@monoes/monograph 1.2.0 → 1.2.1

package/dist/src/pipeline/phases/scope-resolution.js

@@ -171,49 +171,93 @@ function extractCallSites(source, filePath, fileNodeId, ext) {
     }
     return sites;
 }
-// ── Stage 3: Build import map from DB ─────────────────────────────────────────
-/** Returns a map of imported name → source file path for a given file node */
-function buildImportMap(ctx, fileNodeId, symbolNodes) {
-    const importMap = new Map();
+// ── Stage 3: Build import maps from DB (batch) ────────────────────────────────
+/**
+ * Load all IMPORTS edges once and return a map of fileNodeId → (name → filePath).
+ * Eliminates the N+1 pattern of querying per-file inside the main loop.
+ */
+function buildAllImportMaps(ctx, symbolNodes) {
+    const result = new Map();
     if (!ctx.db)
-        return importMap;
-    // Get IMPORTS edges for this file to find which modules it imports
+        return result;
+    // Build a lookup: fileNodeId → filePath from symbolNodes
+    const idToFilePath = new Map();
+    for (const n of symbolNodes) {
+        if (n.label === 'File' && n.filePath) {
+            idToFilePath.set(n.id, n.filePath);
+            // Also register the alternate makeId form
+            const altId = makeId(n.filePath.replace(/\//g, '_'), 'file');
+            if (altId !== n.id)
+                idToFilePath.set(altId, n.filePath);
+        }
+    }
+    // Load ALL IMPORTS edges in one query
     const importsRows = ctx.db
-        .prepare(`SELECT target_id FROM edges WHERE source_id = ? AND relation = 'IMPORTS'`)
-        .all(fileNodeId);
+        .prepare(`SELECT source_id, target_id FROM edges WHERE relation = 'IMPORTS'`)
+        .all();
     for (const row of importsRows) {
-        const targetId = row.target_id;
-        // Find a File node that matches the resolved target
-        const fileNode = symbolNodes.find(n => n.label === 'File' && (n.id === targetId ||
-            makeId(n.filePath?.replace(/\//g, '_') ?? '', 'file') === targetId));
-        if (fileNode?.filePath) {
-            // Extract the module name from the last path segment without extension
-            const parts = fileNode.filePath.split('/');
-            const baseName = parts[parts.length - 1].replace(/\.\w+$/, '');
-            importMap.set(baseName, fileNode.filePath);
-            importMap.set(fileNode.filePath, fileNode.filePath);
+        const targetPath = idToFilePath.get(row.target_id);
+        if (!targetPath)
+            continue;
+        let fileMap = result.get(row.source_id);
+        if (!fileMap) {
+            fileMap = new Map();
+            result.set(row.source_id, fileMap);
         }
+        const parts = targetPath.split('/');
+        const baseName = parts[parts.length - 1].replace(/\.\w+$/, '');
+        fileMap.set(baseName, targetPath);
+        fileMap.set(targetPath, targetPath);
     }
-    return importMap;
+    return result;
+}
+/** Returns the pre-built import map for a given file node (empty map if not found). */
+function getImportMap(allImportMaps, fileNodeId) {
+    return allImportMaps.get(fileNodeId) ?? new Map();
 }
-// ── Stage 4 + 5: Resolve target node ─────────────────────────────────────────
-function resolveTarget(ctx, site, callerFilePath, importMap) {
+// ── Stage 4 helpers: preloaded function/method index ──────────────────────────
+/**
+ * Load all Function/Method/Constructor nodes once.
+ * Returns two indices:
+ * - byFilePath: filePath → name → id[] (for resolveTarget candidate lookup)
+ * - nameCounts: name → total occurrences across all files (for ambiguity check)
+ */
+function buildFunctionIndex(ctx) {
+    const byFilePath = new Map();
+    const nameCounts = new Map();
     if (!ctx.db)
-        return null;
+        return { byFilePath, nameCounts };
+    const rows = ctx.db
+        .prepare(`SELECT id, name, file_path FROM nodes WHERE label IN ('Function', 'Method', 'Constructor') AND file_path IS NOT NULL`)
+        .all();
+    for (const row of rows) {
+        // byFilePath index
+        let fileMap = byFilePath.get(row.file_path);
+        if (!fileMap) {
+            fileMap = new Map();
+            byFilePath.set(row.file_path, fileMap);
+        }
+        let ids = fileMap.get(row.name);
+        if (!ids) {
+            ids = [];
+            fileMap.set(row.name, ids);
+        }
+        ids.push(row.id);
+        // global count for ambiguity detection
+        nameCounts.set(row.name, (nameCounts.get(row.name) ?? 0) + 1);
+    }
+    return { byFilePath, nameCounts };
+}
+// ── Stage 4 + 5: Resolve target node (index-based, no per-call DB query) ──────
+function resolveTarget(site, callerFilePath, importMap, fnIndex) {
     const methodName = site.methodName;
     if (!methodName)
         return null;
-    let candidateFilePaths = [];
+    let candidateFilePaths;
     if (site.form === 'method' && site.receiverName) {
         // Stage 3: Infer receiver type — look up receiver in import map
