@monoes/monograph 1.2.0 → 1.2.1

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

@@ -1,31 +1,24 @@
-import { readFileSync } from 'fs';
+import { readFileSync, statSync } from 'fs';
 import { extractMiddlewareChain } from '../pipeline/phases/middleware-extractor.js';
+const MAX_FILE_BYTES = 1_048_576; // 1 MiB guard for middleware source reads
 // ── Implementation ─────────────────────────────────────────────────────────────
 export function getMonographRouteMap(db, input) {
-    // 1. Query all Route nodes
-    let routeRows = db
-        .prepare("SELECT * FROM nodes WHERE label = 'Route'")
-        .all();
-    // 2. Apply prefix filter
+    // 1. Build SQL-level filters to avoid loading the whole Route table into JS
+    const conditions = ["label = 'Route'"];
+    const params = [];
     if (input.prefix) {
-        const prefix = input.prefix;
-        routeRows = routeRows.filter((row) => {
-            const name = row.name;
-            // name is like "GET /api/users" — find the path part
-            const spaceIdx = name.indexOf(' ');
-            const path = spaceIdx >= 0 ? name.slice(spaceIdx + 1) : name;
-            return path.startsWith(prefix);
-        });
+        // Route name format: "METHOD /path" — prefix applies to path portion after first space
+        conditions.push("name LIKE ?");
+        params.push(`% ${input.prefix}%`);
     }
-    // 3. Apply method filter
     if (input.method) {
         const methodUpper = input.method.toUpperCase();
-        routeRows = routeRows.filter((row) => {
-            const name = row.name;
-            return name.startsWith(methodUpper + ' ') || name.startsWith('ANY ');
-        });
+        conditions.push("(name LIKE ? OR name LIKE ?)");
+        params.push(`${methodUpper} %`, 'ANY %');
     }
-    // 4. For each route, find handler via HANDLES_ROUTE edge
+    const sql = `SELECT * FROM nodes WHERE ${conditions.join(' AND ')}`;
+    const routeRows = db.prepare(sql).all(...params);
+    // 2. For each route, find handler via HANDLES_ROUTE edge (prepared once)
     const handlerStmt = db.prepare(`SELECT n.name, n.file_path, n.start_line FROM nodes n
      JOIN edges e ON n.id = e.target_id
      WHERE e.source_id = ? AND e.relation = 'HANDLES_ROUTE'
@@ -44,11 +37,14 @@ export function getMonographRouteMap(db, input) {
         if (input.includeMiddleware && input.repoPath && handlerRow?.name && handlerRow?.file_path) {
             try {
                 const absPath = `${input.repoPath}/${handlerRow.file_path}`;
-                const source = readFileSync(absPath, 'utf-8');
-                middlewareChain = extractMiddlewareChain(source, handlerRow.name).middlewareNames;
+                const st = statSync(absPath);
+                if (st.size <= MAX_FILE_BYTES) {
+                    const source = readFileSync(absPath, 'utf-8');
+                    middlewareChain = extractMiddlewareChain(source, handlerRow.name).middlewareNames;
+                }
             }
             catch {
-                // File not found or unreadable — leave middlewareChain as []
+                // File not found, unreadable, or too large — leave middlewareChain as []
             }
         }
         return {

