milens 0.7.1 → 0.7.3

package/dist/store/db.js

@@ -34,43 +34,43 @@ export class Database {
     prepareStatements() {
         return {
             checkHash: this.db.prepare('SELECT hash FROM file_hashes WHERE path = ?'),
-            upsertHash: this.db.prepare(`INSERT INTO file_hashes (path, hash) VALUES (?, ?)
+            upsertHash: this.db.prepare(`INSERT INTO file_hashes (path, hash) VALUES (?, ?)
          ON CONFLICT(path) DO UPDATE SET hash = excluded.hash, analyzed_at = datetime('now')`),
-            insertSym: this.db.prepare(`INSERT OR REPLACE INTO symbols (id, name, kind, file_path, start_line, end_line, exported, parent_id, signature, role, heat)
+            insertSym: this.db.prepare(`INSERT OR REPLACE INTO symbols (id, name, kind, file_path, start_line, end_line, exported, parent_id, signature, role, heat)
          VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)`),
             updateMeta: this.db.prepare(`UPDATE symbols SET role = ?, heat = ? WHERE id = ?`),
             upsertZone: this.db.prepare(`UPDATE file_hashes SET zone = ? WHERE path = ?`),
-            insertLink: this.db.prepare(`INSERT OR REPLACE INTO links (id, from_id, to_id, type, confidence, line_number)
+            insertLink: this.db.prepare(`INSERT OR REPLACE INTO links (id, from_id, to_id, type, confidence, line_number)
          VALUES (?, ?, ?, ?, ?, ?)`),
-            searchFts: this.db.prepare(`SELECT s.* FROM symbol_fts f
-         JOIN symbols s ON s.rowid = f.rowid
-         WHERE symbol_fts MATCH ?
+            searchFts: this.db.prepare(`SELECT s.* FROM symbol_fts f
+         JOIN symbols s ON s.rowid = f.rowid
+         WHERE symbol_fts MATCH ?
          ORDER BY rank LIMIT ?`),
             byName: this.db.prepare('SELECT * FROM symbols WHERE name = ?'),
             byId: this.db.prepare('SELECT * FROM symbols WHERE id = ?'),
             byFile: this.db.prepare('SELECT * FROM symbols WHERE file_path = ?'),
             linksIn: this.db.prepare('SELECT * FROM links WHERE to_id = ?'),
             linksOut: this.db.prepare('SELECT * FROM links WHERE from_id = ?'),
-            upstream: this.db.prepare(`
-        WITH RECURSIVE upstream(id, depth, via) AS (
-          SELECT from_id, 1, type FROM links WHERE to_id = ? AND type IN ('calls', 'imports', 'extends', 'implements')
-          UNION
-          SELECT l.from_id, u.depth + 1, l.type
-          FROM links l JOIN upstream u ON l.to_id = u.id
-          WHERE u.depth < ? AND l.type IN ('calls', 'imports', 'extends', 'implements')
-        )
-        SELECT DISTINCT s.*, u.depth, u.via FROM upstream u JOIN symbols s ON s.id = u.id ORDER BY u.depth
+            upstream: this.db.prepare(`
+        WITH RECURSIVE upstream(id, depth, via) AS (
+          SELECT from_id, 1, type FROM links WHERE to_id = ? AND type IN ('calls', 'imports', 'extends', 'implements')
+          UNION
+          SELECT l.from_id, u.depth + 1, l.type
+          FROM links l JOIN upstream u ON l.to_id = u.id
+          WHERE u.depth < ? AND l.type IN ('calls', 'imports', 'extends', 'implements')
+        )
+        SELECT DISTINCT s.*, u.depth, u.via FROM upstream u JOIN symbols s ON s.id = u.id ORDER BY u.depth
       `),
-            downstream: this.db.prepare(`
-        WITH RECURSIVE downstream(id, depth, via, path) AS (
-          SELECT to_id, 1, type, ',' || to_id || ',' FROM links WHERE from_id = ? AND type IN ('calls', 'imports', 'extends', 'implements')
-          UNION
-          SELECT l.to_id, d.depth + 1, l.type, d.path || l.to_id || ','
-          FROM links l JOIN downstream d ON l.from_id = d.id
-          WHERE d.depth < ? AND l.type IN ('calls', 'imports', 'extends', 'implements')
-            AND d.path NOT LIKE '%,' || l.to_id || ',%'
-        )
-        SELECT DISTINCT s.*, d.depth, d.via FROM downstream d JOIN symbols s ON s.id = d.id ORDER BY d.depth
+            downstream: this.db.prepare(`
+        WITH RECURSIVE downstream(id, depth, via, path) AS (
+          SELECT to_id, 1, type, ',' || to_id || ',' FROM links WHERE from_id = ? AND type IN ('calls', 'imports', 'extends', 'implements')
+          UNION
+          SELECT l.to_id, d.depth + 1, l.type, d.path || l.to_id || ','
+          FROM links l JOIN downstream d ON l.from_id = d.id
+          WHERE d.depth < ? AND l.type IN ('calls', 'imports', 'extends', 'implements')
+            AND d.path NOT LIKE '%,' || l.to_id || ',%'
+        )
+        SELECT DISTINCT s.*, d.depth, d.via FROM downstream d JOIN symbols s ON s.id = d.id ORDER BY d.depth
       `),
             countSymbols: this.db.prepare('SELECT COUNT(*) as c FROM symbols'),
             countLinks: this.db.prepare('SELECT COUNT(*) as c FROM links'),
@@ -78,17 +78,17 @@ export class Database {
             deleteFileLinks: this.db.prepare('DELETE FROM links WHERE from_id IN (SELECT id FROM symbols WHERE file_path = ?)'),
             deleteFileSymbols: this.db.prepare('DELETE FROM symbols WHERE file_path = ?'),
             topHubs: this.db.prepare('SELECT * FROM symbols WHERE exported = 1 ORDER BY heat DESC LIMIT ?'),
-            testCoverageGaps: this.db.prepare(`
-        SELECT s.* FROM symbols s
-        WHERE s.exported = 1 AND s.heat > 0
-        AND s.id NOT IN (
-          SELECT DISTINCT l.to_id FROM links l
-          JOIN symbols src ON src.id = l.from_id
-          WHERE (src.file_path LIKE '%/test/%' OR src.file_path LIKE '%\\test\\%'
-                 OR src.file_path LIKE '%.test.%' OR src.file_path LIKE '%.spec.%')
-        )
-        ORDER BY s.heat DESC
-        LIMIT ?
