@monoes/monograph 2.24.0 → 2.25.0

package/dist/src/mcp-tools/impact.js

@@ -49,6 +49,13 @@ function reverseBfs(startNodeId, db, maxDepth, options = {}) {
     return visited;
 }
 // ── Implementation ─────────────────────────────────────────────────────────────
+/**
+ * "What breaks if I change this?" — walks outward from a symbol through its
+ * callers, importers, references and subclasses. Returns the affected symbols
+ * by distance, the affected files, the tests that cover any of them
+ * (`affectedTests`) and a risk level. A name that matches several definitions
+ * comes back as candidates rather than a guess.
+ */
 export function getMonographImpact(db, input) {
     const maxDepth = Math.min(input.depth ?? 3, 6);
     // Find the node. Several same-named definitions (say, a test mock) are not
@@ -65,6 +72,7 @@ export function getMonographImpact(db, input) {
             directCallers: [],
             transitiveCallers: [],
             affectedFiles: [],
+            affectedTests: [],
             riskScore: 0,
             riskLevel: 'LOW',
             ambiguous: candidates.length > 1,
@@ -103,6 +111,8 @@ function extractCallerResult(db, startNodeId, visited) {
     const affectedFiles = [
         ...new Set(allAffectedNodes.map((n) => n.filePath).filter((p) => p != null)),
     ];
+    const own = db.prepare('SELECT file_path FROM nodes WHERE id = ?').get(startNodeId);
+    const affectedTests = findAffectedTests(db, [...visited.keys()], own?.file_path ? [own.file_path, ...affectedFiles] : affectedFiles);
     const totalCallerCount = visited.size - 1; // exclude start node
     const rawScore = Math.min(Math.log2(totalCallerCount + 1), 10);
     const riskScore = rawScore / 10;
@@ -110,10 +120,36 @@ function extractCallerResult(db, startNodeId, visited) {
         directCallers,
         transitiveCallers,
         affectedFiles,
+        affectedTests,
         riskScore,
         riskLevel: computeRiskLevel(riskScore),
     };
 }
+/** Test files with a TESTS edge to any impacted node or any impacted file. */
+function findAffectedTests(db, nodeIds, files) {
+    const targets = new Set(nodeIds);
+    if (files.length > 0) {
+        const rows = db
+            .prepare(`SELECT id FROM nodes WHERE label = 'File' AND file_path IN (${files.map(() => '?').join(',')})`)
+            .all(...files);
+        for (const r of rows)
+            targets.add(r.id);
+    }
+    const ids = [...targets];
+    const found = new Set();
+    const CHUNK = 500;
+    for (let i = 0; i < ids.length; i += CHUNK) {
+        const chunk = ids.slice(i, i + CHUNK);
+        const rows = db
+            .prepare(`SELECT DISTINCT s.file_path AS p FROM edges e JOIN nodes s ON s.id = e.source_id
+         WHERE e.relation = 'TESTS' AND e.target_id IN (${chunk.map(() => '?').join(',')})`)
+            .all(...chunk);
+        for (const r of rows)
+            if (r.p)
+                found.add(r.p);
+    }
+    return [...found].sort();
+}
 // ── id-based impact with filtering options ────────────────────────────────────
 export async function monographImpact(db, nodeId, options = {}) {
     const maxDepth = Math.min(options.maxDepth ?? 3, 6);
@@ -124,6 +160,7 @@ export async function monographImpact(db, nodeId, options = {}) {
             directCallers: [],
             transitiveCallers: [],
             affectedFiles: [],
+            affectedTests: [],
             riskScore: 0,
             riskLevel: 'LOW',
         };

package/dist/src/mcp-tools/impact.js.map

@@ -1 +1 @@
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package/dist/src/mcp-tools/index.d.ts

