@cleocode/core 2026.9.8 → 2026.9.9

package/dist/nexus/analyze-orchestrator.js

@@ -1,15 +1,157 @@
 /**
  * Nexus analyze orchestrator — business logic extracted from `cleo nexus analyze`.
  *
- * Runs the code-intelligence pipeline, clears the existing index for full runs,
+ * Stages a replacement code graph and publishes it atomically,
  * refreshes the nexus-bridge, updates the multi-project registry, and sweeps
- * the git log for task–symbol links. All side-effects are best-effort and do
- * not fail the pipeline on error.
+ * the git log for task–symbol links. Post-publication hooks are best-effort.
  *
  * @module nexus/analyze-orchestrator
  * @epic T9833
  * @task T10062
  */
+import { randomUUID } from 'node:crypto';
+import { realpath } from 'node:fs/promises';
+import { resolve } from 'node:path';
+import { sql } from 'drizzle-orm';
+import { z } from 'zod';
+import { worktreeScope } from '../paths.js';
+import { getProjectInfo } from '../project-info.js';
+import { createParserExecutionPort } from '../resources/spawn-wrapper.js';
+import { nexusNodes, nexusRelations } from '../store/schema/cleo-project/nexus-graph.js';
+import { generateProjectHash } from './hash.js';
+import { readKnowledgeIndexAssessment } from './knowledge.js';
+import { resolveSourceRoots } from './source-roots.js';
+/** Compare ownership and observed revisions without treating observation time as a change. */
+function rootFingerprint(roots) {
+    return JSON.stringify({
+        projectId: roots.projectId,
+        projectRoot: roots.projectRoot,
+        sourceRoot: roots.sourceRoot,
+        roots: roots.roots.map((root) => ({
+            requestedPath: root.requestedPath,
+            canonicalPath: root.canonicalPath,
+            graphPrefix: root.graphPrefix,
+            explicitlyIncluded: root.explicitlyIncluded,
+            revision: root.revision,
+            status: root.status,
+            diagnostics: root.diagnostics,
+        })),
+    });
+}
+/** Fail closed when a required root observation did not finish successfully. */
+function requireObservedRoots(roots) {
+    const failed = roots.roots.filter((root) => root.status !== 'available' && root.status !== 'unversioned');
+    if (failed.length)
+        throw new Error(`Source-root observation incomplete; previous graph retained: ${failed.map((root) => `${root.requestedPath}: ${root.diagnostics.join('; ')}`).join(' | ')}`);
+}
+/** Verify persisted parent identity without promoting a legacy path hash into authority. */
+async function readAnalysisIdentity(projectRoot, previousRoots, projectIdOverride) {
+    const canonicalParent = await realpath(projectRoot);
+    if (previousRoots && previousRoots.projectRoot !== canonicalParent)
+        throw new Error('Stored graph ownership differs from the current project root; previous graph retained.');
+    let projectId;
+    try {
+        const info = await getProjectInfo(projectRoot);
+        projectId = info.projectId || info.projectHash;
+    }
+    catch (error) {
+        if (!(error instanceof Error && 'code' in error && error.code === 'ENOENT'))
+            throw error;
+        projectId = previousRoots?.projectId;
+    }
+    if (!projectId)
+        throw new Error('Stable project identity is unavailable; initialize this project or restore its verified project identity.');
+    if (previousRoots && previousRoots.projectId !== projectId)
+        throw new Error('Stored graph identity differs from the current project identity; previous graph retained.');
+    if (projectIdOverride !== undefined && projectIdOverride !== projectId)
+        throw new Error('Explicit analysis identity differs from the verified project identity.');
+    return projectId;
+}
+/** Preserve explicitly selected nested repository scope on routine reindexing. */
+function includedRepositoryScope(db, repoPath) {
+    return db
+        .values(sql `SELECT repositories.value
+    FROM main._nexus_meta, json_each(json_extract(_nexus_meta.value, '$.includedRepositories')) AS repositories
+    WHERE _nexus_meta.key = 'graph_assessment'
+      AND json_extract(_nexus_meta.value, '$.sourceRoot') = ${repoPath}`)
+        .map((row) => {
+        const repository = row[0];
+        if (typeof repository !== 'string')
+            throw new Error('Invalid saved nested repository scope');
+        return repository;
+    });
+}
+/** Read the last committed graph generation without opening a write transaction. */
+function graphGeneration(db) {
+    const value = db.values(sql `SELECT value FROM main._nexus_meta WHERE key = 'graph_generation'`)[0]?.[0];
+    return typeof value === 'string' ? value : null;
+}
+/**
+ * Atomically publish staged rows if the graph has not changed since assessment.