+            testCoverageGaps: this.db.prepare(`
+        SELECT s.* FROM symbols s
+        WHERE s.exported = 1 AND s.heat > 0
+        AND s.id NOT IN (
+          SELECT DISTINCT l.to_id FROM links l
+          JOIN symbols src ON src.id = l.from_id
+          WHERE (src.file_path LIKE '%/test/%' OR src.file_path LIKE '%\\test\\%'
+                 OR src.file_path LIKE '%.test.%' OR src.file_path LIKE '%.spec.%')
+        )
+        ORDER BY s.heat DESC
+        LIMIT ?
       `),
             annotationCount: this.db.prepare('SELECT COUNT(*) as c FROM annotations'),
         };
@@ -131,6 +131,9 @@ export class Database {
             if (!annNames.has('updated_at')) {
                 this.db.exec(`ALTER TABLE annotations ADD COLUMN updated_at TEXT NOT NULL DEFAULT (datetime('now'))`);
             }
+            if (!annNames.has('symbol_hash')) {
+                this.db.exec(`ALTER TABLE annotations ADD COLUMN symbol_hash TEXT`);
+            }
             // Rebuild index if column was renamed
             if (annNames.has('symbol_id')) {
                 this.db.exec(`DROP INDEX IF EXISTS idx_annotations_symbol`);
@@ -258,20 +261,49 @@ export class Database {
         return rows.map(rowToLink);
     }
     findDeadCode(kind, limit = 50) {
-        const frameworkExclude = `AND s.file_path NOT LIKE 'app/%/page.%' AND s.file_path NOT LIKE 'app/%/layout.%'
-      AND s.file_path NOT LIKE 'app/page.%' AND s.file_path NOT LIKE 'app/layout.%'
-      AND s.file_path NOT LIKE 'app/api/%/route.%' AND s.file_path NOT LIKE 'jest.config.%'
-      AND s.file_path NOT LIKE 'src/routes/+page.%' AND s.file_path NOT LIKE 'src/routes/+layout.%'`;
+        // Next.js/SvelteKit/api conventions are matched both at the repo root AND nested
+        // under a package subdirectory (e.g. monorepos with frontend/app/... instead of
+        // app/...) — a root-only 'app/%' pattern silently misses every monorepo layout.
+        const frameworkExclude = `AND s.file_path NOT LIKE 'app/%/page.%' AND s.file_path NOT LIKE '%/app/%/page.%'
+      AND s.file_path NOT LIKE 'app/%/layout.%' AND s.file_path NOT LIKE '%/app/%/layout.%'
+      AND s.file_path NOT LIKE 'app/page.%' AND s.file_path NOT LIKE '%/app/page.%'
+      AND s.file_path NOT LIKE 'app/layout.%' AND s.file_path NOT LIKE '%/app/layout.%'
+      AND s.file_path NOT LIKE 'app/%/loading.%' AND s.file_path NOT LIKE '%/app/%/loading.%'
+      AND s.file_path NOT LIKE 'app/%/error.%' AND s.file_path NOT LIKE '%/app/%/error.%'
+      AND s.file_path NOT LIKE 'app/%/not-found.%' AND s.file_path NOT LIKE '%/app/%/not-found.%'
+      AND s.file_path NOT LIKE 'app/%/template.%' AND s.file_path NOT LIKE '%/app/%/template.%'
+      AND s.file_path NOT LIKE 'app/%/global-error.%' AND s.file_path NOT LIKE '%/app/%/global-error.%'
+      AND s.file_path NOT LIKE 'app/%/default.%' AND s.file_path NOT LIKE '%/app/%/default.%'
+      AND s.file_path NOT LIKE 'app/api/%/route.%' AND s.file_path NOT LIKE '%/app/api/%/route.%'
+      AND s.file_path NOT LIKE 'app/%/route.%' AND s.file_path NOT LIKE '%/app/%/route.%'
+      AND s.file_path NOT LIKE 'jest.config.%'
+      AND s.file_path NOT LIKE 'src/routes/+page.%' AND s.file_path NOT LIKE '%/src/routes/+page.%'
+      AND s.file_path NOT LIKE 'src/routes/+layout.%' AND s.file_path NOT LIKE '%/src/routes/+layout.%'
+      AND s.file_path NOT LIKE '%/alembic/versions/%'
+      AND s.file_path NOT LIKE '%/migrations/%'
+      AND s.file_path NOT LIKE 'api/%' AND s.file_path NOT LIKE '%/api/%'
+      AND NOT ((s.file_path LIKE 'app/%' OR s.file_path LIKE '%/app/%') AND s.name IN ('generateStaticParams', 'metadata', 'generateMetadata', 'viewport', 'generateViewport', 'revalidate', 'dynamic', 'fetchCache', 'runtime', 'preferredRegion', 'maxDuration'))`;
+        // Vue SFC root components imported via <Component/> template tags get their
+        // import link on _top [module], not on the [class] root symbol. Treat the class
+        // as referenced if its file's _top module has incoming links from other files.