@@ -1,4 +1,5 @@
 export * from './api-impact.js';
+export * from './brief.js';
 export * from './context.js';
 export * from './cypher.js';
 export * from './detect-changes.js';

package/dist/src/mcp-tools/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/mcp-tools/index.ts"],"names":[],"mappings":"AAAA,cAAc,iBAAiB,CAAC;AAChC,cAAc,cAAc,CAAC;AAC7B,cAAc,aAAa,CAAC;AAC5B,cAAc,qBAAqB,CAAC;AACpC,cAAc,cAAc,CAAC;AAC7B,cAAc,kBAAkB,CAAC;AACjC,cAAc,iBAAiB,CAAC;AAChC,cAAc,kBAAkB,CAAC;AACjC,cAAc,iBAAiB,CAAC;AAChC,cAAc,aAAa,CAAC;AAC5B,cAAc,iBAAiB,CAAC;AAChC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,YAAY,CAAC;AAC3B,cAAc,aAAa,CAAC;AAC5B,YAAY,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AACzD,cAAc,gBAAgB,CAAC;AAC/B,cAAc,YAAY,CAAC;AAC3B,cAAc,kBAAkB,CAAC;AACjC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,eAAe,CAAC;AAC9B,cAAc,WAAW,CAAC;AAC1B,cAAc,iBAAiB,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/mcp-tools/index.ts"],"names":[],"mappings":"AAAA,cAAc,iBAAiB,CAAC;AAChC,cAAc,YAAY,CAAC;AAC3B,cAAc,cAAc,CAAC;AAC7B,cAAc,aAAa,CAAC;AAC5B,cAAc,qBAAqB,CAAC;AACpC,cAAc,cAAc,CAAC;AAC7B,cAAc,kBAAkB,CAAC;AACjC,cAAc,iBAAiB,CAAC;AAChC,cAAc,kBAAkB,CAAC;AACjC,cAAc,iBAAiB,CAAC;AAChC,cAAc,aAAa,CAAC;AAC5B,cAAc,iBAAiB,CAAC;AAChC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,YAAY,CAAC;AAC3B,cAAc,aAAa,CAAC;AAC5B,YAAY,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AACzD,cAAc,gBAAgB,CAAC;AAC/B,cAAc,YAAY,CAAC;AAC3B,cAAc,kBAAkB,CAAC;AACjC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,eAAe,CAAC;AAC9B,cAAc,WAAW,CAAC;AAC1B,cAAc,iBAAiB,CAAC"}

package/dist/src/mcp-tools/index.js

@@ -1,4 +1,5 @@
 export * from './api-impact.js';
+export * from './brief.js';
 export * from './context.js';
 export * from './cypher.js';
 export * from './detect-changes.js';

package/dist/src/mcp-tools/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/mcp-tools/index.ts"],"names":[],"mappings":"AAAA,cAAc,iBAAiB,CAAC;AAChC,cAAc,cAAc,CAAC;AAC7B,cAAc,aAAa,CAAC;AAC5B,cAAc,qBAAqB,CAAC;AACpC,cAAc,cAAc,CAAC;AAC7B,cAAc,kBAAkB,CAAC;AACjC,cAAc,iBAAiB,CAAC;AAChC,cAAc,kBAAkB,CAAC;AACjC,cAAc,iBAAiB,CAAC;AAChC,cAAc,aAAa,CAAC;AAC5B,cAAc,iBAAiB,CAAC;AAChC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,YAAY,CAAC;AAC3B,cAAc,aAAa,CAAC;AAE5B,cAAc,gBAAgB,CAAC;AAC/B,cAAc,YAAY,CAAC;AAC3B,cAAc,kBAAkB,CAAC;AACjC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,eAAe,CAAC;AAC9B,cAAc,WAAW,CAAC;AAC1B,cAAc,iBAAiB,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/mcp-tools/index.ts"],"names":[],"mappings":"AAAA,cAAc,iBAAiB,CAAC;AAChC,cAAc,YAAY,CAAC;AAC3B,cAAc,cAAc,CAAC;AAC7B,cAAc,aAAa,CAAC;AAC5B,cAAc,qBAAqB,CAAC;AACpC,cAAc,cAAc,CAAC;AAC7B,cAAc,kBAAkB,CAAC;AACjC,cAAc,iBAAiB,CAAC;AAChC,cAAc,kBAAkB,CAAC;AACjC,cAAc,iBAAiB,CAAC;AAChC,cAAc,aAAa,CAAC;AAC5B,cAAc,iBAAiB,CAAC;AAChC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,YAAY,CAAC;AAC3B,cAAc,aAAa,CAAC;AAE5B,cAAc,gBAAgB,CAAC;AAC/B,cAAc,YAAY,CAAC;AAC3B,cAAc,kBAAkB,CAAC;AACjC,cAAc,gBAAgB,CAAC;AAC/B,cAAc,eAAe,CAAC;AAC9B,cAAc,WAAW,CAAC;AAC1B,cAAc,iBAAiB,CAAC"}