         const receiverPath = importMap.get(site.receiverName);
-        if (receiverPath) {
-            candidateFilePaths = [receiverPath];
-        }
-        else {
-            // Receiver not imported — look in same file only
-            candidateFilePaths = [callerFilePath];
-        }
+        candidateFilePaths = receiverPath ? [receiverPath] : [callerFilePath];
     }
     else if (site.form === 'direct') {
         // Direct call: same file first, then all imported files
@@ -222,21 +266,13 @@ function resolveTarget(ctx, site, callerFilePath, importMap) {
     else {
         return null;
     }
-    // Stage 5: Query nodes table for matching function/method/constructor
+    // Stage 5: O(1) lookup in preloaded index instead of per-call DB query
     for (const fp of candidateFilePaths) {
-        const rows = ctx.db
-            .prepare(`
-        SELECT id FROM nodes
-        WHERE name = ?
-          AND label IN ('Function', 'Method', 'Constructor')
-          AND file_path = ?
-        LIMIT 2
-      `)
-            .all(methodName, fp);
-        if (rows.length === 1) {
-            return { targetId: rows[0].id };
+        const ids = fnIndex.get(fp)?.get(methodName);
+        if (ids && ids.length === 1) {
+            return { targetId: ids[0] };
         }
-        // If > 1 match, it's ambiguous — skip this candidate file
+        // ids.length > 1 → ambiguous within this file — skip to next candidate
     }
     return null;
 }
@@ -291,6 +327,7 @@ export const scopeResolutionPhase = {
         let resolvedEdges = 0;
         let skippedDynamic = 0;
         let ambiguous = 0;
+        // ── Batch preload: one query per table instead of one per file/call-site ──
         // Build a map from file_path → file node id using the parse output
         const fileNodesByPath = new Map();
         for (const node of symbolNodes) {
@@ -316,6 +353,10 @@ export const scopeResolutionPhase = {
                 }
             }
         }
+        // Preload all IMPORTS edges → per-file import maps (one DB query total)
+        const allImportMaps = buildAllImportMaps(ctx, symbolNodes);
+        // Preload all Function/Method/Constructor nodes into indices (one DB query total)
+        const { byFilePath: fnIndex, nameCounts } = buildFunctionIndex(ctx);
         for (const [filePath, fileNode] of fileNodesByPath) {
             const ext = extname(filePath).toLowerCase();
             if (!isSupportedExt(ext))
@@ -330,34 +371,23 @@ export const scopeResolutionPhase = {
             }
             // Stage 1+2: Extract call sites
             const callSites = extractCallSites(source, filePath, fileNode.id, ext);
-            // Stage 3: Build import map for this file
-            const importMap = buildImportMap(ctx, fileNode.id, symbolNodes);
+            // Stage 3: Get pre-built import map for this file (O(1))
+            const importMap = getImportMap(allImportMaps, fileNode.id);
             for (const site of callSites) {
                 if (site.form === 'dynamic') {
                     skippedDynamic++;
                     continue;
                 }
-                // Stage 4+5: Resolve target
-                const resolved = resolveTarget(ctx, site, filePath, importMap);
+                // Stage 4+5: Resolve target using preloaded indices (no DB query)
+                const resolved = resolveTarget(site, filePath, importMap, fnIndex);
                 if (!resolved) {
-                    // Could not resolve — treat as ambiguous if we had candidates
-                    // (method calls with unresolvable receivers are simply skipped)
+                    // Could not resolve — method calls with unresolvable receivers are simply skipped
                     continue;
                 }
-                // Check if the resolved target is actually in multiple places (ambiguity check)
-                if (ctx.db && site.methodName) {
-                    const totalMatches = ctx.db
-                        .prepare(`
-              SELECT COUNT(*) as cnt FROM nodes
-              WHERE name = ?
-                AND label IN ('Function', 'Method', 'Constructor')
-            `)
-                        .get(site.methodName);
-                    if (totalMatches.cnt > 1) {
-                        ambiguous++;
-                        // Still emit if we found exactly one in the candidate file — this is per-file ambiguity
-                        // The resolve already picked one candidate, so proceed
-                    }
+                // Ambiguity check using preloaded name counts (no DB query)
+                if (site.methodName && (nameCounts.get(site.methodName) ?? 0) > 1) {
+                    ambiguous++;
+                    // Still emit — we found exactly one candidate in the caller's context
                 }
                 // Stage 6: Emit edge (source is the file node of the caller)
                 const result = emitEdge(ctx, site.callerFileNodeId, resolved.targetId);