+ * Failed inserts, FTS repair, or stale generations roll back the entire replacement.
+ * Code placed in `packages/core/` per Package-Boundary Check — verified against AGENTS.md.
+ * @param db - Owning project graph database with the canonical schema installed.
+ * @param rows - Validated staged nodes, relations and source assessment to publish.
+ * @param expectedGeneration - Previously observed generation; null for the first publication.
+ * @remarks The transaction rejects stale generation preconditions and restores the
+ * prior live rows on failure. Successful replacement does not itself retain an
+ * independently recoverable historical generation.
+ * @example
+ * ```ts
+ * publishNexusGraph(db, stagedRows, expectedGeneration);
+ * ```
+ */
+export function publishNexusGraph(db, rows, expectedGeneration) {
+    const generation = rows.generation ?? randomUUID();
+    if (rows.generation !== undefined) {
+        z.uuid().parse(generation);
+        if (generation === expectedGeneration)
+            throw new Error('Publication generation must be a fresh immutable identity');
+        if (rows.assessment?.generation !== generation)
+            throw new Error('Staged assessment publication generation does not match rows');
+        if (rows.assessment.references?.some((reference) => reference.publicationGeneration !== undefined &&
+            reference.publicationGeneration !== generation))
+            throw new Error('Staged reference publication generation does not match rows');
+    }
+    db.transaction((tx) => {
+        if (graphGeneration(tx) !== expectedGeneration) {
+            throw new Error('Nexus graph changed during indexing; discard staged generation and retry.');
+        }
+        tx.delete(nexusRelations).run();
+        tx.delete(nexusNodes).run();
+        // The optional FTS shadow can contain orphaned rowids; reset it inside
+        // the same transaction so trigger failures restore the previous generation.
+        if (tx.values(sql `SELECT name FROM main.sqlite_master WHERE name = 'nexus_symbols_fts'`)
+            .length > 0) {
+            tx.run(sql `DELETE FROM main.nexus_symbols_fts`);
+        }
+        for (let offset = 0; offset < rows.nodes.length; offset += 500) {
+            tx.insert(nexusNodes)
+                .values(rows.nodes.slice(offset, offset + 500))
+                .run();
+        }
+        for (let offset = 0; offset < rows.relations.length; offset += 500) {
+            tx.insert(nexusRelations)
+                .values(rows.relations.slice(offset, offset + 500))
+                .run();
+        }
+        if (rows.generation !== undefined &&
+            tx.values(sql `
+        SELECT id FROM main.nexus_nodes
+        WHERE json_extract(meta_json, '$.lexicalCapability') = 'typescript-javascript'
+          AND json_extract(meta_json, '$.publicationGeneration') IS NOT ${generation}
+        LIMIT 1
+      `).length > 0) {
+            throw new Error('Staged lexical declaration publication generation does not match rows');
+        }
+        if (rows.assessment) {
+            tx.run(sql `INSERT INTO main._nexus_meta (key, value) VALUES ('graph_assessment', ${JSON.stringify(rows.assessment)})
+        ON CONFLICT(key) DO UPDATE SET value = excluded.value, updated_at = strftime('%s', 'now')`);
+        }
+        tx.run(sql `INSERT INTO main._nexus_meta (key, value) VALUES ('graph_generation', ${generation})
+      ON CONFLICT(key) DO UPDATE SET value = excluded.value, updated_at = strftime('%s', 'now')`);
+    }, { behavior: 'immediate' });
+}
 // ---------------------------------------------------------------------------
 // Public API
 // ---------------------------------------------------------------------------
@@ -17,82 +159,138 @@
  * Run the nexus code-intelligence pipeline on a repository.
  *
  * This function:
- * 1. Derives the project ID.
- * 2. For full runs, clears the existing nexus index.
- * 3. Runs `@cleocode/nexus` pipeline.
+ * 1. Captures the existing parent identity and explicit source roots.
+ * 2. Captures the current graph generation for concurrent-write detection.
+ * 3. Stages and atomically publishes the `@cleocode/nexus` pipeline output.
  * 4. Best-effort: refreshes `nexus-bridge.md`.
  * 5. Best-effort: updates the multi-project registry.
  * 6. Best-effort: sweeps the git log for task–symbol links.