package/dist/src/pipeline/manifest.d.ts

@@ -0,0 +1,34 @@
+import type { MonographDb } from '../storage/db.js';
+import type { IndexScope } from './index-scope.js';
+/**
+ * What the last build actually produced — the one place an agent (or doctor)
+ * can learn how complete the index is without inferring it from query results.
+ */
+export interface IndexManifest {
+    /** Increments on every committed build; lets a cache tie itself to one build. */
+    generation: number;
+    builtAt: string;
+    durationMs: number;
+    scope: IndexScope;
+    commit: string | null;
+    /** Version of the symbol-id scheme; ids from different versions are not comparable. */
+    identityVersion: number;
+    nodes: Record<string, number>;
+    edges: Record<string, number>;
+    /** Code symbols and files with a natural-language summary indexed. */
+    summarized: number;
+    /** Files the parser skipped or recovered from, with the first few named. */
+    parseWarnings: {
+        count: number;
+        sample: string[];
+    };
+}
+export declare function readManifest(db: MonographDb): IndexManifest | null;
+export declare function writeManifest(db: MonographDb, input: {
+    startedAt: number;
+    scope: IndexScope;
+    commit: string | null;
+    summarized: number;
+    parseErrors: string[];
+}): IndexManifest;
+//# sourceMappingURL=manifest.d.ts.map

package/dist/src/pipeline/manifest.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"manifest.d.ts","sourceRoot":"","sources":["../../../src/pipeline/manifest.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAC;AAEpD,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,kBAAkB,CAAC;AAKnD;;;GAGG;AACH,MAAM,WAAW,aAAa;IAC5B,iFAAiF;IACjF,UAAU,EAAE,MAAM,CAAC;IACnB,OAAO,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,MAAM,CAAC;IACnB,KAAK,EAAE,UAAU,CAAC;IAClB,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB,uFAAuF;IACvF,eAAe,EAAE,MAAM,CAAC;IACxB,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAC9B,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAC9B,sEAAsE;IACtE,UAAU,EAAE,MAAM,CAAC;IACnB,4EAA4E;IAC5E,aAAa,EAAE;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,EAAE,CAAA;KAAE,CAAC;CACpD;AAED,wBAAgB,YAAY,CAAC,EAAE,EAAE,WAAW,GAAG,aAAa,GAAG,IAAI,CASlE;AAaD,wBAAgB,aAAa,CAC3B,EAAE,EAAE,WAAW,EACf,KAAK,EAAE;IACL,SAAS,EAAE,MAAM,CAAC;IAClB,KAAK,EAAE,UAAU,CAAC;IAClB,MAAM,EAAE,MAAM,GAAG,IAAI,CAAC;IACtB,UAAU,EAAE,MAAM,CAAC;IACnB,WAAW,EAAE,MAAM,EAAE,CAAC;CACvB,GACA,aAAa,CAqBf"}

package/dist/src/pipeline/manifest.js

@@ -0,0 +1,38 @@
+import { SYMBOL_ID_VERSION } from '../types.js';
+const MANIFEST_KEY = 'manifest';
+const MAX_LISTED_WARNINGS = 20;
+export function readManifest(db) {
+    try {
+        const row = db.prepare('SELECT value FROM index_meta WHERE key = ?').get(MANIFEST_KEY);
+        return row ? JSON.parse(row.value) : null;
+    }
+    catch {
+        return null;
+    }
+}
+function countBy(db, table, column) {
+    const rows = db
+        .prepare(`SELECT ${column} AS k, COUNT(*) AS n FROM ${table} GROUP BY ${column}`)
+        .all();
+    return Object.fromEntries(rows.map((r) => [r.k, r.n]));
+}
+export function writeManifest(db, input) {
+    const manifest = {
+        generation: (readManifest(db)?.generation ?? 0) + 1,
+        builtAt: new Date().toISOString(),
+        durationMs: Date.now() - input.startedAt,
+        scope: input.scope,
+        commit: input.commit,
+        identityVersion: SYMBOL_ID_VERSION,
+        nodes: countBy(db, 'nodes', 'label'),
+        edges: countBy(db, 'edges', 'relation'),
+        summarized: input.summarized,
+        parseWarnings: {
+            count: input.parseErrors.length,
+            sample: input.parseErrors.slice(0, MAX_LISTED_WARNINGS),
+        },
+    };
+    db.prepare('INSERT OR REPLACE INTO index_meta VALUES (?, ?)').run(MANIFEST_KEY, JSON.stringify(manifest));
+    return manifest;
+}
+//# sourceMappingURL=manifest.js.map