package/dist/src/pipeline/phases/scope-resolution.js.map

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

@@ -1,6 +1,10 @@
 import type { PipelinePhase, PipelineContext } from './types.js';
 export declare class PipelineRunner {
     private readonly phases;
+    /** Topo-sorted phase names, computed once in constructor for O(1) phase map lookups. */
+    private readonly sortedNames;
+    /** O(1) phase lookup by name. */
+    private readonly phaseMap;
     constructor(phases: PipelinePhase<unknown>[]);
     run(ctx: PipelineContext): Promise<Map<string, unknown>>;
 }

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

@@ -1 +1 @@
-{"version":3,"file":"runner.d.ts","sourceRoot":"","sources":["../../../src/pipeline/runner.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAE,eAAe,EAAE,MAAM,YAAY,CAAC;AAGjE,qBAAa,cAAc;IACzB,OAAO,CAAC,QAAQ,CAAC,MAAM,CAA2B;gBAEtC,MAAM,EAAE,aAAa,CAAC,OAAO,CAAC,EAAE;IAMtC,GAAG,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;CAyB/D;AAuCD,MAAM,WAAW,qBAAqB;IACpC,6FAA6F;IAC7F,gBAAgB,CAAC,EAAE,OAAO,CAAC;CAC5B;AAED;;;;GAIG;AACH,wBAAsB,iBAAiB,CACrC,EAAE,EAAE,OAAO,gBAAgB,EAAE,QAAQ,EACrC,YAAY,EAAE,MAAM,EAAE,EACtB,OAAO,GAAE,qBAA0B,GAClC,OAAO,CAAC,IAAI,CAAC,CAoBf"}
+{"version":3,"file":"runner.d.ts","sourceRoot":"","sources":["../../../src/pipeline/runner.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAE,eAAe,EAAE,MAAM,YAAY,CAAC;AAGjE,qBAAa,cAAc;IACzB,OAAO,CAAC,QAAQ,CAAC,MAAM,CAA2B;IAClD,wFAAwF;IACxF,OAAO,CAAC,QAAQ,CAAC,WAAW,CAAW;IACvC,iCAAiC;IACjC,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAsC;gBAEnD,MAAM,EAAE,aAAa,CAAC,OAAO,CAAC,EAAE;IAMtC,GAAG,CAAC,GAAG,EAAE,eAAe,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;CAiC/D;AAuCD,MAAM,WAAW,qBAAqB;IACpC,6FAA6F;IAC7F,gBAAgB,CAAC,EAAE,OAAO,CAAC;CAC5B;AAED;;;;GAIG;AACH,wBAAsB,iBAAiB,CACrC,EAAE,EAAE,OAAO,gBAAgB,EAAE,QAAQ,EACrC,YAAY,EAAE,MAAM,EAAE,EACtB,OAAO,GAAE,qBAA0B,GAClC,OAAO,CAAC,IAAI,CAAC,CAyBf"}

package/dist/src/pipeline/runner.js

@@ -1,32 +1,46 @@
 import { MonographError } from '../types.js';
 export class PipelineRunner {
     phases;
+    /** Topo-sorted phase names, computed once in constructor for O(1) phase map lookups. */
+    sortedNames;
+    /** O(1) phase lookup by name. */
+    phaseMap;
     constructor(phases) {
         this.phases = phases;
-        // Validate: detect cycles and unknown deps
-        topoSort(phases);
+        this.sortedNames = topoSort(phases);
+        this.phaseMap = new Map(phases.map(p => [p.name, p]));
     }
     async run(ctx) {
         const outputs = new Map();
-        const phaseMap = new Map(this.phases.map(p => [p.name, p]));
         // Lazily-created promise per phase — ensures dep promises exist before they are awaited
         const promises = new Map();
         const getOrCreatePromise = (name) => {
             if (promises.has(name))
                 return promises.get(name);
-            const phase = phaseMap.get(name);
+            const phase = this.phaseMap.get(name);
             const p = (async () => {
                 // Wait for all dep phases to finish
                 await Promise.all(phase.deps.map(dep => getOrCreatePromise(dep)));
                 ctx.onProgress?.({ phase: phase.name });
-                const output = await phase.execute(ctx, outputs);
-                outputs.set(phase.name, output);
+                try {
+                    const output = await phase.execute(ctx, outputs);
+                    outputs.set(phase.name, output);
+                }
+                catch (err) {
+                    const msg = err instanceof Error ? err.message : String(err);
+                    throw new MonographError(`Phase '${phase.name}' failed: ${msg}`);
+                }
             })();
             promises.set(name, p);
             return p;
         };
-        // Kick off all phases — each self-manages its dep wait via lazy promise creation
-        await Promise.all(this.phases.map(phase => getOrCreatePromise(phase.name)));
+        // Use allSettled so every in-flight phase completes before we return.
+        // This ensures the DB is not closed while phases are still writing to it,
+        // which would otherwise cause unhandled rejections that hang the process.
+        const results = await Promise.allSettled(this.sortedNames.map(name => getOrCreatePromise(name)));
+        const failed = results.find(r => r.status === 'rejected');
+        if (failed)
+            throw failed.reason;
         return outputs;
     }
 }
@@ -72,14 +86,19 @@ export async function runIncrementalAst(db, changedFiles, options = {}) {
     if (preserveInferred) {
         if (changedFiles.length > 0) {
             const placeholders = changedFiles.map(() => '?').join(',');
+            // Use a CTE to resolve file_path→id once, then delete edges referencing those ids.
+            // This avoids passing changedFiles twice (N*2 params) and lets SQLite reuse the scan.
             db.prepare(`
+        WITH changed_ids AS (
+          SELECT id FROM nodes WHERE file_path IN (${placeholders})
+        )
         DELETE FROM edges
         WHERE confidence = 'EXTRACTED'
         AND (
-          source_id IN (SELECT id FROM nodes WHERE file_path IN (${placeholders}))
-          OR target_id IN (SELECT id FROM nodes WHERE file_path IN (${placeholders}))
+          source_id IN (SELECT id FROM changed_ids)
+          OR target_id IN (SELECT id FROM changed_ids)
         )
-      `).run(...changedFiles, ...changedFiles);
+      `).run(...changedFiles);
         }
         else {
             db.prepare(`DELETE FROM edges WHERE confidence = 'EXTRACTED'`).run();