+        const vueRootGuard = `AND NOT (s.file_path LIKE '%.vue' AND s.kind = 'class' AND EXISTS (
+      SELECT 1 FROM symbols s2
+      JOIN links l2 ON l2.to_id = s2.id AND l2.type != 'contains'
+      WHERE s2.file_path = s.file_path AND s2.kind = 'module' AND s2.name = '_top'
+      AND EXISTS (SELECT 1 FROM links l3 WHERE l3.to_id = s2.id AND l3.type = 'imports')
+    ))`;
         const sql = kind
-            ? `SELECT s.* FROM symbols s
-         LEFT JOIN links l ON l.to_id = s.id AND l.type != 'contains'
-         WHERE s.exported = 1 AND s.kind = ? AND s.kind != 'section' AND l.id IS NULL
-         ${frameworkExclude}
+            ? `SELECT s.* FROM symbols s
+         LEFT JOIN links l ON l.to_id = s.id AND l.type != 'contains'
+         WHERE s.exported = 1 AND s.kind = ? AND s.kind != 'section' AND l.id IS NULL
+         ${frameworkExclude}
+         ${vueRootGuard}
          LIMIT ?`
-            : `SELECT s.* FROM symbols s
-         LEFT JOIN links l ON l.to_id = s.id AND l.type != 'contains'
-         WHERE s.exported = 1 AND s.kind != 'section' AND l.id IS NULL
-         ${frameworkExclude}
+            : `SELECT s.* FROM symbols s
+         LEFT JOIN links l ON l.to_id = s.id AND l.type != 'contains'
+         WHERE s.exported = 1 AND s.kind != 'section' AND l.id IS NULL
+         ${frameworkExclude}
+         ${vueRootGuard}
          LIMIT ?`;
         const rows = kind
             ? this.db.prepare(sql).all(kind, limit)
@@ -285,20 +317,38 @@ export class Database {
      * findDeadCode (which requires zero incoming links of any kind).
      */
     findTestOnlyReferenced(limit = 50) {
-        const frameworkExclude = `AND s.file_path NOT LIKE 'app/%/page.%' AND s.file_path NOT LIKE 'app/%/layout.%'
-      AND s.file_path NOT LIKE 'app/page.%' AND s.file_path NOT LIKE 'app/layout.%'
-      AND s.file_path NOT LIKE 'app/api/%/route.%' AND s.file_path NOT LIKE 'jest.config.%'
-      AND s.file_path NOT LIKE 'src/routes/+page.%' AND s.file_path NOT LIKE 'src/routes/+layout.%'`;
+        // Next.js/SvelteKit/api conventions are matched both at the repo root AND nested
+        // under a package subdirectory (e.g. monorepos with frontend/app/... instead of
+        // app/...) — a root-only 'app/%' pattern silently misses every monorepo layout.
+        const frameworkExclude = `AND s.file_path NOT LIKE 'app/%/page.%' AND s.file_path NOT LIKE '%/app/%/page.%'
+      AND s.file_path NOT LIKE 'app/%/layout.%' AND s.file_path NOT LIKE '%/app/%/layout.%'
+      AND s.file_path NOT LIKE 'app/page.%' AND s.file_path NOT LIKE '%/app/page.%'
+      AND s.file_path NOT LIKE 'app/layout.%' AND s.file_path NOT LIKE '%/app/layout.%'
+      AND s.file_path NOT LIKE 'app/%/loading.%' AND s.file_path NOT LIKE '%/app/%/loading.%'
+      AND s.file_path NOT LIKE 'app/%/error.%' AND s.file_path NOT LIKE '%/app/%/error.%'
+      AND s.file_path NOT LIKE 'app/%/not-found.%' AND s.file_path NOT LIKE '%/app/%/not-found.%'
+      AND s.file_path NOT LIKE 'app/%/template.%' AND s.file_path NOT LIKE '%/app/%/template.%'
+      AND s.file_path NOT LIKE 'app/%/global-error.%' AND s.file_path NOT LIKE '%/app/%/global-error.%'
+      AND s.file_path NOT LIKE 'app/%/default.%' AND s.file_path NOT LIKE '%/app/%/default.%'
+      AND s.file_path NOT LIKE 'app/api/%/route.%' AND s.file_path NOT LIKE '%/app/api/%/route.%'
+      AND s.file_path NOT LIKE 'app/%/route.%' AND s.file_path NOT LIKE '%/app/%/route.%'
+      AND s.file_path NOT LIKE 'jest.config.%'
+      AND s.file_path NOT LIKE 'src/routes/+page.%' AND s.file_path NOT LIKE '%/src/routes/+page.%'
+      AND s.file_path NOT LIKE 'src/routes/+layout.%' AND s.file_path NOT LIKE '%/src/routes/+layout.%'
+      AND s.file_path NOT LIKE '%/alembic/versions/%'
+      AND s.file_path NOT LIKE '%/migrations/%'
+      AND s.file_path NOT LIKE 'api/%' AND s.file_path NOT LIKE '%/api/%'
+      AND NOT ((s.file_path LIKE 'app/%' OR s.file_path LIKE '%/app/%') AND s.name IN ('generateStaticParams', 'metadata', 'generateMetadata', 'viewport', 'generateViewport', 'revalidate', 'dynamic', 'fetchCache', 'runtime', 'preferredRegion', 'maxDuration'))`;
         // Get ALL exported symbols that HAVE at least one incoming link (not caught by findDeadCode).