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

@@ -1 +1 @@
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+{"version":3,"file":"route-map.js","sourceRoot":"","sources":["../../../src/mcp-tools/route-map.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,YAAY,EAAE,QAAQ,EAAE,MAAM,IAAI,CAAC;AAE5C,OAAO,EAAE,sBAAsB,EAAE,MAAM,4CAA4C,CAAC;AAmBpF,MAAM,cAAc,GAAG,SAAS,CAAC,CAAC,0CAA0C;AAE5E,kFAAkF;AAElF,MAAM,UAAU,oBAAoB,CAClC,EAAqB,EACrB,KAA2F;IAE3F,4EAA4E;IAC5E,MAAM,UAAU,GAAa,CAAC,iBAAiB,CAAC,CAAC;IACjD,MAAM,MAAM,GAAc,EAAE,CAAC;IAE7B,IAAI,KAAK,CAAC,MAAM,EAAE,CAAC;QACjB,uFAAuF;QACvF,UAAU,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC;QAC/B,MAAM,CAAC,IAAI,CAAC,KAAK,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC;IACpC,CAAC;IAED,IAAI,KAAK,CAAC,MAAM,EAAE,CAAC;QACjB,MAAM,WAAW,GAAG,KAAK,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC;QAC/C,UAAU,CAAC,IAAI,CAAC,8BAA8B,CAAC,CAAC;QAChD,MAAM,CAAC,IAAI,CAAC,GAAG,WAAW,IAAI,EAAE,OAAO,CAAC,CAAC;IAC3C,CAAC;IAED,MAAM,GAAG,GAAG,6BAA6B,UAAU,CAAC,IAAI,CAAC,OAAO,CAAC,EAAE,CAAC;IACpE,MAAM,SAAS,GAAG,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,GAAG,MAAM,CAA8B,CAAC;IAE9E,yEAAyE;IACzE,MAAM,WAAW,GAAG,EAAE,CAAC,OAAO,CAC5B;;;aAGS,CACV,CAAC;IAEF,MAAM,MAAM,GAAoB,SAAS,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE;QACpD,MAAM,WAAW,GAAG,GAAG,CAAC,EAAY,CAAC;QACrC,MAAM,IAAI,GAAG,GAAG,CAAC,IAAc,CAAC;QAEhC,2DAA2D;QAC3D,MAAM,QAAQ,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;QACnC,MAAM,MAAM,GAAG,QAAQ,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC;QAC/D,MAAM,IAAI,GAAG,QAAQ,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,QAAQ,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;QAE7D,kBAAkB;QAClB,MAAM,UAAU,GAAG,WAAW,CAAC,GAAG,CAAC,WAAW,CAEjC,CAAC;QAEd,uDAAuD;QACvD,IAAI,eAAe,GAAa,EAAE,CAAC;QACnC,IAAI,KAAK,CAAC,iBAAiB,IAAI,KAAK,CAAC,QAAQ,IAAI,UAAU,EAAE,IAAI,IAAI,UAAU,EAAE,SAAS,EAAE,CAAC;YAC3F,IAAI,CAAC;gBACH,MAAM,OAAO,GAAG,GAAG,KAAK,CAAC,QAAQ,IAAI,UAAU,CAAC,SAAS,EAAE,CAAC;gBAC5D,MAAM,EAAE,GAAG,QAAQ,CAAC,OAAO,CAAC,CAAC;gBAC7B,IAAI,EAAE,CAAC,IAAI,IAAI,cAAc,EAAE,CAAC;oBAC9B,MAAM,MAAM,GAAG,YAAY,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;oBAC9C,eAAe,GAAG,sBAAsB,CAAC,MAAM,EAAE,UAAU,CAAC,IAAI,CAAC,CAAC,eAAe,CAAC;gBACpF,CAAC;YACH,CAAC;YAAC,MAAM,CAAC;gBACP,yEAAyE;YAC3E,CAAC;QACH,CAAC;QAED,OAAO;YACL,MAAM;YACN,IAAI;YACJ,WAAW,EAAE,UAAU,EAAE,IAAI,IAAI,IAAI;YACrC,WAAW,EAAE,UAAU,EAAE,SAAS,IAAI,IAAI;YAC1C,WAAW,EAAE,UAAU,EAAE,UAAU,IAAI,IAAI;YAC3C,WAAW;YACX,eAAe;SAChB,CAAC;IACJ,CAAC,CAAC,CAAC;IAEH,OAAO,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,CAAC;AAC1C,CAAC"}

package/dist/src/mcp-tools/shape-check.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"shape-check.d.ts","sourceRoot":"","sources":["../../../src/mcp-tools/shape-check.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,QAAQ,MAAM,gBAAgB,CAAC;AAC3C,OAAO,EAIL,KAAK,UAAU,EAChB,MAAM,gCAAgC,CAAC;AAIxC,MAAM,WAAW,gBAAgB;IAC/B,KAAK,EAAE;QACL,IAAI,EAAE,MAAM,CAAC;QACb,MAAM,EAAE,MAAM,CAAC;QACf,WAAW,EAAE,MAAM,CAAC;QACpB,WAAW,EAAE,MAAM,CAAC;KACrB,GAAG,IAAI,CAAC;IACT,KAAK,EAAE,UAAU,CAAC;IAClB,SAAS,EAAE;QAAE,IAAI,EAAE,MAAM,CAAC;QAAC,QAAQ,EAAE,MAAM,CAAA;KAAE,EAAE,CAAC;IAChD,OAAO,EAAE,MAAM,CAAC;CACjB;AAkBD;;;;;;;;GAQG;AACH,wBAAgB,aAAa,CAC3B,EAAE,EAAE,QAAQ,CAAC,QAAQ,EACrB,QAAQ,EAAE,MAAM,EAChB,OAAO,EAAE;IAAE,KAAK,CAAC,EAAE,MAAM,CAAC;IAAC,IAAI,CAAC,EAAE,MAAM,CAAA;CAAE,GACzC,gBAAgB,CAgIlB"}