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

@@ -1 +1 @@
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+{"version":3,"file":"runner.js","sourceRoot":"","sources":["../../../src/pipeline/runner.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,cAAc,EAAE,MAAM,aAAa,CAAC;AAE7C,MAAM,OAAO,cAAc;IACR,MAAM,CAA2B;IAClD,wFAAwF;IACvE,WAAW,CAAW;IACvC,iCAAiC;IAChB,QAAQ,CAAsC;IAE/D,YAAY,MAAgC;QAC1C,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC;QACrB,IAAI,CAAC,WAAW,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC;QACpC,IAAI,CAAC,QAAQ,GAAG,IAAI,GAAG,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;IACxD,CAAC;IAED,KAAK,CAAC,GAAG,CAAC,GAAoB;QAC5B,MAAM,OAAO,GAAG,IAAI,GAAG,EAAmB,CAAC;QAE3C,wFAAwF;QACxF,MAAM,QAAQ,GAAG,IAAI,GAAG,EAAyB,CAAC;QAElD,MAAM,kBAAkB,GAAG,CAAC,IAAY,EAAiB,EAAE;YACzD,IAAI,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAC;gBAAE,OAAO,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAE,CAAC;YACnD,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAE,CAAC;YACvC,MAAM,CAAC,GAAG,CAAC,KAAK,IAAI,EAAE;gBACpB,oCAAoC;gBACpC,MAAM,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,kBAAkB,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;gBAClE,GAAG,CAAC,UAAU,EAAE,CAAC,EAAE,KAAK,EAAE,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;gBACxC,IAAI,CAAC;oBACH,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,OAAO,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC;oBACjD,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;gBAClC,CAAC;gBAAC,OAAO,GAAG,EAAE,CAAC;oBACb,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;oBAC7D,MAAM,IAAI,cAAc,CAAC,UAAU,KAAK,CAAC,IAAI,aAAa,GAAG,EAAE,CAAC,CAAC;gBACnE,CAAC;YACH,CAAC,CAAC,EAAE,CAAC;YACL,QAAQ,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC;YACtB,OAAO,CAAC,CAAC;QACX,CAAC,CAAC;QAEF,sEAAsE;QACtE,0EAA0E;QAC1E,0EAA0E;QAC1E,MAAM,OAAO,GAAG,MAAM,OAAO,CAAC,UAAU,CAAC,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,kBAAkB,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;QACjG,MAAM,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,UAAU,CAAsC,CAAC;QAC/F,IAAI,MAAM;YAAE,MAAM,MAAM,CAAC,MAAM,CAAC;QAChC,OAAO,OAAO,CAAC;IACjB,CAAC;CACF;AAED,SAAS,QAAQ,CAAC,MAAgC;IAChD,MAAM,KAAK,GAAG,IAAI,GAAG,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC;IAC/C,MAAM,QAAQ,GAAG,IAAI,GAAG,EAAkB,CAAC;IAC3C,MAAM,OAAO,GAAG,IAAI,GAAG,EAAoB,CAAC;IAE5C,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;QACvB,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;QACpC,KAAK,MAAM,GAAG,IAAI,CAAC,CAAC,IAAI,EAAE,CAAC;YACzB,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;gBACpB,MAAM,IAAI,cAAc,CAAC,UAAU,CAAC,CAAC,IAAI,+BAA+B,GAAG,GAAG,CAAC,CAAC;YAClF,CAAC;YACD,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC;YACnC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;YACjB,OAAO,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC;QACxB,CAAC;IACH,CAAC;IAED,MAAM,KAAK,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC;IACrF,MAAM,MAAM,GAAa,EAAE,CAAC;IAE5B,OAAO,KAAK,CAAC,MAAM,EAAE,CAAC;QACpB,MAAM,IAAI,GAAG,KAAK,CAAC,KAAK,EAAG,CAAC;QAC5B,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QAClB,KAAK,MAAM,IAAI,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC,EAAE,CAAC;YAC7C,MAAM,GAAG,GAAG,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC;YAC1C,QAAQ,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC;YACxB,IAAI,GAAG,KAAK,CAAC;gBAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QAClC,CAAC;IACH,CAAC;IAED,IAAI,MAAM,CAAC,MAAM,KAAK,MAAM,CAAC,MAAM,EAAE,CAAC;QACpC,MAAM,IAAI,cAAc,CAAC,wCAAwC,CAAC,CAAC;IACrE,CAAC;IAED,OAAO,MAAM,CAAC;AAChB,CAAC;AAOD;;;;GAIG;AACH,MAAM,CAAC,KAAK,UAAU,iBAAiB,CACrC,EAAqC,EACrC,YAAsB,EACtB,UAAiC,EAAE;IAEnC,MAAM,EAAE,gBAAgB,GAAG,IAAI,EAAE,GAAG,OAAO,CAAC;IAE5C,IAAI,gBAAgB,EAAE,CAAC;QACrB,IAAI,YAAY,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC5B,MAAM,YAAY,GAAG,YAAY,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;YAC3D,mFAAmF;YACnF,sFAAsF;YACtF,EAAE,CAAC,OAAO,CAAC;;qDAEoC,YAAY;;;;;;;;OAQ1D,CAAC,CAAC,GAAG,CAAC,GAAG,YAAY,CAAC,CAAC;QAC1B,CAAC;aAAM,CAAC;YACN,EAAE,CAAC,OAAO,CAAC,kDAAkD,CAAC,CAAC,GAAG,EAAE,CAAC;QACvE,CAAC;IACH,CAAC;SAAM,CAAC;QACN,EAAE,CAAC,OAAO,CAAC,mBAAmB,CAAC,CAAC,GAAG,EAAE,CAAC;IACxC,CAAC;AACH,CAAC"}