         // No SQL LIMIT here: the JS post-filter below narrows this down to test-only-referenced
         // symbols, which can be a small minority of low-heat candidates — applying `limit` before
         // that filter would silently drop real orphans that don't happen to rank in the top N by heat.
-        const sql = `SELECT s.*, COUNT(l.id) as incoming_count FROM symbols s
-         JOIN links l ON l.to_id = s.id AND l.type != 'contains'
-         WHERE s.exported = 1 AND s.kind != 'section'
-         ${frameworkExclude}
-         GROUP BY s.id
-         HAVING incoming_count > 0
+        const sql = `SELECT s.*, COUNT(l.id) as incoming_count FROM symbols s
+         JOIN links l ON l.to_id = s.id AND l.type != 'contains'
+         WHERE s.exported = 1 AND s.kind != 'section'
+         ${frameworkExclude}
+         GROUP BY s.id
+         HAVING incoming_count > 0
          ORDER BY s.heat DESC`;
         const rows = this.db.prepare(sql).all();
         const candidates = rows.map(rowToSymbol);
@@ -319,25 +369,25 @@ export class Database {
         return results.slice(0, limit);
     }
     getTypeHierarchy(symbolId) {
-        const ancestors = this.db.prepare(`
-      WITH RECURSIVE up(id, depth) AS (
-        SELECT to_id, 1 FROM links WHERE from_id = ? AND type IN ('extends', 'implements')
-        UNION
-        SELECT l.to_id, u.depth + 1
-        FROM links l JOIN up u ON l.from_id = u.id
-        WHERE l.type IN ('extends', 'implements') AND u.depth < 10
-      )
-      SELECT DISTINCT s.*, u.depth FROM up u JOIN symbols s ON s.id = u.id ORDER BY u.depth
+        const ancestors = this.db.prepare(`
+      WITH RECURSIVE up(id, depth) AS (
+        SELECT to_id, 1 FROM links WHERE from_id = ? AND type IN ('extends', 'implements')
+        UNION
+        SELECT l.to_id, u.depth + 1
+        FROM links l JOIN up u ON l.from_id = u.id
+        WHERE l.type IN ('extends', 'implements') AND u.depth < 10
+      )
+      SELECT DISTINCT s.*, u.depth FROM up u JOIN symbols s ON s.id = u.id ORDER BY u.depth
     `).all(symbolId);
-        const descendants = this.db.prepare(`
-      WITH RECURSIVE down(id, depth) AS (
-        SELECT from_id, 1 FROM links WHERE to_id = ? AND type IN ('extends', 'implements')
-        UNION
-        SELECT l.from_id, d.depth + 1
-        FROM links l JOIN down d ON l.to_id = d.id
-        WHERE l.type IN ('extends', 'implements') AND d.depth < 10
-      )
-      SELECT DISTINCT s.*, d.depth FROM down d JOIN symbols s ON s.id = d.id ORDER BY d.depth
+        const descendants = this.db.prepare(`
+      WITH RECURSIVE down(id, depth) AS (
+        SELECT from_id, 1 FROM links WHERE to_id = ? AND type IN ('extends', 'implements')
+        UNION
+        SELECT l.from_id, d.depth + 1
+        FROM links l JOIN down d ON l.to_id = d.id
+        WHERE l.type IN ('extends', 'implements') AND d.depth < 10
+      )
+      SELECT DISTINCT s.*, d.depth FROM down d JOIN symbols s ON s.id = d.id ORDER BY d.depth
     `).all(symbolId);
         return {
             ancestors: ancestors.map(r => ({ symbol: rowToSymbol(r), depth: r.depth })),
@@ -349,21 +399,52 @@ export class Database {
         const toSyms = this.findSymbolByName(toName);
         if (fromSyms.length === 0 || toSyms.length === 0)
             return null;
-        const fromId = fromSyms[0].id;
-        const toId = toSyms[0].id;
-        const toIds = new Set(toSyms.map(s => s.id));
-        const rows = this.db.prepare(`
-      WITH RECURSIVE chain(node_id, depth, via, path_ids) AS (
-        SELECT l.to_id, 1, l.type, ',' || l.from_id || ',' || l.to_id || ','
-        FROM links l WHERE l.from_id = ? AND l.type != 'contains'
-        UNION ALL
-        SELECT l.to_id, c.depth + 1, l.type, c.path_ids || l.to_id || ','
-        FROM links l JOIN chain c ON l.from_id = c.node_id
-        WHERE l.type != 'contains' AND c.depth < ?
-          AND c.path_ids NOT LIKE '%,' || l.to_id || ',%'
-      )
-      SELECT node_id, depth, via, path_ids FROM chain ORDER BY depth
-    `).all(fromId, maxDepth);
+        return this.findPathFromId(fromSyms[0].id, toSyms.map(s => s.id), maxDepth);
+    }
+    /**
+     * Same as findPath, but takes an already-resolved source symbol id instead
+     * of re-resolving by name. Needed when the caller has disambiguated among
+     * several same-named symbols (e.g. picking the right file-scoped `_top`
+     * module out of many) — passing the name back through findPath() would
+     * silently re-resolve to an arbitrary same-named symbol and discard that
+     * disambiguation.