package/dist/src/pipeline/manifest.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"manifest.js","sourceRoot":"","sources":["../../../src/pipeline/manifest.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AAGhD,MAAM,YAAY,GAAG,UAAU,CAAC;AAChC,MAAM,mBAAmB,GAAG,EAAE,CAAC;AAuB/B,MAAM,UAAU,YAAY,CAAC,EAAe;IAC1C,IAAI,CAAC;QACH,MAAM,GAAG,GAAG,EAAE,CAAC,OAAO,CAAC,4CAA4C,CAAC,CAAC,GAAG,CAAC,YAAY,CAExE,CAAC;QACd,OAAO,GAAG,CAAC,CAAC,CAAE,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAmB,CAAC,CAAC,CAAC,IAAI,CAAC;IAC/D,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,CAAC;IACd,CAAC;AACH,CAAC;AAED,SAAS,OAAO,CACd,EAAe,EACf,KAAwB,EACxB,MAAc;IAEd,MAAM,IAAI,GAAG,EAAE;SACZ,OAAO,CAAC,UAAU,MAAM,6BAA6B,KAAK,aAAa,MAAM,EAAE,CAAC;SAChF,GAAG,EAAgC,CAAC;IACvC,OAAO,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;AACzD,CAAC;AAED,MAAM,UAAU,aAAa,CAC3B,EAAe,EACf,KAMC;IAED,MAAM,QAAQ,GAAkB;QAC9B,UAAU,EAAE,CAAC,YAAY,CAAC,EAAE,CAAC,EAAE,UAAU,IAAI,CAAC,CAAC,GAAG,CAAC;QACnD,OAAO,EAAE,IAAI,IAAI,EAAE,CAAC,WAAW,EAAE;QACjC,UAAU,EAAE,IAAI,CAAC,GAAG,EAAE,GAAG,KAAK,CAAC,SAAS;QACxC,KAAK,EAAE,KAAK,CAAC,KAAK;QAClB,MAAM,EAAE,KAAK,CAAC,MAAM;QACpB,eAAe,EAAE,iBAAiB;QAClC,KAAK,EAAE,OAAO,CAAC,EAAE,EAAE,OAAO,EAAE,OAAO,CAAC;QACpC,KAAK,EAAE,OAAO,CAAC,EAAE,EAAE,OAAO,EAAE,UAAU,CAAC;QACvC,UAAU,EAAE,KAAK,CAAC,UAAU;QAC5B,aAAa,EAAE;YACb,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM;YAC/B,MAAM,EAAE,KAAK,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,EAAE,mBAAmB,CAAC;SACxD;KACF,CAAC;IACF,EAAE,CAAC,OAAO,CAAC,iDAAiD,CAAC,CAAC,GAAG,CAC/D,YAAY,EACZ,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,CACzB,CAAC;IACF,OAAO,QAAQ,CAAC;AAClB,CAAC"}