package/dist/src/query/cypher-parser.d.ts

@@ -48,4 +48,24 @@ export declare function cypherToSql(parsed: CypherQuery): {
  * Never throws — all errors are returned in the CypherResult.error field.
  */
 export declare function executeCypherQuery(db: Database.Database, query: string): CypherResult;
+/**
+ * Format a CypherResult as structured text for LLM consumption.
+ *
+ * Rows that contain *_filePath and *_startLine fields are rendered with
+ * "file:line" navigation hints so LLMs can jump directly to the symbol.
+ * Plain key=value pairs are rendered for all other fields.
+ *
+ * @example
+ * ```
+ * monograph_cypher result (3 rows, 2ms)
+ *
+ * Row 1:
+ *   n.name = buildAsync
+ *   n.filePath = src/server.ts:42
+ *
+ * Row 2:
+ *   ...
+ * ```
+ */
+export declare function formatCypherResult(result: CypherResult): string;
 //# sourceMappingURL=cypher-parser.d.ts.map

package/dist/src/query/cypher-parser.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"cypher-parser.d.ts","sourceRoot":"","sources":["../../../src/query/cypher-parser.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,QAAQ,MAAM,gBAAgB,CAAC;AAI3C,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,GAAG,cAAc,CAAC;IAC9B,KAAK,EAAE;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,KAAK,CAAC,EAAE,MAAM,CAAC;QAAC,KAAK,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAA;KAAE,CAAC;IACzE,KAAK,CAAC,EAAE;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,KAAK,CAAC,EAAE,MAAM,CAAC;QAAC,KAAK,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAA;KAAE,CAAC;IAC1E,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,WAAW,CAAC,EAAE;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;IAC9D,YAAY,EAAE,KAAK,CAAC;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;CACvD;AAED,MAAM,WAAW,YAAY;IAC3B,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAAC,EAAE,CAAC;IAC/C,SAAS,EAAE,MAAM,CAAC;IAClB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AA2HD;;;GAGG;AACH,wBAAgB,gBAAgB,CAAC,KAAK,EAAE,MAAM,GAAG;IAAE,MAAM,EAAE,WAAW,GAAG,IAAI,CAAC;IAAC,KAAK,CAAC,EAAE,MAAM,CAAA;CAAE,CA8F9F;AAkDD;;;GAGG;AACH,wBAAgB,WAAW,CAAC,MAAM,EAAE,WAAW,GAAG;IAAE,GAAG,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,OAAO,EAAE,CAAA;CAAE,CA8CnF;AAID;;;GAGG;AACH,wBAAgB,kBAAkB,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,EAAE,KAAK,EAAE,MAAM,GAAG,YAAY,CAoBrF"}
+{"version":3,"file":"cypher-parser.d.ts","sourceRoot":"","sources":["../../../src/query/cypher-parser.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,QAAQ,MAAM,gBAAgB,CAAC;AAI3C,MAAM,WAAW,WAAW;IAC1B,IAAI,EAAE,MAAM,GAAG,cAAc,CAAC;IAC9B,KAAK,EAAE;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,KAAK,CAAC,EAAE,MAAM,CAAC;QAAC,KAAK,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAA;KAAE,CAAC;IACzE,KAAK,CAAC,EAAE;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,KAAK,CAAC,EAAE,MAAM,CAAC;QAAC,KAAK,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAA;KAAE,CAAC;IAC1E,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,WAAW,CAAC,EAAE;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;IAC9D,YAAY,EAAE,KAAK,CAAC;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;CACvD;AAED,MAAM,WAAW,YAAY;IAC3B,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAAC,EAAE,CAAC;IAC/C,SAAS,EAAE,MAAM,CAAC;IAClB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AA2HD;;;GAGG;AACH,wBAAgB,gBAAgB,CAAC,KAAK,EAAE,MAAM,GAAG;IAAE,MAAM,EAAE,WAAW,GAAG,IAAI,CAAC;IAAC,KAAK,CAAC,EAAE,MAAM,CAAA;CAAE,CA8F9F;AAkDD;;;GAGG;AACH,wBAAgB,WAAW,CAAC,MAAM,EAAE,WAAW,GAAG;IAAE,GAAG,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,OAAO,EAAE,CAAA;CAAE,CA8CnF;AAID;;;GAGG;AACH,wBAAgB,kBAAkB,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,EAAE,KAAK,EAAE,MAAM,GAAG,YAAY,CAoBrF;AAID;;;;;;;;;;;;;;;;;;GAkBG;AACH,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,YAAY,GAAG,MAAM,CA4D/D"}