package/dist/src/mcp-tools/shape-check.js

@@ -1,9 +1,13 @@
-import { readFileSync } from 'fs';
+import { readFileSync, statSync } from 'fs';
 import { join } from 'path';
 import { extractHandlerReturnKeys, extractAccessedKeys, compareShapes, } from '../analysis/shape-extractor.js';
 // ── Internal helpers ───────────────────────────────────────────────────────────
+const MAX_FILE_BYTES = 1_048_576; // 1 MiB guard
 function safeReadFile(absPath) {
     try {
+        const st = statSync(absPath);
+        if (st.size > MAX_FILE_BYTES)
+            return '';
         return readFileSync(absPath, 'utf-8');
     }
     catch {
@@ -36,18 +40,18 @@ export function getShapeCheck(db, repoPath, options) {
             .get(options.file);
     }
     else if (options.route) {
-        // Search by name substring (name is like "GET /api/users")
-        // We match against path part of the name to avoid matching the method token
-        const allRoutes = db
-            .prepare("SELECT * FROM nodes WHERE label = 'Route'")
-            .all();
-        const searchTerm = options.route.toLowerCase();
-        routeRow = allRoutes.find((row) => {
-            const name = row.name.toLowerCase();
-            const spaceIdx = name.indexOf(' ');
-            const path = spaceIdx >= 0 ? name.slice(spaceIdx + 1) : name;
-            return path.includes(searchTerm);
-        });
+        // Search by name substring (name is like "GET /api/users") using SQL LIKE to avoid full scan
+        // The route path follows the first space, so we match anywhere after it via a LIKE pattern.
+        const likeTerm = `% ${options.route.toLowerCase()}%`;
+        routeRow = db
+            .prepare("SELECT * FROM nodes WHERE label = 'Route' AND lower(name) LIKE ? LIMIT 1")
+            .get(likeTerm);
+        // Fallback: match anywhere in the name (e.g. no space prefix)
+        if (!routeRow) {
+            routeRow = db
+                .prepare("SELECT * FROM nodes WHERE label = 'Route' AND lower(name) LIKE ? LIMIT 1")
+                .get(`%${options.route.toLowerCase()}%`);
+        }
     }
     if (!routeRow) {
         return {

package/dist/src/mcp-tools/shape-check.js.map

@@ -1 +1 @@
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package/dist/src/parsers/loader.js

@@ -77,15 +77,16 @@ export async function getParser(ext) {
         return { parser: parserCache.get(ext), config };
     }
     try {
+        const lang = config.getLanguage();
+        if (!lang)
+            throw new Error('getLanguage() returned undefined');
         const parser = new Parser();
-        parser.setLanguage(config.getLanguage());
+        parser.setLanguage(lang);
         parserCache.set(ext, parser);
         return { parser, config };
     }
-    catch (err) {
-        // Grammar unavailable at runtime (ABI mismatch, native build failure, etc.).
-        // Log a warning and skip the language gracefully.
-        console.warn(`[monograph] warning: grammar for "${config.name}" (${ext}) could not be loaded: ${err}`);
+    catch {
+        // Grammar unavailable at runtime (ABI mismatch, native build failure, etc.) — skip silently.
         return null;
     }
 }

package/dist/src/parsers/loader.js.map

@@ -1 +1 @@
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package/dist/src/pipeline/cluster-only.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"cluster-only.d.ts","sourceRoot":"","sources":["../../../src/pipeline/cluster-only.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,QAAQ,MAAM,gBAAgB,CAAC;AAK3C,MAAM,WAAW,iBAAiB;IAChC,cAAc,EAAE,MAAM,CAAC;IACvB,SAAS,EAAE,MAAM,CAAC;CACnB;AAED;;;;GAIG;AACH,wBAAsB,cAAc,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,GAAG,OAAO,CAAC,iBAAiB,CAAC,CAgDtF"}

package/dist/src/pipeline/cluster-only.js

@@ -34,18 +34,22 @@ export async function runClusterOnly(db) {
             }
         }
     }
-    // Write community assignments back to DB
+    // Write community assignments back to DB and count in a single pass
     const updateStmt = db.prepare('UPDATE nodes SET community_id = ? WHERE id = ?');
+    const communityIds = new Set();
+    let nodeCount = 0;
     const updateAll = db.transaction(() => {
-        for (const [nodeId, commId] of Object.entries(communities)) {
+        for (const nodeId in communities) {
+            const commId = communities[nodeId];
             updateStmt.run(commId, nodeId);
+            communityIds.add(commId);
+            nodeCount++;
         }
     });
     updateAll();
-    const communityIds = new Set(Object.values(communities));
     return {
         communityCount: communityIds.size,
-        nodeCount: Object.keys(communities).length,
+        nodeCount,
     };
 }
 //# sourceMappingURL=cluster-only.js.map