+     */
+    findPathFromId(fromId, toNameOrIds, maxDepth = 5) {
+        const toIds = Array.isArray(toNameOrIds)
+            ? new Set(toNameOrIds)
+            : new Set(this.findSymbolByName(toNameOrIds).map(s => s.id));
+        if (toIds.size === 0)
+            return null;
+        // Anchor branch 2 seeds the search by descending ONE 'contains' hop from the exact
+        // origin symbol into its own contained methods, then taking one real edge from there.
+        // This only ever applies to the literal starting symbol (later branches never re-descend
+        // into contains children mid-path) — a class/struct/trait passed as `fromId` typically
+        // has zero direct calls/imports edges of its own (its real behavior lives in its
+        // methods), so without this seed the search dead-ends immediately at depth 0 for any
+        // class-to-X query. Safe: it can't produce a false "relationship" between unrelated
+        // sibling methods, since it's scoped to fromId's own children only, never applied again
+        // to a class reached later in the chain.
+        const rows = this.db.prepare(`
+      WITH RECURSIVE chain(node_id, depth, via, path_ids) AS (
+        SELECT l.to_id, 1, l.type, ',' || l.from_id || ',' || l.to_id || ','
+        FROM links l WHERE l.from_id = ? AND l.type != 'contains'
+        UNION ALL
+        SELECT l2.to_id, 2, l2.type, ',' || l.from_id || ',' || l.to_id || ',' || l2.to_id || ','
+        FROM links l JOIN links l2 ON l2.from_id = l.to_id
+        WHERE l.from_id = ? AND l.type = 'contains' AND l2.type != 'contains'
+        UNION ALL
+        SELECT l.to_id, c.depth + 1, l.type, c.path_ids || l.to_id || ','
+        FROM links l JOIN chain c ON l.from_id = c.node_id
+        WHERE l.type != 'contains' AND c.depth < ?
+          AND c.path_ids NOT LIKE '%,' || l.to_id || ',%'
+        UNION ALL
+        SELECT l.from_id, c.depth + 1, l.type, c.path_ids || l.from_id || ','
+        FROM links l JOIN chain c ON l.to_id = c.node_id
+        WHERE l.type = 'contains' AND c.depth < ?
+          AND c.path_ids NOT LIKE '%,' || l.from_id || ',%'
+      )
+      SELECT node_id, depth, via, path_ids FROM chain ORDER BY depth
+    `).all(fromId, fromId, maxDepth, maxDepth);
         // Find the first (shortest-depth) row matching the target
         const targetRow = rows.find(r => toIds.has(r.node_id));
         if (!targetRow)
@@ -376,12 +457,21 @@ export class Database {
             const sym = this.findSymbolById(idChain[i]);
             if (!sym)
                 continue;
-            // Determine via for this hop: lookup link from idChain[i] → idChain[i+1]
+            // Determine via for this hop: lookup link from idChain[i] → idChain[i+1]. Prefer a
+            // real calls/imports/etc. edge when one exists between the two nodes; only report
+            // 'contains' (in either direction — the traversal now allows both a class-to-method
+            // seed step and a method-to-class arrival step) when that's the only relationship.
             let via = 'calls';
             if (i < idChain.length - 1) {
                 const linkRow = this.db.prepare('SELECT type FROM links WHERE from_id = ? AND to_id = ? AND type != ? LIMIT 1').get(idChain[i], idChain[i + 1], 'contains');
-                if (linkRow)
+                if (linkRow) {
                     via = linkRow.type;
+                }
+                else {
+                    const containsRow = this.db.prepare('SELECT type FROM links WHERE ((from_id = ? AND to_id = ?) OR (from_id = ? AND to_id = ?)) AND type = ? LIMIT 1').get(idChain[i], idChain[i + 1], idChain[i + 1], idChain[i], 'contains');
+                    if (containsRow)
+                        via = containsRow.type;
+                }
             }
             result.push({ symbol: sym, depth: i, via });
         }
@@ -427,14 +517,14 @@ export class Database {
         };
     }
     getConfidenceDistribution() {
-        const rows = this.db.prepare(`
-      SELECT
-        SUM(CASE WHEN confidence >= 0.9 THEN 1 ELSE 0 END) as high,
-        SUM(CASE WHEN confidence >= 0.7 AND confidence < 0.9 THEN 1 ELSE 0 END) as medium,
-        SUM(CASE WHEN confidence < 0.7 THEN 1 ELSE 0 END) as low,
-        COUNT(*) as total
-      FROM links
-      WHERE type != 'contains'
+        const rows = this.db.prepare(`
+      SELECT
+        SUM(CASE WHEN confidence >= 0.9 THEN 1 ELSE 0 END) as high,
+        SUM(CASE WHEN confidence >= 0.7 AND confidence < 0.9 THEN 1 ELSE 0 END) as medium,
+        SUM(CASE WHEN confidence < 0.7 THEN 1 ELSE 0 END) as low,
+        COUNT(*) as total
+      FROM links
+      WHERE type != 'contains'
     `).get();
         return {
             high: rows?.high ?? 0,
@@ -459,7 +549,16 @@ export class Database {
             if (incoming.length === 0) {
                 // Reached an entrypoint — save this path
                 // _top modules represent file-level entrypoints (e.g., top-level code execution)
-                if (sym?.exported || (sym?.kind === 'module' && sym?.name === '_top')) {
+                // Class methods: if the method is contained by an exported class, treat it as
+                // a de facto entrypoint (framework-invoked handlers like NestJS controllers).