package/dist/src/query/cypher-parser.js

@@ -293,4 +293,77 @@ export function executeCypherQuery(db, query) {
         };
     }
 }
+// ── Structured text formatter ──────────────────────────────────────────────────
+/**
+ * Format a CypherResult as structured text for LLM consumption.
+ *
+ * Rows that contain *_filePath and *_startLine fields are rendered with
+ * "file:line" navigation hints so LLMs can jump directly to the symbol.
+ * Plain key=value pairs are rendered for all other fields.
+ *
+ * @example
+ * ```
+ * monograph_cypher result (3 rows, 2ms)
+ *
+ * Row 1:
+ *   n.name = buildAsync
+ *   n.filePath = src/server.ts:42
+ *
+ * Row 2:
+ *   ...
+ * ```
+ */
+export function formatCypherResult(result) {
+    if (result.error) {
+        return `monograph_cypher error: ${result.error}`;
+    }
+    if (result.rows.length === 0) {
+        return `monograph_cypher result (0 rows, ${result.queryTime}ms)\n\nNo results found.`;
+    }
+    const lines = [
+        `monograph_cypher result (${result.rows.length} row${result.rows.length === 1 ? '' : 's'}, ${result.queryTime}ms)`,
+        '',
+    ];
+    for (let i = 0; i < result.rows.length; i++) {
+        lines.push(`Row ${i + 1}:`);
+        const row = result.rows[i];
+        // Group fields by alias prefix (e.g., "n_name", "b_filePath")
+        // and reconstruct "alias.field = value" display, with file:line merging
+        const seen = new Set();
+        for (const key of Object.keys(row)) {
+            if (seen.has(key))
+                continue;
+            seen.add(key);
+            // key format is aliasName_fieldName (e.g. n_filePath, n_startLine)
+            const sepIdx = key.indexOf('_');
+            if (sepIdx === -1) {
+                lines.push(`  ${key} = ${row[key] ?? 'null'}`);
+                continue;
+            }
+            const alias = key.slice(0, sepIdx);
+            const field = key.slice(sepIdx + 1);
+            // Merge filePath + startLine into a single file:line hint
+            if (field === 'filePath') {
+                const startLineKey = `${alias}_startLine`;
+                const startLine = row[startLineKey];
+                seen.add(startLineKey);
+                const filePath = row[key];
+                if (filePath != null && startLine != null) {
+                    lines.push(`  ${alias}.filePath = ${filePath}:${startLine}`);
+                }
+                else if (filePath != null) {
+                    lines.push(`  ${alias}.filePath = ${filePath}`);
+                }
+                continue;
+            }
+            // Skip startLine — already consumed by filePath branch above
+            if (field === 'startLine')
+                continue;
+            lines.push(`  ${alias}.${field} = ${row[key] ?? 'null'}`);
+        }
+        if (i < result.rows.length - 1)
+            lines.push('');
+    }
+    return lines.join('\n');
+}
 //# sourceMappingURL=cypher-parser.js.map

