11 +144,19 @@ function metadataText(metaJson) {
  * @returns True if the edge was created or already existed; false on error
  */
 export async function linkMemoryToCode(projectRoot, memoryId, codeSymbol) {
+    if (memoryId.startsWith('decision:')) {
+        const result = await linkDecisionToCodeEvidence(projectRoot, memoryId, {
+            symbols: [codeSymbol],
+            apply: true,
+        });
+        return (result.links.some((link) => link.targetId === codeSymbol) &&
+            !result.findings.some((finding) => finding.state === 'failed'));
+    }
     try {
         const brainDb = await getBrainDb(projectRoot);
         // Ensure nexus.db is initialized so we can verify the target node exists
-        await getNexusDb();
-        const nexusNative = getNexusNativeDb();
+        await getNexusDb(projectRoot);
+        const nexusNative = getNexusNativeDb(projectRoot);
         if (!nexusNative)
             return false;
         // Verify the nexus node exists (read-only check)
@@ -212,7 +221,13 @@ export async function linkMemoryToCode(projectRoot, memoryId, codeSymbol) {
  * @param filesModifiedJson - JSON array of file paths (may be null)
  * @param projectRoot - Absolute path to project root
  * @param nexusNative - Optional pre-loaded nexus database handle
- * @returns Count of edges written
+ * @returns Count of newly written edges; repeated calls preserve existing history.
+ * @remarks Only canonical file nodes are eligible. File evidence does not establish symbol-level changes;
+ * revision is explicitly unrecorded when the observation does not supply one.
+ * @example
+ * ```ts
+ * const written = await linkObservationToModifiedFiles(observationId, filePathsJson, projectRoot, undefined);
+ * ```
  */
 export async function linkObservationToModifiedFiles(obsId, filesModifiedJson, projectRoot, nexusNative) {
     let edgeCount = 0;
@@ -223,7 +238,7 @@ export async function linkObservationToModifiedFiles(obsId, filesModifiedJson, p
         const brainNative = getBrainNativeDb(projectRoot);
         if (!brainNative)
             return 0;
-        const nexusDb = nexusNative ?? getNexusNativeDb();
+        const nexusDb = nexusNative ?? getNexusNativeDb(projectRoot);
         if (!nexusDb)
             return 0;
         const filesArray = JSON.parse(filesModifiedJson);
@@ -235,20 +250,26 @@ export async function linkObservationToModifiedFiles(obsId, filesModifiedJson, p
                 continue;
             // Find nexus node by exact file path match
             const nexusNode = nexusDb
-                .prepare('SELECT id FROM nexus_nodes WHERE file_path = ? LIMIT 1')
-                .get(filePath);
-            if (!nexusNode)
+                .prepare("SELECT id FROM main.nexus_nodes WHERE id = ? AND file_path = ? AND kind = 'file'")
+                .get(filePath, filePath);
+            if (typeof nexusNode?.id !== 'string')
                 continue;
             // Write modified_by edge (file → observation)
             try {
-                brainNative
+                const inserted = brainNative
                     .prepare(`
-            INSERT OR IGNORE INTO brain_page_edges
+            INSERT OR IGNORE INTO main.brain_page_edges
               (from_id, to_id, edge_type, weight, provenance, created_at)
-            VALUES (?, ?, 'modified_by', 1.0, 'auto:file-modify', ?)
+            VALUES (?, ?, 'modified_by', 1.0, ?, ?)
           `)
-                    .run(nexusNode.id, obsId, now);
-                edgeCount++;
+                    .run(nexusNode.id, obsId, JSON.stringify({
+                    source: 'observation.files_modified_json',
+                    observationId: obsId,
+                    precision: 'file',
+                    filePath,
+                    assessedRevision: null,
+                }), now);
+                edgeCount += Number(inserted.changes);
             }
             catch (err) {
                 console.warn('[graph-memory-bridge] modified_by edge insert failed:', err);
@@ -287,7 +308,7 @@ export async function linkObservationToMentionedSymbols(obsId, text, projectRoot
         const brainNative = getBrainNativeDb(projectRoot);
         if (!brainNative)
             return 0;
-        const nexusDb = nexusNative ?? getNexusNativeDb();
+        const nexusDb = nexusNative ?? getNexusNativeDb(projectRoot);
         if (!nexusDb)
             return 0;
         const nexusNames = typedAll(nexusDb.prepare('SELECT id, name FROM nexus_nodes WHERE name IS NOT NULL LIMIT 10000'));
@@ -310,7 +331,9 @@ export async function linkObservationToMentionedSymbols(obsId, text, projectRoot
         const now = new Date().toISOString().replace('T', ' ').slice(0, 19);
         // Write mentions edges
         for (const name of matches) {
-            const nexusNode = nexusNames.find((n) => n.name === name);
+            const matches = nexusNames.filter((node) => node.name === name);
+            const qualified = matches.filter((node) => text.includes(node.id));
+            const nexusNode = qualified.length === 1 ? qualified[0] : matches.length === 1 ? matches[0] : undefined;
             if (!nexusNode)
                 continue;
             try {
@@ -360,7 +383,7 @@ export async function linkDecisionToSymbols(decisionId, contextText, projectRoot
         const brainNative = getBrainNativeDb(projectRoot);
         if (!brainNative)
             return 0;
-        const nexusDb = nexusNative ?? getNexusNativeDb();
+        const nexusDb = nexusNative ?? getNexusNativeDb(projectRoot);
         if (!nexusDb)
             return 0;
         const nexusNames = typedAll(nexusDb.prepare('SELECT id, name FROM nexus_nodes WHERE name IS NOT NULL LIMIT 10000'));
@@ -383,7 +406,9 @@ export async function linkDecisionToSymbols(decisionId, contextText, projectRoot