  *
  * @param params - Analysis configuration
  * @returns Pipeline result with node/relation/file counts and duration
- * @throws {Error} When the pipeline itself fails (best-effort steps never throw)
+ * @throws {Error} When identity, source preconditions or the pipeline fail.
+ * @remarks Root revisions and file hashes are optimistic preconditions, not a
+ * filesystem lock. Publication uses the owning store's synchronous generation CAS;
+ * optional post-publication hooks cannot replace its committed result.
+ * @example
+ * ```ts
+ * const result = await runNexusAnalysis({ repoPath: '/identity', includedRepositories: ['app'] });
+ * ```
  */
 export async function runNexusAnalysis(params) {
-    const { repoPath, projectIdOverride, incremental = false, onProgress } = params;
+    const captured = {
+        ...params,
+        parserLimits: params.parserLimits ? { ...params.parserLimits } : undefined,
+        includedRepositories: params.includedRepositories
+            ? [...params.includedRepositories]
+            : undefined,
+    };
+    const projectRoot = resolve(captured.projectRoot ?? captured.repoPath);
+    const inherited = worktreeScope.getStore();
+    if (inherited?.execution && resolve(inherited.execution.identity.projectRoot) !== projectRoot)
+        throw new Error('Analysis project differs from captured execution scope.');
+    return worktreeScope.run({ ...inherited, worktreeRoot: projectRoot, projectHash: generateProjectHash(projectRoot) }, () => runScopedNexusAnalysis(captured, projectRoot));
+}
+/** Keep the entire asynchronous analysis bound to its captured identity parent. */
+async function runScopedNexusAnalysis(params, projectRoot) {
+    const { projectIdOverride, incremental = false, onProgress } = params;
+    const execution = worktreeScope.getStore()?.execution;
+    execution?.assertActive();
+    const signals = [params.parserLimits?.signal, execution?.signal].filter((signal) => signal !== undefined);
+    const signal = signals.length ? AbortSignal.any(signals) : undefined;
+    signal?.throwIfAborted();
     const startTime = Date.now();
     // SSoT-EXEMPT:pipeline-progress — requires direct DB handle access and a
     // progress callback that is CLI-only. Extracted here to keep the core
     // runnable without the CLI layer, but the DB/pipeline imports still happen
     // via dynamic imports so the CLI controls when heavy deps are loaded.
-    const [{ getNexusDb, nexusSchema }, { runPipeline }] = await Promise.all([
+    const [{ getNexusDb, nexusSchema }, { runPipeline, walkRepositoryPaths }] = await Promise.all([
         import('@cleocode/core/store/nexus-sqlite'),
         import('@cleocode/nexus/pipeline'),
     ]);
-    const projectId = projectIdOverride ?? Buffer.from(repoPath).toString('base64url').slice(0, 32);
-    const db = await getNexusDb();
+    const db = await getNexusDb(projectRoot);
+    const expectedGeneration = graphGeneration(db);
+    const previousAssessment = await readKnowledgeIndexAssessment(projectRoot);
+    const projectId = await readAnalysisIdentity(projectRoot, previousAssessment?.sourceRoots, projectIdOverride);
+    if (execution && execution.identity.projectId !== projectId)
+        throw new Error('Analysis identity differs from captured execution scope.');
     const tables = {
         nexusNodes: nexusSchema.nexusNodes,
         nexusRelations: nexusSchema.nexusRelations,
     };
-    if (!incremental) {
-        // ADR-090 · T11648: the graph is project-scoped (one project per `cleo.db`),
-        // so a non-incremental reindex clears the WHOLE graph table — the former
-        // `WHERE project_id = ?` predicate is dropped.