package/dist/src/query/cypher-parser.js.map

@@ -1 +1 @@
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package/dist/src/search/embed-batch.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"embed-batch.d.ts","sourceRoot":"","sources":["../../../src/search/embed-batch.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,KAAK,QAAQ,MAAM,gBAAgB,CAAC;AAC3C,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,eAAe,CAAC;AAChD,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAC;AAC5D,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAC;AAC7D,OAAO,EAAmB,eAAe,EAAE,MAAM,+BAA+B,CAAC;AAKjF,MAAM,WAAW,gBAAgB;IAC/B,MAAM,CAAC,EAAE,iBAAiB,CAAC;IAC3B,MAAM,CAAC,EAAE,kBAAkB,CAAC;IAC5B,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED;;;;;;;;GAQG;AACH,wBAAsB,UAAU,CAC9B,KAAK,EAAE,MAAM,EAAE,EACf,MAAM,CAAC,EAAE,gBAAgB,GACxB,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,CA6BrB;AAED,MAAM,WAAW,cAAc;IAC7B,QAAQ,EAAE,MAAM,CAAC;IACjB,OAAO,EAAE,MAAM,CAAC;CACjB;AAcD,wBAAsB,QAAQ,CAC5B,EAAE,EAAE,QAAQ,CAAC,QAAQ,EACrB,QAAQ,EAAE,UAAU,EACpB,KAAK,UAAQ,EACb,QAAQ,UAAQ,GACf,OAAO,CAAC,cAAc,CAAC,CA+CzB;AAgBD,OAAO,EAAE,eAAe,EAAE,CAAC"}
+{"version":3,"file":"embed-batch.d.ts","sourceRoot":"","sources":["../../../src/search/embed-batch.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,KAAK,QAAQ,MAAM,gBAAgB,CAAC;AAC3C,OAAO,KAAK,EAAE,UAAU,EAAE,MAAM,eAAe,CAAC;AAChD,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAC;AAC5D,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAC;AAC7D,OAAO,EAA0C,eAAe,EAAE,MAAM,+BAA+B,CAAC;AAKxG,MAAM,WAAW,gBAAgB;IAC/B,MAAM,CAAC,EAAE,iBAAiB,CAAC;IAC3B,MAAM,CAAC,EAAE,kBAAkB,CAAC;IAC5B,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED;;;;;;;;GAQG;AACH,wBAAsB,UAAU,CAC9B,KAAK,EAAE,MAAM,EAAE,EACf,MAAM,CAAC,EAAE,gBAAgB,GACxB,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,CA6BrB;AAED,MAAM,WAAW,cAAc;IAC7B,QAAQ,EAAE,MAAM,CAAC;IACjB,OAAO,EAAE,MAAM,CAAC;CACjB;AAcD,wBAAsB,QAAQ,CAC5B,EAAE,EAAE,QAAQ,CAAC,QAAQ,EACrB,QAAQ,EAAE,UAAU,EACpB,KAAK,UAAQ,EACb,QAAQ,UAAQ,GACf,OAAO,CAAC,cAAc,CAAC,CAkDzB;AAgBD,OAAO,EAAE,eAAe,EAAE,CAAC"}

package/dist/src/search/embed-batch.js

@@ -1,7 +1,7 @@
 /**
  * Batch-embed all symbol nodes that don't yet have an embedding stored.
  */
-import { upsertEmbedding, countEmbeddings } from '../storage/embedding-store.js';
+import { upsertEmbedding, ensureEmbeddingSchema, countEmbeddings } from '../storage/embedding-store.js';
 import { embedText } from './embedder.js';
 const BATCH_SIZE = 32;
 /**
@@ -65,6 +65,9 @@ export async function embedAll(db, embedder, force = false, codeOnly = false) {
     // Filter to only rows that need embedding
     const toEmbed = filteredRows.filter((r) => !existingIds.has(r.id));
     skipped = filteredRows.length - toEmbed.length;
+    // Ensure schema migration runs once before any upsert — not per-row.
+    if (toEmbed.length > 0)
+        ensureEmbeddingSchema(db);
     // Process in batches
     for (let i = 0; i < toEmbed.length; i += BATCH_SIZE) {
         const batch = toEmbed.slice(i, i + BATCH_SIZE);