+                const isExportedClassMember = !sym?.exported && sym?.kind === 'method' &&
+                    this.getIncomingLinks(currentId).some(l => {
+                        if (l.type !== 'contains')
+                            return false;
+                        const containingClass = this.findSymbolById(l.fromId);
+                        return containingClass?.exported === true;
+                    });
+                if (sym?.exported || (sym?.kind === 'module' && sym?.name === '_top') || isExportedClassMember) {
                     paths.push({ path: [...currentPath] });
                 }
                 visited.delete(currentId);
@@ -490,34 +589,34 @@ export class Database {
     // ── Route/endpoint detection via link patterns ──
     getEntrypoints() {
         // Symbols with role='entrypoint' OR exported + 0 incoming non-contains links
-        const rows = this.db.prepare(`
-      SELECT s.* FROM symbols s
-      WHERE s.exported = 1
-        AND s.role = 'entrypoint'
-      ORDER BY s.heat DESC
-      LIMIT 50
+        const rows = this.db.prepare(`
+      SELECT s.* FROM symbols s
+      WHERE s.exported = 1
+        AND s.role = 'entrypoint'
+      ORDER BY s.heat DESC
+      LIMIT 50
     `).all();
         return rows.map(rowToSymbol);
     }
     // ── Domain clustering stats ──
     getDomainStats() {
-        const rows = this.db.prepare(`
-      SELECT fh.zone AS domain, COUNT(DISTINCT fh.path) AS file_count,
-             COUNT(s.id) AS symbol_count
-      FROM file_hashes fh
-      LEFT JOIN symbols s ON s.file_path = fh.path
-      WHERE fh.zone IS NOT NULL
-      GROUP BY fh.zone
-      ORDER BY symbol_count DESC
+        const rows = this.db.prepare(`
+      SELECT fh.zone AS domain, COUNT(DISTINCT fh.path) AS file_count,
+             COUNT(s.id) AS symbol_count
+      FROM file_hashes fh
+      LEFT JOIN symbols s ON s.file_path = fh.path
+      WHERE fh.zone IS NOT NULL
+      GROUP BY fh.zone
+      ORDER BY symbol_count DESC
     `).all();
         return rows.map((r) => ({ domain: r.domain, files: r.file_count, symbols: r.symbol_count }));
     }
     // ── Staleness detection ──
     getStaleFiles(hoursOld = 24) {
-        const rows = this.db.prepare(`
-      SELECT path FROM file_hashes
-      WHERE analyzed_at < datetime('now', '-' || ? || ' hours')
-      ORDER BY analyzed_at ASC
+        const rows = this.db.prepare(`
+      SELECT path FROM file_hashes
+      WHERE analyzed_at < datetime('now', '-' || ? || ' hours')
+      ORDER BY analyzed_at ASC
     `).all(hoursOld);
         return rows.map((r) => r.path);
     }
@@ -543,14 +642,14 @@ export class Database {
             return;
         const placeholders = filePaths.map(() => '?').join(',');
         // Delete links where either end references a symbol in the changed files
-        this.db.prepare(`
-      DELETE FROM links WHERE from_id IN (SELECT id FROM symbols WHERE file_path IN (${placeholders}))
+        this.db.prepare(`
+      DELETE FROM links WHERE from_id IN (SELECT id FROM symbols WHERE file_path IN (${placeholders}))
     `).run(...filePaths);
-        this.db.prepare(`
-      DELETE FROM links WHERE to_id IN (SELECT id FROM symbols WHERE file_path IN (${placeholders}))
+        this.db.prepare(`
+      DELETE FROM links WHERE to_id IN (SELECT id FROM symbols WHERE file_path IN (${placeholders}))
     `).run(...filePaths);
-        this.db.prepare(`
-      DELETE FROM symbols WHERE file_path IN (${placeholders})
+        this.db.prepare(`
+      DELETE FROM symbols WHERE file_path IN (${placeholders})
     `).run(...filePaths);
     }
     /** Delete file_hashes rows for paths not in the given set (orphan cleanup after incremental analyze) */
@@ -558,52 +657,52 @@ export class Database {
         if (knownPaths.length === 0)
             return 0;
         const placeholders = knownPaths.map(() => '?').join(',');
-        const result = this.db.prepare(`
-      DELETE FROM file_hashes WHERE path NOT IN (${placeholders})
+        const result = this.db.prepare(`
+      DELETE FROM file_hashes WHERE path NOT IN (${placeholders})
     `).run(...knownPaths);
         return result.changes;
     }
     // ── Tool usage tracking ──
     logToolUsage(tool, durationMs, tokensOut, tokensSaved, repo) {
-        this.db.prepare(`INSERT INTO tool_usage (tool, duration_ms, tokens_out, tokens_saved, repo)
+        this.db.prepare(`INSERT INTO tool_usage (tool, duration_ms, tokens_out, tokens_saved, repo)
        VALUES (?, ?, ?, ?, ?)`).run(tool, durationMs, tokensOut, tokensSaved, repo ?? null);
     }
     getToolUsageStats(repo) {
         const repoFilter = repo ? `WHERE repo = ?` : '';
         const repoParam = repo ? [repo] : [];
-        const totals = this.db.prepare(`
-      SELECT COUNT(*) as total_calls,
-             COALESCE(SUM(tokens_saved), 0) as total_saved,
-             COALESCE(SUM(tokens_out), 0) as total_out,
-             COALESCE(SUM(duration_ms), 0) as total_ms
-      FROM tool_usage
-      ${repoFilter}
+        const totals = this.db.prepare(`
+      SELECT COUNT(*) as total_calls,
+             COALESCE(SUM(tokens_saved), 0) as total_saved,