-        try {
-            db.delete(nexusSchema.nexusNodes).run();
-        }
-        catch {
-            // table may be empty — ignore
-        }
-        try {
-            db.delete(nexusSchema.nexusRelations).run();
-        }
-        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 requestedSource = resolve(params.repoPath);
+    const includedRepositories = params.includedRepositories ?? includedRepositoryScope(db, requestedSource);
+    const rootRequest = {
+        projectId,
+        projectRoot,
+        sourceRoot: requestedSource,
+        includedRepositories,
+        signal,
+        ...(execution ? { deadline: execution.deadlineAt } : {}),
+    };
+    const sourceRoots = await resolveSourceRoots(rootRequest);
+    requireObservedRoots(sourceRoots);
+    execution?.assertActive();
+    const repoPath = sourceRoots.sourceRoot;
+    const assessedRevision = sourceRoots.roots[0]?.revision ?? null;
+    const unchangedRoots = previousAssessment?.sourceRoots !== undefined &&
+        rootFingerprint(previousAssessment.sourceRoots) === rootFingerprint(sourceRoots);
+    const useIncremental = incremental && expectedGeneration !== null && unchangedRoots;
+    let committedAssessment = null;
+    const recheckRoots = async () => {
+        execution?.assertActive();
+        if ((await readAnalysisIdentity(projectRoot, previousAssessment?.sourceRoots, projectIdOverride)) !== projectId)
+            throw new Error('Project identity changed during indexing; previous graph retained.');
+        const currentRoots = await resolveSourceRoots(rootRequest);
+        requireObservedRoots(currentRoots);
+        execution?.assertActive();
+        signal?.throwIfAborted();
+        if (rootFingerprint(currentRoots) !== rootFingerprint(sourceRoots))
+            throw new Error('Source ownership or revision changed during indexing; previous graph retained.');
+    };
+    const recheckFiles = async (assessment) => {
+        // Git observation yields. Reuse the full walker after it so an edit,
+        // addition, rename or deletion during that await cannot publish stale bytes.
+        const failures = [];
+        const currentFiles = await walkRepositoryPaths(repoPath, undefined, (report) => {
+            if (report.status === 'failed')
+                failures.push(report.path);
+        }, includedRepositories);
+        const recorded = new Map(assessment.files
+            .filter((file) => file.contentHash)
+            .map((file) => [file.path, file.contentHash]));
+        if (failures.length ||
+            currentFiles.length !== recorded.size ||
+            currentFiles.some((file) => !file.contentHash || recorded.get(file.path) !== file.contentHash))
+            throw new Error('Source files changed before publication; previous graph retained.');
+    };
     const result = await runPipeline(repoPath, projectId, db, tables, onProgress, {
-        incremental,
+        parserExecution: createParserExecutionPort(),
+        parserLimits: { ...params.parserLimits, signal },
+        incremental: useIncremental,
+        assessedRevision,
+        sourceRoots,
+        includedRepositories,
+        publishGraph: async (rows) => {
+            await recheckRoots();
+            if (!rows.assessment?.sourceRoots ||
+                rootFingerprint(rows.assessment.sourceRoots) !== rootFingerprint(sourceRoots))
+                throw new Error('Staged source ownership does not match the assessed roots.');
+            await recheckFiles(rows.assessment);
+            execution?.assertActive();
+            signal?.throwIfAborted();
+            publishNexusGraph(db, rows, expectedGeneration);
+            committedAssessment = rows.assessment;
+        },
     });
+    if (!committedAssessment && previousAssessment) {
+        // Incremental no-op still needs current provenance: Git or source bytes can
+        // change while the pipeline scans without ever invoking the publisher.
+        await recheckRoots();
+        await recheckFiles(previousAssessment);
+        execution?.assertActive();
+        signal?.throwIfAborted();
+    }
     // Best-effort: refresh nexus-bridge.md
     try {
         const { refreshNexusBridge } = await import('@cleocode/core/internal');
@@ -127,11 +325,12 @@ export async function runNexusAnalysis(params) {
     return {
         projectId,
         repoPath,
-        incremental,
+        incremental: useIncremental,
         nodeCount: result.nodeCount,
         relationCount: result.relationCount,
         fileCount: result.fileCount,
         durationMs: Date.now() - startTime,
+        assessment: committedAssessment ?? previousAssessment,
     };
 }
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package/dist/nexus/api-contracts.d.ts

@@ -14,7 +14,7 @@
  * @task T1569
  * @task T1117
  */
-import type { ContractCompatibilityMatrix, SymbolReference } from '@cleocode/contracts';
+import type { ContractCompatibilityMatrix, NexusTaskSymbolsResult } from '@cleocode/contracts';
 import { type EngineResult } from '../engine-result.js';
 /**
  * Extract HTTP, gRPC, and topic contracts from a project and store them in nexus.db.