package/dist/src/pipeline/orchestrator.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"orchestrator.d.ts","sourceRoot":"","sources":["../../../src/pipeline/orchestrator.ts"],"names":[],"mappings":"AAOA,OAAO,KAAK,EAAE,gBAAgB,EAAqB,MAAM,aAAa,CAAC;AACvE,OAAO,EAAoB,KAAK,eAAe,EAA2B,MAAM,iBAAiB,CAAC;AA2BlG,OAAO,KAAK,EAAmB,eAAe,EAAE,MAAM,YAAY,CAAC;AAgBnE,MAAM,WAAW,YAAa,SAAQ,OAAO,CAAC,eAAe,CAAC;IAC5D,UAAU,CAAC,EAAE,CAAC,CAAC,EAAE,gBAAgB,KAAK,IAAI,CAAC;IAC3C,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,oGAAoG;IACpG,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB;;;;OAIG;IACH,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED;;;;;GAKG;AACH,MAAM,MAAM,WAAW,GACnB;IACE,MAAM,EAAE,OAAO,CAAC;IAChB,KAAK,EAAE;QAAE,MAAM,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;IACzC,KAAK,EAAE;QAAE,MAAM,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;CAC1C,GACD;IACE,MAAM,EAAE,SAAS,CAAC;IAClB,MAAM,EAAE,QAAQ,GAAG,OAAO,CAAC;IAC3B,OAAO,EAAE,MAAM,CAAC;IAChB,wEAAwE;IACxE,MAAM,CAAC,EAAE,eAAe,CAAC;CAC1B,CAAC;AAQN,wBAAsB,UAAU,CAC9B,QAAQ,EAAE,MAAM,EAChB,OAAO,GAAE,YAAiB,GACzB,OAAO,CAAC,WAAW,CAAC,CAiBtB;AAsQD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAsB,qBAAqB,CACzC,QAAQ,EAAE,MAAM,EAChB,eAAe,EAAE,MAAM,EAAE,EACzB,OAAO,GAAE,YAAiB,GACzB,OAAO,CAAC,WAAW,GAAG,IAAI,CAAC,CAa7B"}
+{"version":3,"file":"orchestrator.d.ts","sourceRoot":"","sources":["../../../src/pipeline/orchestrator.ts"],"names":[],"mappings":"AAOA,OAAO,KAAK,EAAE,gBAAgB,EAAqB,MAAM,aAAa,CAAC;AACvE,OAAO,EAAoB,KAAK,eAAe,EAA2B,MAAM,iBAAiB,CAAC;AAgClG,OAAO,KAAK,EAAmB,eAAe,EAAE,MAAM,YAAY,CAAC;AAgBnE,MAAM,WAAW,YAAa,SAAQ,OAAO,CAAC,eAAe,CAAC;IAC5D,UAAU,CAAC,EAAE,CAAC,CAAC,EAAE,gBAAgB,KAAK,IAAI,CAAC;IAC3C,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,oGAAoG;IACpG,WAAW,CAAC,EAAE,OAAO,CAAC;IACtB;;;;OAIG;IACH,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED;;;;;GAKG;AACH,MAAM,MAAM,WAAW,GACnB;IACE,MAAM,EAAE,OAAO,CAAC;IAChB,KAAK,EAAE;QAAE,MAAM,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;IACzC,KAAK,EAAE;QAAE,MAAM,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;CAC1C,GACD;IACE,MAAM,EAAE,SAAS,CAAC;IAClB,MAAM,EAAE,QAAQ,GAAG,OAAO,CAAC;IAC3B,OAAO,EAAE,MAAM,CAAC;IAChB,wEAAwE;IACxE,MAAM,CAAC,EAAE,eAAe,CAAC;CAC1B,CAAC;AAQN,wBAAsB,UAAU,CAC9B,QAAQ,EAAE,MAAM,EAChB,OAAO,GAAE,YAAiB,GACzB,OAAO,CAAC,WAAW,CAAC,CAiBtB;AA8OD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAsB,qBAAqB,CACzC,QAAQ,EAAE,MAAM,EAChB,eAAe,EAAE,MAAM,EAAE,EACzB,OAAO,GAAE,YAAiB,GACzB,OAAO,CAAC,WAAW,GAAG,IAAI,CAAC,CAa7B"}