+             COALESCE(SUM(tokens_out), 0) as total_out,
+             COALESCE(SUM(duration_ms), 0) as total_ms
+      FROM tool_usage
+      ${repoFilter}
     `).get(...repoParam);
-        const byTool = this.db.prepare(`
-      SELECT tool, COUNT(*) as calls,
-             COALESCE(SUM(tokens_saved), 0) as tokens_saved,
-             COALESCE(SUM(tokens_out), 0) as tokens_out,
-             CAST(COALESCE(AVG(duration_ms), 0) AS INTEGER) as avg_ms
-      FROM tool_usage
-      ${repoFilter}
-      GROUP BY tool
-      ORDER BY calls DESC
+        const byTool = this.db.prepare(`
+      SELECT tool, COUNT(*) as calls,
+             COALESCE(SUM(tokens_saved), 0) as tokens_saved,
+             COALESCE(SUM(tokens_out), 0) as tokens_out,
+             CAST(COALESCE(AVG(duration_ms), 0) AS INTEGER) as avg_ms
+      FROM tool_usage
+      ${repoFilter}
+      GROUP BY tool
+      ORDER BY calls DESC
     `).all(...repoParam);
-        const byDay = this.db.prepare(`
-      SELECT date(called_at) as date, COUNT(*) as calls,
-             COALESCE(SUM(tokens_saved), 0) as tokens_saved
-      FROM tool_usage
-      ${repoFilter}
-      GROUP BY date(called_at)
-      ORDER BY date DESC
-      LIMIT 30
+        const byDay = this.db.prepare(`
+      SELECT date(called_at) as date, COUNT(*) as calls,
+             COALESCE(SUM(tokens_saved), 0) as tokens_saved
+      FROM tool_usage
+      ${repoFilter}
+      GROUP BY date(called_at)
+      ORDER BY date DESC
+      LIMIT 30
     `).all(...repoParam);
-        const recentCalls = this.db.prepare(`
-      SELECT tool, called_at, duration_ms, tokens_saved
-      FROM tool_usage
-      ${repoFilter}
-      ORDER BY id DESC
-      LIMIT 50
+        const recentCalls = this.db.prepare(`
+      SELECT tool, called_at, duration_ms, tokens_saved
+      FROM tool_usage
+      ${repoFilter}
+      ORDER BY id DESC
+      LIMIT 50
     `).all(...repoParam);
         return {
             totalCalls: totals.total_calls,
@@ -622,7 +721,10 @@ export class Database {
     }
     // ── Test file detection ──
     isTestFile(filePath) {
-        return /[/\\]test[/\\]/.test(filePath) || /\.(test|spec)\./.test(filePath);
+        const codeExt = /\.(ts|tsx|js|jsx|mjs|cjs|py|go|rb|java|php|rs)$/i;
+        if (!codeExt.test(filePath))
+            return false;
+        return /[/\\]tests?[/\\]/.test(filePath) || /\.(test|spec)\./i.test(filePath);
     }
     // ── Heat / hubs ──
     getTopHubs(limit) {
@@ -644,10 +746,10 @@ export class Database {
         if (candidateIds.length === 0)
             return new Set();
         const placeholders = candidateIds.map(() => '?').join(',');
-        const rows = this.db.prepare(`
-      SELECT DISTINCT l.to_id
-      FROM links l JOIN symbols src ON src.id = l.from_id
-      WHERE l.to_id IN (${placeholders}) AND l.type != 'contains'
+        const rows = this.db.prepare(`
+      SELECT DISTINCT l.to_id
+      FROM links l JOIN symbols src ON src.id = l.from_id
+      WHERE l.to_id IN (${placeholders}) AND l.type != 'contains'
     `).all(...candidateIds);
         const testedIds = new Set();
         for (const row of rows) {
@@ -682,27 +784,27 @@ export class Database {
         if (changedSymbolIds.length === 0)
             return { testFiles: [], changedSymbols: [] };
         const placeholders = changedSymbolIds.map(() => '?').join(',');
-        const testFilesDirect = this.db.prepare(`
-      SELECT DISTINCT src.file_path
-      FROM links l
-      JOIN symbols src ON src.id = l.from_id
-      WHERE l.to_id IN (${placeholders})
-        AND (src.file_path LIKE '%/test/%' OR src.file_path LIKE '%\\test\\%'
-             OR src.file_path LIKE '%.test.%' OR src.file_path LIKE '%.spec.%')
+        const testFilesDirect = this.db.prepare(`
+      SELECT DISTINCT src.file_path
+      FROM links l
+      JOIN symbols src ON src.id = l.from_id
+      WHERE l.to_id IN (${placeholders})
+        AND (src.file_path LIKE '%/test/%' OR src.file_path LIKE '%\\test\\%'
+             OR src.file_path LIKE '%.test.%' OR src.file_path LIKE '%.spec.%')
     `).all(...changedSymbolIds);
-        const testFilesUpstream = this.db.prepare(`
-      WITH RECURSIVE upstream(id, depth) AS (
-        SELECT from_id, 1 FROM links WHERE to_id IN (${placeholders})
-          AND type IN ('calls', 'imports', 'extends', 'implements')
-        UNION
-        SELECT l.from_id, u.depth + 1
-        FROM links l JOIN upstream u ON l.to_id = u.id
-        WHERE l.type IN ('calls', 'imports', 'extends', 'implements') AND u.depth < 5
-      )
-      SELECT DISTINCT s.file_path FROM upstream u
-      JOIN symbols s ON s.id = u.id
-      WHERE (s.file_path LIKE '%/test/%' OR s.file_path LIKE '%\\test\\%'
-             OR s.file_path LIKE '%.test.%' OR s.file_path LIKE '%.spec.%')
+        const testFilesUpstream = this.db.prepare(`
+      WITH RECURSIVE upstream(id, depth) AS (
+        SELECT from_id, 1 FROM links WHERE to_id IN (${placeholders})
+          AND type IN ('calls', 'imports', 'extends', 'implements')
+        UNION
+        SELECT l.from_id, u.depth + 1
+        FROM links l JOIN upstream u ON l.to_id = u.id
