homegraph 1.4.1 → 1.5.1

package/dist/db/index.js

@@ -38,7 +38,7 @@ var __importStar = (this && this.__importStar) || (function () {
     };
 })();
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.DATABASE_FILENAME = exports.DatabaseConnection = void 0;
+exports.DATABASE_FILENAME = exports.DatabaseConnection = exports.isNativeSqliteAvailable = exports.isNodeSqliteAvailable = exports.WASM_FALLBACK_FIX_RECIPE = void 0;
 exports.getDatabasePath = getDatabasePath;
 exports.removeDatabaseFiles = removeDatabaseFiles;
 const sqlite_adapter_1 = require("./sqlite-adapter");
@@ -46,6 +46,10 @@ const fs = __importStar(require("fs"));
 const path = __importStar(require("path"));
 const migrations_1 = require("./migrations");
 const directory_1 = require("../directory");
+var sqlite_adapter_2 = require("./sqlite-adapter");
+Object.defineProperty(exports, "WASM_FALLBACK_FIX_RECIPE", { enumerable: true, get: function () { return sqlite_adapter_2.WASM_FALLBACK_FIX_RECIPE; } });
+Object.defineProperty(exports, "isNodeSqliteAvailable", { enumerable: true, get: function () { return sqlite_adapter_2.isNodeSqliteAvailable; } });
+Object.defineProperty(exports, "isNativeSqliteAvailable", { enumerable: true, get: function () { return sqlite_adapter_2.isNativeSqliteAvailable; } });
 /**
  * Apply connection-level PRAGMAs. Shared by `initialize` and `open` so the two
  * paths can't drift.
@@ -56,15 +60,15 @@ const directory_1 = require("../directory");
  * the lock instead of throwing "database is locked" immediately. See issue #238.
  *
  * The 5s window (was 120s) rides out a normal incremental sync; the old
- * 2-minute wait presented as a frozen, hung agent. With WAL, reads never block
- * on a writer, so this timeout only governs cross-process write contention
- * (e.g. the git-hook `homegraph sync` running while the MCP server writes).
+ * 2-minute wait presented as a frozen, hung agent. With WAL (node:sqlite or
+ * better-sqlite3), reads never block on a writer, so this timeout only governs
+ * cross-process write contention. The WASM fallback remaps WAL → DELETE.
  */
 function configureConnection(db) {
     db.pragma('busy_timeout = 5000'); // MUST be first — see above
     db.pragma('foreign_keys = ON');
-    db.pragma('journal_mode = WAL'); // node:sqlite supports WAL on every platform
-    db.pragma('synchronous = NORMAL'); // safe with WAL mode
+    db.pragma('journal_mode = WAL'); // native: WAL; wasm remaps to DELETE
+    db.pragma('synchronous = NORMAL'); // safe with WAL; wasm remaps to FULL
     // Keep SQLite's per-connection footprint small. On multi-hundred-MB indexes,
     // a 64MB cache + 256MB mmap (× main + query-pool workers) was a major driver
     // of multi-GB process RSS. 16MB cache / 64MB mmap is enough for interactive
@@ -135,8 +139,228 @@ class DatabaseConnection {
         if (currentVersion < migrations_1.CURRENT_SCHEMA_VERSION) {
             (0, migrations_1.runMigrations)(db, currentVersion);
         }
+        // Self-heal a bulk-load window that never closed (crash between
+        // beginBulkNodeLoad and endBulkNodeLoad): the FTS triggers are missing and
+        // nodes_fts is stale. Rebuild + recreate so search stays in sync.
+        conn.healBulkNodeLoad();
         return conn;
     }
+    /**
+     * FTS maintenance triggers dropped/recreated around a bulk load.
+     * Names must match schema.sql.
+     */
+    static FTS_TRIGGER_NAMES = ['nodes_ai', 'nodes_ad', 'nodes_au'];
+    /**
+     * Enter bulk-load mode: drop the per-row FTS sync triggers so mass node
+     * inserts skip per-row tokenization. MUST be paired with endBulkNodeLoad()
+     * (use try/finally); a crash inside the window is healed on the next open().