package/dist/src/search/embed-batch.js.map

@@ -1 +1 @@
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+{"version":3,"file":"embed-batch.js","sourceRoot":"","sources":["../../../src/search/embed-batch.ts"],"names":[],"mappings":"AAAA;;GAEG;AAMH,OAAO,EAAE,eAAe,EAAE,qBAAqB,EAAE,eAAe,EAAE,MAAM,+BAA+B,CAAC;AACxG,OAAO,EAAE,SAAS,EAAE,MAAM,eAAe,CAAC;AAE1C,MAAM,UAAU,GAAG,EAAE,CAAC;AAQtB;;;;;;;;GAQG;AACH,MAAM,CAAC,KAAK,UAAU,UAAU,CAC9B,KAAe,EACf,MAAyB;IAEzB,0EAA0E;IAC1E,MAAM,OAAO,GAAG,MAAM,EAAE,MAAM,CAAC;IAC/B,KAAK,OAAO,CAAC;IAEb,IAAI,MAAM,EAAE,MAAM,EAAE,CAAC;QACnB,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,MAAM,CAAC,oBAAoB,CAAC,CAAC;QAC5D,MAAM,QAAQ,GAAG,IAAI,YAAY,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;QACjD,OAAO,QAAQ,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC;IACpC,CAAC;IAED,sBAAsB;IACtB,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,MAAM,CAAC,eAAe,CAAC,CAAC;IACtD,MAAM,UAAU,GAAG,MAAM,WAAW,EAAE,CAAC;IACvC,MAAM,SAAS,GAAG,MAAM,EAAE,SAAS,IAAI,UAAU,CAAC;IAClD,MAAM,OAAO,GAAe,EAAE,CAAC;IAE/B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,IAAI,SAAS,EAAE,CAAC;QACjD,MAAM,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,CAAC;QAC5C,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,KAAK,CAAC,GAAG,CAAC,KAAK,EAAE,IAAI,EAAE,EAAE;YACvB,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC,IAAI,EAAE,UAAU,CAAC,CAAC;YACjD,OAAO,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;QAC5B,CAAC,CAAC,CACH,CAAC;QACF,OAAO,CAAC,IAAI,CAAC,GAAG,YAAY,CAAC,CAAC;IAChC,CAAC;IAED,OAAO,OAAO,CAAC;AACjB,CAAC;AAOD;;;;;;;;;GASG;AACH,MAAM,WAAW,GAAG,IAAI,GAAG,CAAC,CAAC,UAAU,EAAE,QAAQ,EAAE,OAAO,EAAE,QAAQ,EAAE,WAAW,EAAE,MAAM,EAAE,QAAQ,EAAE,aAAa,EAAE,UAAU,EAAE,OAAO,EAAE,WAAW,CAAC,CAAC,CAAC;AAEvJ,MAAM,CAAC,KAAK,UAAU,QAAQ,CAC5B,EAAqB,EACrB,QAAoB,EACpB,KAAK,GAAG,KAAK,EACb,QAAQ,GAAG,KAAK;IAEhB,IAAI,QAAQ,GAAG,CAAC,CAAC;IACjB,IAAI,OAAO,GAAG,CAAC,CAAC;IAEhB,0EAA0E;IAC1E,MAAM,IAAI,GAAG,EAAE;SACZ,OAAO,CACN;;sBAEgB,CACjB;SACA,GAAG,EAAiG,CAAC;IAExG,MAAM,YAAY,GAAG,QAAQ,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IAEpF,qDAAqD;IACrD,MAAM,WAAW,GAAG,KAAK;QACvB,CAAC,CAAC,IAAI,GAAG,EAAU;QACnB,CAAC,CAAC,IAAI,GAAG,CAEH,EAAE,CAAC,OAAO,CAAC,gCAAgC,CAAC,CAAC,GAAG,EACjD,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CACxB,CAAC;IAEN,0CAA0C;IAC1C,MAAM,OAAO,GAAG,YAAY,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;IACnE,OAAO,GAAG,YAAY,CAAC,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;IAE/C,qEAAqE;IACrE,IAAI,OAAO,CAAC,MAAM,GAAG,CAAC;QAAE,qBAAqB,CAAC,EAAE,CAAC,CAAC;IAElD,qBAAqB;IACrB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,IAAI,UAAU,EAAE,CAAC;QACpD,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,CAAC;QAC/C,MAAM,OAAO,CAAC,GAAG,CACf,KAAK,CAAC,GAAG,CAAC,KAAK,EAAE,GAAG,EAAE,EAAE;YACtB,MAAM,IAAI,GAAG,aAAa,CAAC,GAAG,CAAC,CAAC;YAChC,IAAI,CAAC;gBACH,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC,IAAI,EAAE,QAAQ,CAAC,CAAC;gBAC/C,eAAe,CAAC,EAAE,EAAE,GAAG,CAAC,EAAE,EAAE,MAAM,CAAC,CAAC;gBACpC,QAAQ,EAAE,CAAC;YACb,CAAC;YAAC,MAAM,CAAC;gBACP,kDAAkD;gBAClD,OAAO,EAAE,CAAC;YACZ,CAAC;QACH,CAAC,CAAC,CACH,CAAC;IACJ,CAAC;IAED,OAAO,EAAE,QAAQ,EAAE,OAAO,EAAE,CAAC;AAC/B,CAAC;AAED,iFAAiF;AAEjF,SAAS,aAAa,CAAC,GAKtB;IACC,MAAM,KAAK,GAAa,CAAC,GAAG,CAAC,IAAI,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC;IAC9C,IAAI,GAAG,CAAC,UAAU,IAAI,GAAG,CAAC,UAAU,KAAK,GAAG,CAAC,IAAI;QAAE,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,CAAC;IAC9E,IAAI,GAAG,CAAC,SAAS;QAAE,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC;IAC7C,OAAO,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;AACzB,CAAC;AAED,OAAO,EAAE,eAAe,EAAE,CAAC"}

package/dist/src/search/hybrid-query.d.ts

@@ -24,6 +24,10 @@ export interface HybridResult extends RankedResult {
     filePath: string | null;
     label: string;
     score: number;
+    /** First line of the symbol in its source file (1-based, null if unknown). */
+    startLine?: number | null;
+    /** Last line of the symbol in its source file (1-based, null if unknown). */
+    endLine?: number | null;
 }
 /**
  * Run a hybrid BM25 + cosine search.