@@ -55,9 +55,5 @@ export declare function nexusConduitScan(projectRoot: string): Promise<EngineRes
  *
  * @task T1569
  */
-export declare function nexusTaskSymbols(taskId: string, projectRoot: string): Promise<EngineResult<{
-    taskId: string;
-    count: number;
-    symbols: SymbolReference[];
-}>>;
+export declare function nexusTaskSymbols(taskId: string, projectRoot: string): Promise<EngineResult<NexusTaskSymbolsResult>>;
 //# sourceMappingURL=api-contracts.d.ts.map

package/dist/nexus/api-contracts.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"api-contracts.d.ts","sourceRoot":"","sources":["../../src/nexus/api-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAEH,OAAO,KAAK,EACV,2BAA2B,EAE3B,eAAe,EAChB,MAAM,qBAAqB,CAAC;AAC7B,OAAO,EAAE,KAAK,YAAY,EAA8B,MAAM,qBAAqB,CAAC;AAUpF;;;;GAIG;AAEH,wBAAsB,kBAAkB,CACtC,SAAS,EAAE,MAAM,EACjB,QAAQ,EAAE,MAAM,GACf,OAAO,CACR,YAAY,CAAC;IACX,SAAS,EAAE,MAAM,CAAC;IAClB,QAAQ,EAAE,MAAM,CAAC;IACjB,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,UAAU,EAAE,MAAM,CAAC;CACpB,CAAC,CACH,CAsBA;AAED;;;;GAIG;AAEH,wBAAsB,kBAAkB,CACtC,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,MAAM,EAClB,WAAW,EAAE,MAAM,GAClB,OAAO,CAAC,YAAY,CAAC,2BAA2B,CAAC,CAAC,CAsCpD;AAED;;;;GAIG;AAEH,wBAAsB,uBAAuB,CAC3C,SAAS,EAAE,MAAM,EACjB,QAAQ,EAAE,MAAM,GACf,OAAO,CAAC,YAAY,CAAC,OAAO,CAAC,CAAC,CAOhC;AAED;;;;GAIG;AAEH,wBAAsB,gBAAgB,CACpC,WAAW,EAAE,MAAM,GAClB,OAAO,CAAC,YAAY,CAAC;IAAE,OAAO,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,CAAC,CAAC,CAO5D;AAED;;;;GAIG;AAEH,wBAAsB,gBAAgB,CACpC,MAAM,EAAE,MAAM,EACd,WAAW,EAAE,MAAM,GAClB,OAAO,CACR,YAAY,CAAC;IACX,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,MAAM,CAAC;IACd,OAAO,EAAE,eAAe,EAAE,CAAC;CAC5B,CAAC,CACH,CAOA"}
+{"version":3,"file":"api-contracts.d.ts","sourceRoot":"","sources":["../../src/nexus/api-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAEH,OAAO,KAAK,EACV,2BAA2B,EAE3B,sBAAsB,EACvB,MAAM,qBAAqB,CAAC;AAC7B,OAAO,EAAE,KAAK,YAAY,EAA8B,MAAM,qBAAqB,CAAC;AAYpF;;;;GAIG;AAEH,wBAAsB,kBAAkB,CACtC,SAAS,EAAE,MAAM,EACjB,QAAQ,EAAE,MAAM,GACf,OAAO,CACR,YAAY,CAAC;IACX,SAAS,EAAE,MAAM,CAAC;IAClB,QAAQ,EAAE,MAAM,CAAC;IACjB,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,UAAU,EAAE,MAAM,CAAC;CACpB,CAAC,CACH,CAsBA;AAED;;;;GAIG;AAEH,wBAAsB,kBAAkB,CACtC,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,MAAM,EAClB,WAAW,EAAE,MAAM,GAClB,OAAO,CAAC,YAAY,CAAC,2BAA2B,CAAC,CAAC,CAsCpD;AAED;;;;GAIG;AAEH,wBAAsB,uBAAuB,CAC3C,SAAS,EAAE,MAAM,EACjB,QAAQ,EAAE,MAAM,GACf,OAAO,CAAC,YAAY,CAAC,OAAO,CAAC,CAAC,CAOhC;AAED;;;;GAIG;AAEH,wBAAsB,gBAAgB,CACpC,WAAW,EAAE,MAAM,GAClB,OAAO,CAAC,YAAY,CAAC;IAAE,OAAO,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,CAAC,CAAC,CAO5D;AAED;;;;GAIG;AAEH,wBAAsB,gBAAgB,CACpC,MAAM,EAAE,MAAM,EACd,WAAW,EAAE,MAAM,GAClB,OAAO,CAAC,YAAY,CAAC,sBAAsB,CAAC,CAAC,CAkB/C"}

package/dist/nexus/api-contracts.js

@@ -17,6 +17,8 @@
 import { engineError, engineSuccess } from '../engine-result.js';
 import { linkConduitMessagesToSymbols } from '../memory/graph-memory-bridge.js';
 import { extractGrpcContracts, extractHttpContracts, extractTopicContracts, matchContracts, } from './api-extractors/index.js';
+import { assessKnowledgeCoverage, recordKnowledgeGap } from './knowledge.js';
+import { getTaskKnowledgeEvidence } from './task-evidence.js';
 import { getSymbolsForTask, runGitLogTaskLinker } from './tasks-bridge.js';
 /**
  * Extract HTTP, gRPC, and topic contracts from a project and store them in nexus.db.