+        WHERE l.type IN ('calls', 'imports', 'extends', 'implements') AND u.depth < 5
+      )
+      SELECT DISTINCT s.file_path FROM upstream u
+      JOIN symbols s ON s.id = u.id
+      WHERE (s.file_path LIKE '%/test/%' OR s.file_path LIKE '%\\test\\%'
+             OR s.file_path LIKE '%.test.%' OR s.file_path LIKE '%.spec.%')
     `).all(...changedSymbolIds);
         const allTestFiles = [...new Set([
                 ...testFilesDirect.map((r) => r.file_path),
@@ -736,30 +838,41 @@ export class Database {
         const target = this.findSymbolById(symbolId);
         if (!target)
             return [];
-        const incoming = this.getIncomingLinks(symbolId).filter(l => l.type !== 'contains');
-        const outgoing = this.getOutgoingLinks(symbolId).filter(l => l.type !== 'contains');
-        const targetLinks = new Set();
-        for (const link of incoming)
-            targetLinks.add(link.fromId);
-        for (const link of outgoing)
-            targetLinks.add(link.toId);
+        const CONTAINER_KINDS = new Set(['class', 'struct', 'trait']);
+        const buildSig = (id) => {
+            const sig = new Set();
+            const sym = this.findSymbolById(id);
+            const incoming = this.getIncomingLinks(id).filter(l => l.type !== 'contains');
+            const outgoing = this.getOutgoingLinks(id).filter(l => l.type !== 'contains');
+            for (const link of incoming)
+                sig.add(link.fromId);
+            for (const link of outgoing)
+                sig.add(link.toId);
+            if (sym && CONTAINER_KINDS.has(sym.kind)) {
+                const contained = this.getOutgoingLinks(id).filter(l => l.type === 'contains');
+                for (const cl of contained) {
+                    const mIn = this.getIncomingLinks(cl.toId).filter(l => l.type !== 'contains');
+                    const mOut = this.getOutgoingLinks(cl.toId).filter(l => l.type !== 'contains');
+                    for (const link of mIn)
+                        sig.add(link.fromId);
+                    for (const link of mOut)
+                        sig.add(link.toId);
+                }
+            }
+            return sig;
+        };
+        const targetSig = buildSig(symbolId);
         // Search across all exported symbols, not just same-file siblings
         const allSymbols = this.getAllSymbols().filter(s => s.id !== symbolId && s.exported);
         const results = [];
         for (const candidate of allSymbols) {
-            const candIncoming = this.getIncomingLinks(candidate.id).filter(l => l.type !== 'contains');
-            const candOutgoing = this.getOutgoingLinks(candidate.id).filter(l => l.type !== 'contains');
-            const candidateLinks = new Set();
-            for (const link of candIncoming)
-                candidateLinks.add(link.fromId);
-            for (const link of candOutgoing)
-                candidateLinks.add(link.toId);
+            const candidateSig = buildSig(candidate.id);
             let intersection = 0;
-            for (const id of targetLinks) {
-                if (candidateLinks.has(id))
+            for (const id of targetSig) {
+                if (candidateSig.has(id))
                     intersection++;
             }
-            const union = new Set([...targetLinks, ...candidateLinks]).size;
+            const union = new Set([...targetSig, ...candidateSig]).size;
             const similarity = union > 0 ? intersection / union : 0;
             if (similarity >= 0.15) {
                 results.push({ symbol: candidate, similarity: Math.round(similarity * 100) / 100 });
@@ -778,7 +891,7 @@ export class Database {
         const expiresAt = ttlHours
             ? new Date(Date.now() + ttlHours * 3600_000).toISOString().replace('T', ' ').slice(0, 19)
             : null;
-        const result = this.db.prepare(`INSERT INTO annotations (symbol, key, value, agent, session_id, expires_at)
+        const result = this.db.prepare(`INSERT INTO annotations (symbol, key, value, agent, session_id, expires_at)
        VALUES (?, ?, ?, ?, ?, ?)`).run(symbolId, key, value, agent ?? null, sessionId ?? null, expiresAt);
         return result.lastInsertRowid;
     }
@@ -833,12 +946,12 @@ export class Database {
         this.db.prepare('INSERT INTO metric_history (metric_name, value) VALUES (?, ?)').run(name, value);
     }
     getMetricHistory(name, daysBack = 30) {
-        return this.db.prepare(`SELECT value, recorded_at as recordedAt FROM metric_history
-       WHERE metric_name = ? AND recorded_at >= datetime('now', ?)
+        return this.db.prepare(`SELECT value, recorded_at as recordedAt FROM metric_history
+       WHERE metric_name = ? AND recorded_at >= datetime('now', ?)
        ORDER BY recorded_at DESC`).all(name, `-${daysBack} days`);
     }
     getMetricTrend(name) {
-        const rows = this.db.prepare(`SELECT value FROM metric_history
+        const rows = this.db.prepare(`SELECT value FROM metric_history
        WHERE metric_name = ? ORDER BY recorded_at DESC LIMIT 2`).all(name);
         if (rows.length === 0)
             return { current: 0, previous: null, change: null };