package/dist/src/pipeline/orchestrator.js

@@ -6,7 +6,9 @@ import { ExtractionCache } from '../cache/extraction-cache.js';
 import { generateGraphReport } from '../reporting/graph-report.js';
 import { closeDb, openDb } from '../storage/db.js';
 import { acquireBuildLock, describeBuildLockHolder } from './build-lock.js';
-import { isWithinScope, readIndexScope, scopeForOptions, writeIndexScope } from './index-scope.js';
+import { readIndexScope, scopeForOptions, writeIndexScope } from './index-scope.js';
+import { writeManifest } from './manifest.js';
+import { agentRegistryPhase } from './phases/agent-registry.js';
 import { bridgeResolverPhase } from './phases/bridge-resolver.js';
 import { communitiesPhase } from './phases/communities.js';
 import { contextualProximityPhase } from './phases/contextual-proximity.js';
@@ -25,9 +27,12 @@ import { processesPhase } from './phases/processes.js';
 import { routesPhase } from './phases/routes.js';
 import { scanPhase } from './phases/scan.js';
 import { clearWorkspacePackageMapCache, scopeResolutionPhase } from './phases/scope-resolution.js';
+import { staleSweepPhase } from './phases/stale-sweep.js';
 import { structurePhase } from './phases/structure.js';
 import { suggestPhase } from './phases/suggest.js';
+import { summariesPhase } from './phases/summaries.js';
 import { surprisesPhase } from './phases/surprises.js';
+import { testsEdgesPhase } from './phases/tests-edges.js';
 import { toolsPhase } from './phases/tools.js';
 import { variablesPhase } from './phases/variables-phase.js';
 import { wildcardSynthesisPhase } from './phases/wildcard-phase.js';
@@ -138,6 +143,7 @@ async function buildAsyncLocked(repoPath, dbPath, fullOptions, options) {
     // phases below are async. This is still safe: every phase writes through
     // this same single connection, so SQLite serializes them regardless of how
     // the JS event loop interleaves the awaits between phases.
+    const buildStartedAt = Date.now();
     db.exec('BEGIN');
     try {
         const graph = new Graph({ multi: true, type: 'directed' });
@@ -168,11 +174,15 @@ async function buildAsyncLocked(repoPath, dbPath, fullOptions, options) {
             scopeResolutionPhase,
             bridgeResolverPhase,
             mroPhase,
+            staleSweepPhase,
             communitiesPhase,
             processesPhase,
             godNodesPhase,
             surprisesPhase,
             suggestPhase,
+            agentRegistryPhase,
+            summariesPhase,
+            testsEdgesPhase,
         ]);
         const outputs = await runner.run(ctx);
         // MONO-2: surface parse-time errors (malformed files, failed grammar loads,
@@ -192,38 +202,6 @@ async function buildAsyncLocked(repoPath, dbPath, fullOptions, options) {
                 process.stderr.write(`[monograph] ${summary}\n`);
             }
         }
-        // Sweep orphaned rows for files that were renamed/deleted since the last build.
-        // This MUST run unconditionally — even when every remaining file cache-hit
-        // (ctx.allFilesCached === true), a file may have been deleted from disk between
-        // builds, which produces zero cache misses but still leaves ghost rows in the DB
-        // unless we compare the DB's known file set against the current on-disk set.
-        //
-        // The sweep is confined to the current build's source domain (`activeScope`).
-        // A narrowed build never looked at files outside its domain, so their absence
-        // from `filePaths` says nothing about whether they still exist on disk —
-        // deleting those rows is how a code-only refresh used to erase every Document
-        // node in the graph.
-        const scanOut = outputs.get('scan');
-        if (scanOut) {
-            const liveFiles = new Set(scanOut.filePaths.map((f) => resolve(f)));
-            const staleFiles = db.prepare('SELECT DISTINCT file_path FROM nodes WHERE file_path IS NOT NULL').all()
-                .map((r) => r.file_path)
-                .filter((f) => isWithinScope(f, activeScope) && !liveFiles.has(resolve(ctx.repoPath, f)));
-            if (staleFiles.length > 0) {
-                const deleteStale = db.transaction((files) => {
-                    const deleteEdges = db.prepare(`
-            DELETE FROM edges WHERE source_id IN (SELECT id FROM nodes WHERE file_path = ?)
-               OR target_id IN (SELECT id FROM nodes WHERE file_path = ?)
-          `);
-                    const deleteNodesStmt = db.prepare('DELETE FROM nodes WHERE file_path = ?');
-                    for (const f of files) {
-                        deleteEdges.run(f, f);
-                        deleteNodesStmt.run(f);
-                    }
-                });
-                deleteStale(staleFiles);
-            }
-        }
         // Populate churnScore on File nodes from git history (6-month window)
         try {
             const churnResult = await analyzeChurn(ctx.repoPath, '6m');
@@ -266,6 +244,13 @@ async function buildAsyncLocked(repoPath, dbPath, fullOptions, options) {
         }
         db.prepare("INSERT OR REPLACE INTO index_meta VALUES ('indexed_at', ?)").run(new Date().toISOString());
         writeIndexScope(db, activeScope);
+        writeManifest(db, {
+            startedAt: buildStartedAt,
+            scope: activeScope,
+            commit: hash ?? null,
+            summarized: outputs.get('summaries')?.summarized ?? 0,
+            parseErrors,
+        });
         const after = countGraph(db);
         db.exec('COMMIT');
         // Skip expensive report regeneration when all files were cached (nothing changed) —

package/dist/src/pipeline/orchestrator.js.map

@@ -1 +1 @@
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package/dist/src/pipeline/phases/agent-registry.d.ts

