@monoes/monograph 1.2.4 → 1.2.6

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@monoes/monograph",
-  "version": "1.2.4",
+  "version": "1.2.6",
   "type": "module",
   "description": "Native TypeScript code intelligence engine for monomind",
   "main": "dist/src/index.js",
@@ -46,7 +46,6 @@
     "tree-sitter-vue": "^0.2.1"
   },
   "optionalDependencies": {
-    "@anthropic-ai/sdk": "^0.39.0",
     "@huggingface/transformers": "^3.1.0"
   },
   "devDependencies": {

package/src/pipeline/orchestrator.ts

@@ -85,6 +85,38 @@ export async function buildAsync(repoPath: string, options: BuildOptions = {}):
 
     const outputs = await runner.run(ctx);
 
+    // Every full build reuses the same DB in place (no truncate-on-open), and no
+    // phase ever deletes nodes for files that were renamed/deleted since the last
+    // build. Left unchecked, orphaned rows (and their FTS/edge fallout) accumulate
+    // forever across repeated rebuilds. Sweep them here, once, after scan knows the
+    // authoritative current file set.
+    const scanOut = outputs.get('scan') as { filePaths: string[] } | undefined;
+    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() as { file_path: string }[]
+      )
+        .map((r) => r.file_path)
+        .filter((f) => !liveFiles.has(resolve(f)));
+      if (staleFiles.length > 0) {
+        const deleteStale = db.transaction((files: string[]) => {
+          // Edges FK-reference nodes with no ON DELETE CASCADE, and a stale node
+          // can be referenced from either side (another file's export pointing at
+          // it, or it importing another file) — clear both directions first.
+          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);
+      }
+    }
+
     const hash = getCurrentCommitHash(resolve(repoPath));
     if (hash) {
       db.prepare("INSERT OR REPLACE INTO index_meta VALUES ('last_commit_hash', ?)").run(hash);

package/src/pipeline/phases/communities.ts

@@ -107,7 +107,7 @@ export function computeAllCohesionScores(
 export const communitiesPhase: PipelinePhase<CommunitiesOutput> = {
   name: 'communities',
   deps: ['parse', 'cross-file', 'mro'],
-  async execute(_ctx, deps) {
+  async execute(ctx, deps) {
     const { resolvedEdges } = deps.get('cross-file') as CrossFileOutput;
     const { allEdges } = deps.get('parse') as ParseOutput;
     const allUsedEdges: MonographEdge[] = [...allEdges, ...resolvedEdges];
@@ -142,6 +142,26 @@ export const communitiesPhase: PipelinePhase<CommunitiesOutput> = {
     // Compute all cohesion scores in one O(N+E) pass instead of O(K*(N+E))
     const cohesionScores = computeAllCohesionScores(memberships, allUsedEdges);
 
+    // Persist community assignments to the DB
+    if (memberships.size > 0) {
+      const commSizes = new Map<number, number>();
+      for (const commId of memberships.values()) {
+        commSizes.set(commId, (commSizes.get(commId) ?? 0) + 1);
+      }
+      const updateNode = ctx.db.prepare('UPDATE nodes SET community_id = ? WHERE id = ?');
+      const upsertComm = ctx.db.prepare(
+        'INSERT OR REPLACE INTO communities (id, label, size, cohesion_score) VALUES (?, ?, ?, ?)',
+      );
+      ctx.db.transaction(() => {
+        for (const [nodeId, commId] of memberships) {
+          updateNode.run(commId, nodeId);
+        }
+        for (const [commId, label] of communityLabels) {
+          upsertComm.run(commId, label, commSizes.get(commId) ?? 0, cohesionScores.get(commId) ?? 0);
+        }
+      })();
+    }
+
     return { memberships, communityLabels, cohesionScores };
   },
 };

package/src/pipeline/phases/tools.ts

@@ -124,17 +124,26 @@ export const toolsPhase: PipelinePhase<ToolsOutput> = {
             return n.includes(lowerTool) || (n.length > 0 && lowerTool.includes(n));
           });
 
-          if (matches.length === 1) {
-            const edgeId = makeId(toolNodeId, matches[0].id, 'handles_tool');
+          if (matches.length >= 1) {
+            // Pick best match: exact name > name contains tool > tool contains name
+            const scored = matches
+              .map(row => {
+                const n = row.name.toLowerCase().replace(/[_-]/g, '');
+                const score = n === lowerTool ? 3 : n.includes(lowerTool) ? 2 : 1;
+                return { row, score };
+              })
+              .sort((a, b) => b.score - a.score);
+            const { row: best, score } = scored[0];
+            const edgeId = makeId(toolNodeId, best.id, 'handles_tool');
             handlesEdges.push({
               id: edgeId,
               sourceId: toolNodeId,
-              targetId: matches[0].id,
+              targetId: best.id,
               relation: 'HANDLES_TOOL',
               confidence: 'EXTRACTED',
-              confidenceScore: 0.85,
+              confidenceScore: score === 3 ? 0.95 : 0.75,
             });
-            def.handlerNodeId = matches[0].id;
+            def.handlerNodeId = best.id;
           }
         }