package/dist/src/pipeline/cluster-only.js.map

@@ -1 +1 @@
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package/dist/src/pipeline/orchestrator.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"orchestrator.d.ts","sourceRoot":"","sources":["../../../src/pipeline/orchestrator.ts"],"names":[],"mappings":"AAwBA,OAAO,KAAK,EAAE,eAAe,EAAmB,MAAM,YAAY,CAAC;AAEnE,OAAO,KAAK,EAAE,gBAAgB,EAAqB,MAAM,aAAa,CAAC;AAWvE,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;CACjB;AAED,wBAAsB,UAAU,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,GAAE,YAAiB,GAAG,OAAO,CAAC,IAAI,CAAC,CAkC5F"}
+{"version":3,"file":"orchestrator.d.ts","sourceRoot":"","sources":["../../../src/pipeline/orchestrator.ts"],"names":[],"mappings":"AAwBA,OAAO,KAAK,EAAE,eAAe,EAAmB,MAAM,YAAY,CAAC;AAEnE,OAAO,KAAK,EAAE,gBAAgB,EAAqB,MAAM,aAAa,CAAC;AAWvE,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;CACvB;AAED,wBAAsB,UAAU,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,GAAE,YAAiB,GAAG,OAAO,CAAC,IAAI,CAAC,CAsD5F"}

package/dist/src/pipeline/orchestrator.js

@@ -35,6 +35,25 @@ function getCurrentCommitHash(repoPath) {
 export async function buildAsync(repoPath, options = {}) {
     const dbPath = resolve(join(repoPath, '.monomind', 'monograph.db'));
     const fullOptions = { ...DEFAULT_OPTIONS, ...options };
+    // Incremental guard: if the caller requested skip-when-fresh and force is
+    // not set, check staleness before opening the DB for a full write cycle.
+    if (options.incremental && !options.force) {
+        const { existsSync: _existsSync } = await import('fs');
+        if (_existsSync(dbPath)) {
+            const { checkStaleness } = await import('../staleness/git-staleness.js');
+            const tmpDb = openDb(dbPath);
+            try {
+                const report = checkStaleness(tmpDb, resolve(repoPath));
+                if (!report.isStale && report.currentCommit !== null) {
+                    options.onProgress?.({ phase: 'skip', message: 'Index is fresh — skipping rebuild' });
+                    return; // Already up-to-date
+                }
+            }
+            finally {
+                closeDb(tmpDb);
+            }
+        }
+    }
     const db = openDb(dbPath);
     try {
         const graph = new Graph({ multi: true, type: 'directed' });