         const now = new Date().toISOString().replace('T', ' ').slice(0, 19);
         // Write documents edges
         for (const name of matches) {
-            const nexusNode = nexusNames.find((n) => n.name === name);
+            const matches = nexusNames.filter((node) => node.name === name);
+            const qualified = matches.filter((node) => contextText.includes(node.id));
+            const nexusNode = qualified.length === 1 ? qualified[0] : matches.length === 1 ? matches[0] : undefined;
             if (!nexusNode)
                 continue;
             try {
@@ -432,8 +457,8 @@ export async function autoLinkMemories(projectRoot) {
     try {
         await getBrainDb(projectRoot);
         const brainNative = getBrainNativeDb(projectRoot);
-        await getNexusDb();
-        const nexusNative = getNexusNativeDb();
+        await getNexusDb(projectRoot);
+        const nexusNative = getNexusNativeDb(projectRoot);
         if (!brainNative || !nexusNative)
             return result;
         // Load all brain page nodes that are memory entity types
@@ -651,13 +676,18 @@ export async function queryMemoriesForCode(projectRoot, symbol) {
         ORDER BY e.weight DESC, n.quality_score DESC
         LIMIT 50
       `), symbol);
-        result.memories = rows.map((r) => ({
+        result.memories = rows
+            .filter((row) => isCurrentDecisionCodeEvidence(brainNative, row.provenance))
+            .map((r) => ({
             nodeId: r.id,
             nodeType: r.node_type,
             label: r.label,
             qualityScore: r.quality_score,
             edgeWeight: r.weight,
-            matchStrategy: r.provenance?.replace('auto:', '') ?? 'manual',
+            matchStrategy: readDecisionCodeEvidence(r.provenance)
+                ? 'explicit-decision-evidence'
+                : (r.provenance?.replace('auto:', '') ?? 'manual'),
+            provenance: readDecisionCodeEvidence(r.provenance) ?? undefined,
         }));
     }
     catch (err) {
@@ -683,8 +713,8 @@ export async function queryCodeForMemory(projectRoot, memoryId) {
     try {
         await getBrainDb(projectRoot);
         const brainNative = getBrainNativeDb(projectRoot);
-        await getNexusDb();
-        const nexusNative = getNexusNativeDb();
+        await getNexusDb(projectRoot);
+        const nexusNative = getNexusNativeDb(projectRoot);
         if (!brainNative || !nexusNative)
             return result;
         const brainEdges = typedAll(brainNative.prepare(`
@@ -699,6 +729,8 @@ export async function queryCodeForMemory(projectRoot, memoryId) {
             return result;
         // Fetch nexus node metadata for each target (read-only)
         for (const edge of brainEdges) {
+            if (!isCurrentDecisionCodeEvidence(brainNative, edge.provenance))
+                continue;
             const nexusNode = nexusNative
                 .prepare('SELECT id, label, file_path, kind FROM nexus_nodes WHERE id = ? LIMIT 1')
                 .get(edge.to_id);
@@ -709,7 +741,10 @@ export async function queryCodeForMemory(projectRoot, memoryId) {
                     filePath: nexusNode.file_path,
                     kind: nexusNode.kind,
                     edgeWeight: edge.weight,
-                    matchStrategy: edge.provenance?.replace('auto:', '') ?? 'manual',
+                    matchStrategy: readDecisionCodeEvidence(edge.provenance)
+                        ? 'explicit-decision-evidence'
+                        : (edge.provenance?.replace('auto:', '') ?? 'manual'),
+                    provenance: readDecisionCodeEvidence(edge.provenance) ?? undefined,
                 });
             }
         }
@@ -733,12 +768,12 @@ export async function listCodeLinks(projectRoot, limit = 100) {
     try {
         await getBrainDb(projectRoot);
         const brainNative = getBrainNativeDb(projectRoot);
-        await getNexusDb();
-        const nexusNative = getNexusNativeDb();
+        await getNexusDb(projectRoot);
+        const nexusNative = getNexusNativeDb(projectRoot);
         if (!brainNative || !nexusNative)
             return entries;
         const rows = typedAll(brainNative.prepare(`
-        SELECT e.from_id, e.to_id, e.weight, e.created_at,
+        SELECT e.from_id, e.to_id, e.weight, e.created_at, e.provenance,
                n.node_type, n.label
         FROM brain_page_edges e
         JOIN brain_page_nodes n ON n.id = e.from_id
@@ -747,10 +782,13 @@ export async function listCodeLinks(projectRoot, limit = 100) {
         LIMIT ?
       `), limit);
         for (const row of rows) {
+            if (!isCurrentDecisionCodeEvidence(brainNative, row.provenance))
+                continue;
             const nexusNode = nexusNative
                 .prepare('SELECT id, label, file_path, kind FROM nexus_nodes WHERE id = ? LIMIT 1')
                 .get(row.to_id);
             entries.push({
+                provenance: readDecisionCodeEvidence(row.provenance) ?? undefined,
                 brainNodeId: row.from_id,
                 brainNodeType: row.node_type,
                 brainNodeLabel: row.label,
@@ -910,8 +948,8 @@ export async function linkConduitMessagesToSymbols(projectRoot) {
             await getBrainDb(projectRoot);
             const brainNative = getBrainNativeDb(projectRoot);
             // Ensure nexus.db is available for symbol lookup
-            await getNexusDb();
-            const nexusNative = getNexusNativeDb();
+            await getNexusDb(projectRoot);
+            const nexusNative = getNexusNativeDb(projectRoot);
             if (!brainNative || !nexusNative)
                 return result;
             // T11545: plasticity weight lives in the sibling nexus_relation_weights