@@ -0,0 +1,33 @@
+import type { PipelinePhase } from '../types.js';
+export interface AgentDefinition {
+    kind: 'Agent' | 'Skill';
+    name: string;
+    filePath: string;
+    description: string;
+    whenToUse: string;
+    tags: string[];
+    category: string;
+    /** Markdown after the frontmatter. */
+    body: string;
+}
+/**
+ * Reads the flat `key: value` frontmatter agent and skill files use. Only the
+ * keys the graph needs; nested blocks such as `capability:` are ignored.
+ */
+export declare function parseDefinition(kind: AgentDefinition['kind'], filePath: string, source: string): AgentDefinition | null;
+/** Agents under `.claude/agents/**` and skills at `.claude/skills/<name>/SKILL.md`. */
+export declare function readDefinitions(repoPath: string): AgentDefinition[];
+/** The searchable description of a definition, for the summaries index. */
+export declare function definitionText(p: Record<string, unknown>, name: string): string;
+/**
+ * Indexes the agent and skill definitions as `Agent` / `Skill` nodes, so "which
+ * agent handles X" and "which code does this agent touch" are graph queries.
+ * `.claude/` is excluded from the file scan on purpose (it is mirrored into
+ * several platform trees), so this reads the root tree directly. Rebuilt from
+ * scratch each build; a definition's REFERENCES edges point at the repository
+ * files its text names.
+ */
+export declare const agentRegistryPhase: PipelinePhase<{
+    definitions: number;
+}>;
+//# sourceMappingURL=agent-registry.d.ts.map

package/dist/src/pipeline/phases/agent-registry.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/pipeline/phases/agent-registry.js