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

@@ -1 +1 @@
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+{"version":3,"file":"orchestrator.js","sourceRoot":"","sources":["../../../src/pipeline/orchestrator.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAC;AACrC,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAC;AACzC,OAAO,KAAK,MAAM,YAAY,CAAC;AAC/B,OAAO,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,kBAAkB,CAAC;AACnD,OAAO,EAAE,cAAc,EAAE,MAAM,aAAa,CAAC;AAC7C,OAAO,EAAE,SAAS,EAAE,MAAM,kBAAkB,CAAC;AAC7C,OAAO,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AACvD,OAAO,EAAE,UAAU,EAAE,MAAM,mBAAmB,CAAC;AAC/C,OAAO,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAC;AACrD,OAAO,EAAE,WAAW,EAAE,MAAM,oBAAoB,CAAC;AACjD,OAAO,EAAE,UAAU,EAAE,MAAM,mBAAmB,CAAC;AAC/C,OAAO,EAAE,QAAQ,EAAE,MAAM,iBAAiB,CAAC;AAC3C,OAAO,EAAE,cAAc,EAAE,MAAM,wBAAwB,CAAC;AACxD,OAAO,EAAE,oBAAoB,EAAE,MAAM,8BAA8B,CAAC;AACpE,OAAO,EAAE,QAAQ,EAAE,MAAM,iBAAiB,CAAC;AAC3C,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAC;AAC3D,OAAO,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AACvD,OAAO,EAAE,aAAa,EAAE,MAAM,uBAAuB,CAAC;AACtD,OAAO,EAAE,cAAc,EAAE,MAAM,uBAAuB,CAAC;AACvD,OAAO,EAAE,YAAY,EAAE,MAAM,qBAAqB,CAAC;AACnD,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAC7D,OAAO,EAAE,sBAAsB,EAAE,MAAM,4BAA4B,CAAC;AACpE,OAAO,EAAE,oBAAoB,EAAE,MAAM,8BAA8B,CAAC;AACpE,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAC;AAElE,OAAO,EAAE,eAAe,EAAE,MAAM,YAAY,CAAC;AAE7C,OAAO,EAAE,mBAAmB,EAAE,MAAM,8BAA8B,CAAC;AAEnE,SAAS,oBAAoB,CAAC,QAAgB;IAC5C,IAAI,CAAC;QACH,OAAO,QAAQ,CAAC,oBAAoB,EAAE,EAAE,GAAG,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;IACpF,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,IAAI,CAAC;IACd,CAAC;AACH,CAAC;AASD,MAAM,CAAC,KAAK,UAAU,UAAU,CAAC,QAAgB,EAAE,UAAwB,EAAE;IAC3E,MAAM,MAAM,GAAG,OAAO,CAAC,IAAI,CAAC,QAAQ,EAAE,WAAW,EAAE,cAAc,CAAC,CAAC,CAAC;IACpE,MAAM,WAAW,GAAoB,EAAE,GAAG,eAAe,EAAE,GAAG,OAAO,EAAE,CAAC;IAExE,0EAA0E;IAC1E,yEAAyE;IACzE,IAAI,OAAO,CAAC,WAAW,IAAI,CAAC,OAAO,CAAC,KAAK,EAAE,CAAC;QAC1C,MAAM,EAAE,UAAU,EAAE,WAAW,EAAE,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,CAAC;QACvD,IAAI,WAAW,CAAC,MAAM,CAAC,EAAE,CAAC;YACxB,MAAM,EAAE,cAAc,EAAE,GAAG,MAAM,MAAM,CAAC,+BAA+B,CAAC,CAAC;YACzE,MAAM,KAAK,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC;YAC7B,IAAI,CAAC;gBACH,MAAM,MAAM,GAAG,cAAc,CAAC,KAAK,EAAE,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC;gBACxD,IAAI,CAAC,MAAM,CAAC,OAAO,IAAI,MAAM,CAAC,aAAa,KAAK,IAAI,EAAE,CAAC;oBACrD,OAAO,CAAC,UAAU,EAAE,CAAC,EAAE,KAAK,EAAE,MAAM,EAAE,OAAO,EAAE,mCAAmC,EAAE,CAAC,CAAC;oBACtF,OAAO,CAAC,qBAAqB;gBAC/B,CAAC;YACH,CAAC;oBAAS,CAAC;gBACT,OAAO,CAAC,KAAK,CAAC,CAAC;YACjB,CAAC;QACH,CAAC;IACH,CAAC;IAED,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC;IAE1B,IAAI,CAAC;QACH,MAAM,KAAK,GAAG,IAAI,KAAK,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,IAAI,EAAE,UAAU,EAAE,CAAC,CAAC;QAC3D,MAAM,GAAG,GAAoB;YAC3B,QAAQ,EAAE,OAAO,CAAC,QAAQ,CAAC;YAC3B,EAAE,EAAE,KAAK;YACT,UAAU,EAAE,OAAO,CAAC,UAAU,IAAI,CAAC,GAAG,EAAE,GAAE,CAAC,CAAC;YAC5C,OAAO,EAAE,WAAW;SACrB,CAAC;QAEF,MAAM,MAAM,GAAG,IAAI,cAAc,CAAC;YAChC,SAAS,EAAE,oBAAoB,EAAE,cAAc,EAAE,UAAU,EAAE,cAAc;YAC3E,aAAa,EAAE,WAAW,EAAE,UAAU,EAAE,QAAQ;YAChD,cAAc,EAAE,sBAAsB,EAAE,mBAAmB,EAAE,oBAAoB;YACjF,QAAQ,EAAE,gBAAgB,EAAE,cAAc,EAAE,aAAa,EAAE,cAAc,EAAE,YAAY;SACxF,CAAC,CAAC;QAEH,MAAM,OAAO,GAAG,MAAM,MAAM,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;QAEtC,MAAM,IAAI,GAAG,oBAAoB,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC;QACrD,IAAI,IAAI,EAAE,CAAC;YACT,EAAE,CAAC,OAAO,CAAC,kEAAkE,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QAC3F,CAAC;QAED,MAAM,UAAU,GAAG,OAAO,CAAC,GAAG,CAAC,SAAS,CAAmD,CAAC;QAC5F,MAAM,SAAS,GAAG,UAAU,EAAE,SAAS,IAAI,EAAE,CAAC;QAC9C,MAAM,mBAAmB,CAAC,OAAO,CAAC,QAAQ,CAAC,EAAE,SAAS,EAAE,MAAM,EAAE,SAAS,CAAC,CAAC;IAC7E,CAAC;YAAS,CAAC;QACT,OAAO,CAAC,EAAE,CAAC,CAAC;IACd,CAAC;AACH,CAAC"}

package/dist/src/pipeline/phases/boundary.d.ts

@@ -20,6 +20,8 @@ export interface BoundaryViolation {
 export declare function loadMonographConfig(repoRoot: string): MonographConfig;
 /**
  * Classify a file path into a zone name. Returns null if no zone matches.
+ * Compiles the glob patterns on every call — use classifyZoneCompiled with
+ * precompiled zones for hot paths.
  */
 export declare function classifyZone(filePath: string, zones: ZoneConfig[]): string | null;
 /**