@@ -126,8 +128,15 @@ export async function nexusConduitScan(projectRoot) {
 // SSoT-EXEMPT:engine-migration-T1569
 export async function nexusTaskSymbols(taskId, projectRoot) {
     try {
-        const symbols = await getSymbolsForTask(taskId, projectRoot);
-        return engineSuccess({ taskId, count: symbols.length, symbols });
+        const coverage = await assessKnowledgeCoverage(projectRoot);
+        const taskEvidence = await getTaskKnowledgeEvidence(taskId, projectRoot, coverage);
+        const symbols = await getSymbolsForTask(taskId, projectRoot, taskEvidence);
+        if (symbols.length === 0) {
+            recordKnowledgeGap(coverage, coverage.maintenanceState === 'pending' ? 'partial' : 'missing', coverage.maintenanceState === 'pending'
+                ? 'Task evidence assessment is deferred; zero matches do not establish missing evidence.'
+                : 'No task evidence has been resolved to indexed symbols.');
+        }
+        return engineSuccess({ taskId, count: symbols.length, symbols, coverage });
     }
     catch (error) {
         return engineError('E_INTERNAL', error instanceof Error ? error.message : String(error));

package/dist/nexus/api-contracts.js.map

@@ -1 +1 @@
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+{"version":3,"file":"api-contracts.js","sourceRoot":"","sources":["../../src/nexus/api-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAOH,OAAO,EAAqB,WAAW,EAAE,aAAa,EAAE,MAAM,qBAAqB,CAAC;AACpF,OAAO,EAAE,4BAA4B,EAAE,MAAM,kCAAkC,CAAC;AAChF,OAAO,EACL,oBAAoB,EACpB,oBAAoB,EACpB,qBAAqB,EACrB,cAAc,GACf,MAAM,2BAA2B,CAAC;AACnC,OAAO,EAAE,uBAAuB,EAAE,kBAAkB,EAAE,MAAM,gBAAgB,CAAC;AAC7E,OAAO,EAAE,wBAAwB,EAAE,MAAM,oBAAoB,CAAC;AAC9D,OAAO,EAAE,iBAAiB,EAAE,mBAAmB,EAAE,MAAM,mBAAmB,CAAC;AAE3E;;;;GAIG;AACH,qCAAqC;AACrC,MAAM,CAAC,KAAK,UAAU,kBAAkB,CACtC,SAAiB,EACjB,QAAgB;IAWhB,IAAI,CAAC;QACH,MAAM,CAAC,aAAa,EAAE,aAAa,EAAE,cAAc,CAAC,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC;YACvE,oBAAoB,CAAC,SAAS,EAAE,QAAQ,CAAC;YACzC,oBAAoB,CAAC,SAAS,EAAE,QAAQ,CAAC;YACzC,qBAAqB,CAAC,SAAS,EAAE,QAAQ,CAAC;SAC3C,CAAC,CAAC;QAEH,MAAM,IAAI,GAAG,aAAa,EAAE,MAAM,IAAI,CAAC,CAAC;QACxC,MAAM,IAAI,GAAG,aAAa,EAAE,MAAM,IAAI,CAAC,CAAC;QACxC,MAAM,KAAK,GAAG,cAAc,EAAE,MAAM,IAAI,CAAC,CAAC;QAC1C,OAAO,aAAa,CAAC;YACnB,SAAS;YACT,QAAQ;YACR,IAAI;YACJ,IAAI;YACJ,KAAK;YACL,UAAU,EAAE,IAAI,GAAG,IAAI,GAAG,KAAK;SAChC,CAAC,CAAC;IACL,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,OAAO,WAAW,CAAC,YAAY,EAAE,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC;IAC3F,CAAC;AACH,CAAC;AAED;;;;GAIG;AACH,qCAAqC;AACrC,MAAM,CAAC,KAAK,UAAU,kBAAkB,CACtC,UAAkB,EAClB,UAAkB,EAClB,WAAmB;IAEnB,IAAI,CAAC;QACH,MAAM,SAAS,GAAG,MAAM,CAAC,IAAI,CAAC,UAAU,EAAE,WAAW,CAAC,CAAC,QAAQ,EAAE,IAAI,WAAW,CAAC;QACjF,MAAM,SAAS,GAAG,MAAM,CAAC,IAAI,CAAC,UAAU,EAAE,WAAW,CAAC,CAAC,QAAQ,EAAE,IAAI,WAAW,CAAC;QAEjF,MAAM,CAAC,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,KAAK,EAAE,MAAM,CAAC,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC;YACrE,oBAAoB,CAAC,UAAU,EAAE,SAAS,CAAC;YAC3C,oBAAoB,CAAC,UAAU,EAAE,SAAS,CAAC;YAC3C,qBAAqB,CAAC,UAAU,EAAE,SAAS,CAAC;YAC5C,oBAAoB,CAAC,UAAU,EAAE,SAAS,CAAC;YAC3C,oBAAoB,CAAC,UAAU,EAAE,SAAS,CAAC;YAC3C,qBAAqB,CAAC,UAAU,EAAE,SAAS,CAAC;SAC7C,CAAC,CAAC;QAEH,MAAM,UAAU,GAAG,CAAC,GAAG,CAAC,KAAK,IAAI,EAAE,CAAC,EAAE,GAAG,CAAC,KAAK,IAAI,EAAE,CAAC,EAAE,GAAG,CAAC,MAAM,IAAI,EAAE,CAAC,CAAC,CAAC;QAC3E,MAAM,UAAU,GAAG,CAAC,GAAG,CAAC,KAAK,IAAI,EAAE,CAAC,EAAE,GAAG,CAAC,KAAK,IAAI,EAAE,CAAC,EAAE,GAAG,CAAC,MAAM,IAAI,EAAE,CAAC,CAAC,CAAC;QAC3E,MAAM,OAAO,GAAoB,cAAc,CAAC,UAAU,EAAE,UAAU,CAAC,CAAC;QAExE,MAAM,eAAe,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,aAAa,KAAK,YAAY,CAAC,CAAC,MAAM,CAAC;QACvF,MAAM,iBAAiB,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,aAAa,KAAK,cAAc,CAAC,CAAC,MAAM,CAAC;QAC3F,MAAM,YAAY,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,aAAa,KAAK,SAAS,CAAC,CAAC,MAAM,CAAC;QACjF,MAAM,oBAAoB,GACxB,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,eAAe,GAAG,OAAO,CAAC,MAAM,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;QAEhF,MAAM,MAAM,GAAgC;YAC1C,UAAU;YACV,UAAU;YACV,OAAO;YACP,eAAe;YACf,iBAAiB;YACjB,YAAY;YACZ,oBAAoB;YACpB,eAAe,EAAE,EAAE;SACpB,CAAC;QACF,OAAO,aAAa,CAAC,MAAM,CAAC,CAAC;IAC/B,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,OAAO,WAAW,CAAC,YAAY,EAAE,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC;IAC3F,CAAC;AACH,CAAC;AAED;;;;GAIG;AACH,qCAAqC;AACrC,MAAM,CAAC,KAAK,UAAU,uBAAuB,CAC3C,SAAiB,EACjB,QAAgB;IAEhB,IAAI,CAAC;QACH,MAAM,MAAM,GAAG,MAAM,mBAAmB,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAC;QAC9D,OAAO,aAAa,CAAC,MAAM,CAAC,CAAC;IAC/B,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,OAAO,WAAW,CAAC,YAAY,EAAE,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC;IAC3F,CAAC;AACH,CAAC;AAED;;;;GAIG;AACH,qCAAqC;AACrC,MAAM,CAAC,KAAK,UAAU,gBAAgB,CACpC,WAAmB;IAEnB,IAAI,CAAC;QACH,MAAM,MAAM,GAAG,MAAM,4BAA4B,CAAC,WAAW,CAAC,CAAC;QAC/D,OAAO,aAAa,CAAC,MAAM,CAAC,CAAC;IAC/B,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,OAAO,WAAW,CAAC,YAAY,EAAE,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC;IAC3F,CAAC;AACH,CAAC;AAED;;;;GAIG;AACH,qCAAqC;AACrC,MAAM,CAAC,KAAK,UAAU,gBAAgB,CACpC,MAAc,EACd,WAAmB;IAEnB,IAAI,CAAC;QACH,MAAM,QAAQ,GAAG,MAAM,uBAAuB,CAAC,WAAW,CAAC,CAAC;QAC5D,MAAM,YAAY,GAAG,MAAM,wBAAwB,CAAC,MAAM,EAAE,WAAW,EAAE,QAAQ,CAAC,CAAC;QACnF,MAAM,OAAO,GAAG,MAAM,iBAAiB,CAAC,MAAM,EAAE,WAAW,EAAE,YAAY,CAAC,CAAC;QAC3E,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACzB,kBAAkB,CAChB,QAAQ,EACR,QAAQ,CAAC,gBAAgB,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,EAC/D,QAAQ,CAAC,gBAAgB,KAAK,SAAS;gBACrC,CAAC,CAAC,uFAAuF;gBACzF,CAAC,CAAC,wDAAwD,CAC7D,CAAC;QACJ,CAAC;QACD,OAAO,aAAa,CAAC,EAAE,MAAM,EAAE,KAAK,EAAE,OAAO,CAAC,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,CAAC,CAAC;IAC7E,CAAC;IAAC,OAAO,KAAK,EAAE,CAAC;QACf,OAAO,WAAW,CAAC,YAAY,EAAE,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC;IAC3F,CAAC;AACH,CAAC"}

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

@@ -1 +1 @@
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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 { KnowledgeSymbolAmbiguityError, resolveKnowledgeSymbol } from './knowledge.js';
 import { buildSymbolMissError } from './symbol-miss.js';
 /**
  * Retrieve caller/callee context and process participation for a named symbol.