@@ -0,0 +1,153 @@
+import { existsSync, readdirSync, readFileSync, statSync } from 'node:fs';
+import { join, relative } from 'node:path';
+import { insertEdges } from '../../storage/edge-store.js';
+import { insertNodes } from '../../storage/node-store.js';
+import { toNormLabel } from '../../types.js';
+const MAX_FILE_BYTES = 256 * 1024;
+const MAX_REFERENCED_FILES = 20;
+const PATH_RE = /[\w@./-]+\.(?:ts|tsx|mjs|cjs|js|json|md)/g;
+function unquote(v) {
+    const t = v.trim();
+    return /^(".*"|'.*')$/s.test(t) ? t.slice(1, -1).replace(/\\(["'])/g, '$1') : t;
+}
+/**
+ * Reads the flat `key: value` frontmatter agent and skill files use. Only the
+ * keys the graph needs; nested blocks such as `capability:` are ignored.
+ */
+export function parseDefinition(kind, filePath, source) {
+    const m = /^---\r?\n([\s\S]*?)\r?\n---\r?\n?([\s\S]*)$/.exec(source);
+    if (!m)
+        return null;
+    const fields = new Map();
+    for (const line of m[1].split(/\r?\n/)) {
+        const kv = /^([A-Za-z_][\w-]*):\s*(.*)$/.exec(line);
+        if (kv)
+            fields.set(kv[1], kv[2]);
+    }
+    const name = unquote(fields.get('name') ?? '');
+    if (!name)
+        return null;
+    const tags = (fields.get('tags') ?? '')
+        .replace(/^\[|\]$/g, '')
+        .split(',')
+        .map((t) => unquote(t))
+        .filter(Boolean);
+    return {
+        kind,
+        name,
+        filePath,
+        description: unquote(fields.get('description') ?? ''),
+        whenToUse: unquote(fields.get('when_to_use') ?? ''),
+        tags,
+        category: unquote(fields.get('category') ?? ''),
+        body: m[2],
+    };
+}
+function* markdownFiles(dir) {
+    if (!existsSync(dir))
+        return;
+    for (const entry of readdirSync(dir)) {
+        const full = join(dir, entry);
+        const st = statSync(full);
+        if (st.isDirectory())
+            yield* markdownFiles(full);
+        else if (entry.endsWith('.md'))
+            yield full;
+    }
+}
+/** Agents under `.claude/agents/**` and skills at `.claude/skills/<name>/SKILL.md`. */
+export function readDefinitions(repoPath) {
+    const out = [];
+    const add = (kind, abs) => {
+        try {
+            if (statSync(abs).size > MAX_FILE_BYTES)
+                return;
+            const def = parseDefinition(kind, relative(repoPath, abs), readFileSync(abs, 'utf8'));
+            if (def)
+                out.push(def);
+        }
+        catch {
+            /* unreadable definition: skip it, the rest still index */
+        }
+    };
+    for (const abs of markdownFiles(join(repoPath, '.claude', 'agents')))
+        add('Agent', abs);
+    const skills = join(repoPath, '.claude', 'skills');
+    if (existsSync(skills)) {
+        for (const entry of readdirSync(skills)) {
+            const skillFile = join(skills, entry, 'SKILL.md');
+            if (existsSync(skillFile))
+                add('Skill', skillFile);
+        }
+    }
+    return out;
+}
+/** The searchable description of a definition, for the summaries index. */
+export function definitionText(p, name) {
+    const tags = Array.isArray(p.tags) ? p.tags.join(' ') : '';
+    return [name, p.description, p.whenToUse, tags, p.category]
+        .filter((x) => typeof x === 'string' && x)
+        .join(' ');
+}
+/**
+ * Indexes the agent and skill definitions as `Agent` / `Skill` nodes, so "which
+ * agent handles X" and "which code does this agent touch" are graph queries.
+ * `.claude/` is excluded from the file scan on purpose (it is mirrored into
+ * several platform trees), so this reads the root tree directly. Rebuilt from
+ * scratch each build; a definition's REFERENCES edges point at the repository
+ * files its text names.
+ */
+export const agentRegistryPhase = {
+    name: 'agent-registry',
+    deps: ['stale-sweep'],
+    async execute(ctx) {
+        const db = ctx.db;
+        db.exec("DELETE FROM edges WHERE source_id IN (SELECT id FROM nodes WHERE label IN ('Agent','Skill'))");
+        db.exec("DELETE FROM nodes WHERE label IN ('Agent','Skill')");
+        const defs = readDefinitions(ctx.repoPath);
+        if (defs.length === 0)
+            return { definitions: 0 };
+        const fileIds = new Map(db.prepare("SELECT id, file_path FROM nodes WHERE label = 'File'").all().map((r) => [r.file_path, r.id]));
+        const nodes = [];
+        const edges = [];
+        for (const d of defs) {
+            // Path-keyed, not slugged: two definitions can never share an id.
+            const id = `${d.kind.toLowerCase()}:${d.filePath}`;
+            nodes.push({
+                id,
+                label: d.kind,
+                name: d.name,
+                normLabel: toNormLabel(d.name),
+                filePath: d.filePath,
+                startLine: 1,
+                isExported: true,
+                properties: {
+                    description: d.description,
+                    whenToUse: d.whenToUse,
+                    tags: d.tags,
+                    category: d.category,
+                },
+            });
+            const seen = new Set();
+            for (const match of d.body.matchAll(PATH_RE)) {
+                const target = fileIds.get(match[0]);
+                if (!target || seen.has(target) || seen.size >= MAX_REFERENCED_FILES)
+                    continue;
+                seen.add(target);
+                edges.push({
+                    id: `agent-ref:${id}>${target}`,
+                    sourceId: id,
+                    targetId: target,
+                    relation: 'REFERENCES',
+                    confidence: 'INFERRED',
+                    confidenceScore: 0.6,
+                    reason: `${d.kind.toLowerCase()} text names this file`,
+                });
+            }
+        }
+        insertNodes(db, nodes);
+        insertEdges(db, edges);
+        return { definitions: nodes.length };
+    },
+};
+//# sourceMappingURL=agent-registry.js.map

package/dist/src/pipeline/phases/agent-registry.js.map

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package/dist/src/pipeline/phases/communities.d.ts.map

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