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

@@ -1 +1 @@
-{"version":3,"file":"boundary.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/phases/boundary.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,QAAQ,MAAM,gBAAgB,CAAC;AAI3C,MAAM,WAAW,UAAU;IACzB,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;CACd;AAED,MAAM,WAAW,eAAe;IAC9B,KAAK,CAAC,EAAE,UAAU,EAAE,CAAC;IACrB,cAAc,CAAC,EAAE,CAAC,MAAM,EAAE,MAAM,CAAC,EAAE,CAAC;CACrC;AAED,MAAM,WAAW,iBAAiB;IAChC,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,MAAM,CAAC;IACf,YAAY,EAAE,MAAM,CAAC;CACtB;AAgBD;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,QAAQ,EAAE,MAAM,GAAG,eAAe,CASrE;AAED;;GAEG;AACH,wBAAgB,YAAY,CAAC,QAAQ,EAAE,MAAM,EAAE,KAAK,EAAE,UAAU,EAAE,GAAG,MAAM,GAAG,IAAI,CAMjF;AAED;;;;;GAKG;AACH,wBAAgB,wBAAwB,CACtC,EAAE,EAAE,QAAQ,CAAC,QAAQ,EACrB,QAAQ,EAAE,MAAM,GACf,iBAAiB,EAAE,CA0CrB"}
+{"version":3,"file":"boundary.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/phases/boundary.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,QAAQ,MAAM,gBAAgB,CAAC;AAI3C,MAAM,WAAW,UAAU;IACzB,IAAI,EAAE,MAAM,CAAC;IACb,IAAI,EAAE,MAAM,CAAC;CACd;AAED,MAAM,WAAW,eAAe;IAC9B,KAAK,CAAC,EAAE,UAAU,EAAE,CAAC;IACrB,cAAc,CAAC,EAAE,CAAC,MAAM,EAAE,MAAM,CAAC,EAAE,CAAC;CACrC;AAED,MAAM,WAAW,iBAAiB;IAChC,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,MAAM,CAAC;IACf,YAAY,EAAE,MAAM,CAAC;CACtB;AAsCD;;GAEG;AACH,wBAAgB,mBAAmB,CAAC,QAAQ,EAAE,MAAM,GAAG,eAAe,CASrE;AAED;;;;GAIG;AACH,wBAAgB,YAAY,CAAC,QAAQ,EAAE,MAAM,EAAE,KAAK,EAAE,UAAU,EAAE,GAAG,MAAM,GAAG,IAAI,CAMjF;AAED;;;;;GAKG;AACH,wBAAgB,wBAAwB,CACtC,EAAE,EAAE,QAAQ,CAAC,QAAQ,EACrB,QAAQ,EAAE,MAAM,GACf,iBAAiB,EAAE,CAwDrB"}

package/dist/src/pipeline/phases/boundary.js

@@ -13,6 +13,21 @@ function globToRegex(glob) {
         .split(DOUBLE_STAR).join('.*');
     return new RegExp('^' + pattern + '$');
 }
+/** Compile a ZoneConfig[] into CompiledZone[] once to avoid reconstructing RegExps per path. */
+function compileZones(zones) {
+    return zones.map(z => ({ name: z.name, re: globToRegex(z.glob) }));
+}
+/**
+ * Classify a file path into a zone name using precompiled regexes.
+ * Returns null if no zone matches.
+ */
+function classifyZoneCompiled(filePath, compiled) {
+    for (const z of compiled) {
+        if (z.re.test(filePath))
+            return z.name;
+    }
+    return null;
+}
 /**
  * Load .monographrc.json from repoRoot. Returns empty config if not found or invalid.
  */
@@ -30,6 +45,8 @@ export function loadMonographConfig(repoRoot) {
 }
 /**
  * Classify a file path into a zone name. Returns null if no zone matches.
+ * Compiles the glob patterns on every call — use classifyZoneCompiled with
+ * precompiled zones for hot paths.
  */
 export function classifyZone(filePath, zones) {
     for (const zone of zones) {
@@ -51,6 +68,8 @@ export function detectBoundaryViolations(db, repoRoot) {
         return [];
     const zones = config.zones;
     const allowedSet = new Set((config.allowedImports ?? []).map(([from, to]) => `${from}→${to}`));
+    // Precompile zone regexes once — avoids re-constructing RegExp objects per file path.
+    const compiledZones = compileZones(zones);
     const rows = db.prepare(`
     SELECT e.id, e.relation,
            ns.file_path AS src_path,
@@ -60,10 +79,20 @@ export function detectBoundaryViolations(db, repoRoot) {
     JOIN nodes nt ON nt.id = e.target_id
     WHERE ns.file_path IS NOT NULL AND nt.file_path IS NOT NULL
   `).all();
+    // Cache per-path zone classification to avoid O(rows * zones) repeated regex tests.
+    const pathZoneCache = new Map();
+    const classifyPath = (p) => {
+        let zone = pathZoneCache.get(p);
+        if (zone === undefined) {
+            zone = classifyZoneCompiled(p, compiledZones);
+            pathZoneCache.set(p, zone);
+        }
+        return zone;
+    };
     const violations = [];
     for (const row of rows) {
-        const fromZone = classifyZone(row.src_path, zones);
-        const toZone = classifyZone(row.tgt_path, zones);
+        const fromZone = classifyPath(row.src_path);
+        const toZone = classifyPath(row.tgt_path);
         if (fromZone === null || toZone === null)
             continue;
         if (fromZone === toZone)