@@ -33,47 +34,21 @@ import { buildSymbolMissError } from './symbol-miss.js';
 export async function getSymbolContext(symbolName, projectId, repoPath, opts = {}) {
     const limit = opts.limit ?? 20;
     const showContent = opts.showContent ?? false;
-    const { sortMatchingNodes } = await import('./symbol-ranking.js');
-    const db = await getNexusDb();
-    // Fetch only symbol nodes (exclude community/process structural nodes).
-    // ADR-090 · T11648: the graph lives in the PROJECT `cleo.db` (one project per
-    // DB), so the former `project_id = ?` predicate is dropped — only the kind
-    // exclusion remains, pushed into the `idx_nexus_nodes_kind` index.
-    let projectSymbolNodes = [];
-    try {
-        projectSymbolNodes = db
-            .select()
-            .from(nexusSchema.nexusNodes)
-            .where(notInArray(nexusSchema.nexusNodes.kind, ['community', 'process']))
-            .all();
-    }
-    catch {
-        projectSymbolNodes = [];
-    }
-    const lowerSymbol = symbolName.toLowerCase();
-    const rawMatchingNodes = projectSymbolNodes.filter((n) => n['name'] != null && String(n['name']).toLowerCase().includes(lowerSymbol));
-    const matchingNodes = sortMatchingNodes(rawMatchingNodes, symbolName);
+    const db = await getNexusDb(repoPath);
+    const projectSymbolNodes = db
+        .select()
+        .from(nexusSchema.nexusNodes)
+        .where(notInArray(nexusSchema.nexusNodes.kind, ['community', 'process']))
+        .all();
+    const selected = resolveKnowledgeSymbol(symbolName, projectSymbolNodes);
+    const matchingNodes = projectSymbolNodes.filter((node) => node.id === selected?.id);
     if (matchingNodes.length === 0) {
         // 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 = [];
-    try {
-        allRelations = db.select().from(nexusSchema.nexusRelations).all();
-    }
-    catch {
-        allRelations = [];
-    }
-    // Fetch ALL nodes (including community/process) for the nodeById map so community
-    // labels and process names resolve correctly.
-    let allProjectNodes = [];
-    try {
-        allProjectNodes = db.select().from(nexusSchema.nexusNodes).all();
-    }
-    catch {
-        allProjectNodes = projectSymbolNodes;
-    }
+    // Query failures remain explicit errors rather than empty healthy context.
+    const allRelations = db.select().from(nexusSchema.nexusRelations).all();
+    const allProjectNodes = db.select().from(nexusSchema.nexusNodes).all();
     const nodeById = new Map();
     for (const n of allProjectNodes) {
         nodeById.set(String(n['id']), n);
@@ -192,6 +167,8 @@ export async function nexusContext(symbolName, projectId, repoPath, limit, showC
         return engineSuccess(result);
     }
     catch (error) {
+        if (error instanceof KnowledgeSymbolAmbiguityError)
+            return engineError(error.code, error.message, { details: { candidates: error.candidates } });
         return engineError('E_INTERNAL', error instanceof Error ? error.message : String(error));
     }
 }

package/dist/nexus/context.js.map

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

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