package/dist/src/pipeline/phases/boundary.js.map

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

@@ -8,6 +8,20 @@ export declare function computeCohesion(communityId: number, memberships: Map<st
     sourceId: string;
     targetId: string;
 }>): number;
+/**
+ * Compute cohesion scores for all communities in a single O(N+E) pass.
+ *
+ * This replaces calling `computeCohesion` inside a loop, which was O(K*(N+E))
+ * because each call re-scanned all memberships (O(N)) and all edges (O(E)).
+ *
+ * @param memberships - nodeId → communityId map from the clustering step
+ * @param edges - all edges used for the graph (IMPORTS + resolved)
+ * @returns Map of communityId → cohesion score ∈ [0, 1]
+ */
+export declare function computeAllCohesionScores(memberships: Map<string, number>, edges: Array<{
+    sourceId: string;
+    targetId: string;
+}>): Map<number, number>;
 export declare const communitiesPhase: PipelinePhase<CommunitiesOutput>;
 /**
  * Split a community that is too large into smaller sub-groups.

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

@@ -1 +1 @@
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package/dist/src/pipeline/phases/communities.js

@@ -24,6 +24,62 @@ export function computeCohesion(communityId, memberships, edges) {
     }
     return internalCount / maxEdges;
 }
+/**
+ * Compute cohesion scores for all communities in a single O(N+E) pass.
+ *
+ * This replaces calling `computeCohesion` inside a loop, which was O(K*(N+E))
+ * because each call re-scanned all memberships (O(N)) and all edges (O(E)).
+ *
+ * @param memberships - nodeId → communityId map from the clustering step
+ * @param edges - all edges used for the graph (IMPORTS + resolved)
+ * @returns Map of communityId → cohesion score ∈ [0, 1]
+ */
+export function computeAllCohesionScores(memberships, edges) {
+    // Single pass over memberships: build communityId → Set<nodeId>
+    const memberSets = new Map();
+    for (const [nodeId, commId] of memberships) {
+        let s = memberSets.get(commId);
+        if (!s) {
+            s = new Set();
+            memberSets.set(commId, s);
+        }
+        s.add(nodeId);
+    }
+    // Single pass over edges: count unique undirected internal edges per community
+    const internalEdgeCounts = new Map();
+    const seenEdgeKeys = new Map();
+    for (const e of edges) {
+        const commSrc = memberships.get(e.sourceId);
+        const commTgt = memberships.get(e.targetId);
+        if (commSrc === undefined || commTgt === undefined || commSrc !== commTgt)
+            continue;
+        let seen = seenEdgeKeys.get(commSrc);
+        if (!seen) {
+            seen = new Set();
+            seenEdgeKeys.set(commSrc, seen);
+        }
+        const key = e.sourceId < e.targetId
+            ? `${e.sourceId}\0${e.targetId}`
+            : `${e.targetId}\0${e.sourceId}`;
+        if (!seen.has(key)) {
+            seen.add(key);
+            internalEdgeCounts.set(commSrc, (internalEdgeCounts.get(commSrc) ?? 0) + 1);
+        }
+    }
+    // Compute final scores
+    const scores = new Map();
+    for (const [commId, members] of memberSets) {
+        const n = members.size;
+        if (n <= 1) {
+            scores.set(commId, 1);
+            continue;
+        }
+        const maxEdges = (n * (n - 1)) / 2;
+        const internalCount = internalEdgeCounts.get(commId) ?? 0;
+        scores.set(commId, maxEdges > 0 ? internalCount / maxEdges : 1);
+    }
+    return scores;
+}
 export const communitiesPhase = {
     name: 'communities',
     deps: ['parse', 'cross-file', 'mro'],
@@ -58,11 +114,8 @@ export const communitiesPhase = {
             const topNode = [...nodeDegs.entries()].sort((a, b) => b[1] - a[1])[0]?.[0] ?? '';
             communityLabels.set(commId, `community-${commId}(${topNode.slice(0, 20)})`);
         }
-        const communityIds = new Set([...memberships.values()]);
-        const cohesionScores = new Map();
-        for (const cid of communityIds) {
-            cohesionScores.set(cid, computeCohesion(cid, memberships, allUsedEdges));
-        }
+        // Compute all cohesion scores in one O(N+E) pass instead of O(K*(N+E))
+        const cohesionScores = computeAllCohesionScores(memberships, allUsedEdges);
         return { memberships, communityLabels, cohesionScores };
     },
 };

package/dist/src/pipeline/phases/communities.js.map

@@ -1 +1 @@
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package/dist/src/pipeline/phases/contextual-proximity.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"contextual-proximity.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/phases/contextual-proximity.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAmB,MAAM,aAAa,CAAC;AAKlE,MAAM,WAAW,yBAAyB;IACxC,aAAa,EAAE,MAAM,CAAC;IACtB,cAAc,EAAE,MAAM,CAAC;CACxB;AAED,eAAO,MAAM,wBAAwB,EAAE,aAAa,CAAC,yBAAyB,CA4E7E,CAAC"}
+{"version":3,"file":"contextual-proximity.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/phases/contextual-proximity.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,aAAa,EAAmB,MAAM,aAAa,CAAC;AAKlE,MAAM,WAAW,yBAAyB;IACxC,aAAa,EAAE,MAAM,CAAC;IACtB,cAAc,EAAE,MAAM,CAAC;CACxB;AAED,eAAO,MAAM,wBAAwB,EAAE,aAAa,CAAC,yBAAyB,CA6E7E,CAAC"}

package/dist/src/pipeline/phases/contextual-proximity.js

@@ -12,19 +12,28 @@ export const contextualProximityPhase = {
             .all();
         if (rows.length === 0)
             return { coOccursEdges: 0, conceptsScored: 0 };
-        // Group concepts by section
+        // Group concepts by section using ??= to avoid has+get pattern
         const sectionConcepts = new Map();
         for (const { source_id, target_id } of rows) {
-            if (!sectionConcepts.has(source_id))
-                sectionConcepts.set(source_id, []);
-            sectionConcepts.get(source_id).push(target_id);
+            let list = sectionConcepts.get(source_id);
+            if (!list) {
+                list = [];
+                sectionConcepts.set(source_id, list);
+            }
+            list.push(target_id);
         }
-        // Count concept co-occurrences across all sections
+        // Count concept co-occurrences across all sections.
+        // Accumulate conceptDegree in the same pass to avoid a second loop over sectionConcepts.
+        // Use a ternary comparison instead of [a,b].sort() to avoid per-pair array allocation.
         const coOccur = new Map();
+        const conceptDegree = new Map();
         for (const concepts of sectionConcepts.values()) {
             for (let i = 0; i < concepts.length; i++) {
+                conceptDegree.set(concepts[i], (conceptDegree.get(concepts[i]) ?? 0) + 1);
                 for (let j = i + 1; j < concepts.length; j++) {
-                    const [a, b] = [concepts[i], concepts[j]].sort();
+                    // Avoid allocating a 2-element sort array — ternary comparison is equivalent
+                    const a = concepts[i] <= concepts[j] ? concepts[i] : concepts[j];
+                    const b = concepts[i] <= concepts[j] ? concepts[j] : concepts[i];
                     const key = `${a}::${b}`;
                     coOccur.set(key, (coOccur.get(key) ?? 0) + 1);
                 }
@@ -46,15 +55,13 @@ export const contextualProximityPhase = {
                 weight,
             });
         }
-        // Score concept importance 1-5 based on normalized degree (sections it appears in)
-        const conceptDegree = new Map();
-        for (const concepts of sectionConcepts.values()) {
-            for (const cid of concepts) {
-                conceptDegree.set(cid, (conceptDegree.get(cid) ?? 0) + 1);
-            }
-        }
         if (conceptDegree.size > 0) {
-            const maxDeg = [...conceptDegree.values()].reduce((a, b) => Math.max(a, b), 0);
+            // Compute maxDeg with a loop to avoid spread array allocation from [...values()]
+            let maxDeg = 0;
+            for (const deg of conceptDegree.values()) {
+                if (deg > maxDeg)
+                    maxDeg = deg;
+            }
             const update = ctx.db.prepare(`UPDATE nodes SET properties = json_set(COALESCE(properties, '{}'), '$.importance', ?) WHERE id = ?`);
             ctx.db.transaction(() => {
                 for (const [cid, deg] of conceptDegree) {