+     * The window is DB-wide (triggers are schema objects), which is safe because
+     * endBulkNodeLoad() rebuilds nodes_fts from the nodes table wholesale — any
+     * row written by anyone during the window is captured by the rebuild.
+     */
+    beginBulkNodeLoad() {
+        for (const t of DatabaseConnection.FTS_TRIGGER_NAMES) {
+            this.db.exec(`DROP TRIGGER IF EXISTS ${t}`);
+        }
+    }
+    /**
+     * Leave bulk-load mode: rebuild the whole FTS index from the nodes table in
+     * one pass (far cheaper than per-row trigger firings), then recreate the
+     * triggers by re-running schema.sql (idempotent — everything in it is
+     * IF NOT EXISTS).
+     */
+    endBulkNodeLoad() {
+        this.db.exec(`INSERT INTO nodes_fts(nodes_fts) VALUES('rebuild')`);
+        this.recreateFtsTriggers();
+    }
+    /**
+     * NON-UNIQUE secondary indexes maintained per-row during the parse phase's
+     * bulk inserts — the store-architecture arc's first lever (plan §4d: dubbo's
+     * parse-loop wall is 94% store-writer busy, and the #1320 post-mortem showed
+     * statement batching and sorted inserts are ~zero on this path because
+     * B-TREE MAINTENANCE is the floor). A fresh init writes every row of
+     * nodes/unresolved_refs/files exactly once and reads none of them until
+     * resolution, so the parse window can drop all of these and rebuild each in
+     * one table scan afterwards — the same measured trade as the resolution
+     * phase's edge-index window (2.8s → 1.1s inserting, ~0.3s recreating).
+     * Primary keys and UNIQUE constraints stay (upserts and OR-IGNORE dedup
+     * conflict on them).
+     */
+    static BULK_PARSE_INDEX_NAMES = [
+        'idx_nodes_kind',
+        'idx_nodes_name',
+        'idx_nodes_qualified_name',
+        'idx_nodes_file_path',
+        'idx_nodes_language',
+        'idx_nodes_file_line',
+        'idx_nodes_lower_name',
+        'idx_unresolved_from_node',
+        'idx_unresolved_name',
+        'idx_unresolved_file_path',
+        'idx_unresolved_from_name',
+        'idx_unresolved_status',
+        'idx_unresolved_failed_tail',
+        'idx_files_language',
+        'idx_files_modified_at',
+    ];
+    /**
+     * Enter bulk-parse-load mode (FRESH-INIT ONLY — the caller gates on a fresh
+     * DB, because an incremental index deletes per-file rows mid-phase and needs
+     * the file_path indexes): drop every parse-lane secondary index, including
+     * the four non-unique edge indexes (parse inserts contains-edges too; the
+     * UNIQUE identity index stays for INSERT OR IGNORE dedup, and its `source`
+     * prefix keeps source-keyed reads indexed, as in the edge window). MUST be
+     * paired with endBulkParseLoad(); a crash inside the window is healed on the
+     * next DatabaseConnection open (schema.sql re-applies CREATE INDEX IF NOT
+     * EXISTS).
+     */
+    beginBulkParseLoad() {
+        for (const idx of DatabaseConnection.BULK_PARSE_INDEX_NAMES) {
+            this.db.exec(`DROP INDEX IF EXISTS ${idx}`);
+        }
+        this.beginBulkEdgeLoad();
+    }
+    /**
+     * Leave bulk-parse-load mode: recreate everything the window dropped, one
+     * table scan per index, with a yield between statements (same
+     * liveness-watchdog rationale as endBulkEdgeLoad — at kernel scale each
+     * build is a long synchronous scan). The edge indexes are rebuilt here too,
+     * so paths that never enter the resolution phase's own bulk-edge window
+     * (small runs) are left with a complete schema; the batched resolver's
+     * beginBulkEdgeLoad simply re-drops them (DROP IF EXISTS — idempotent).
+     */
+    async endBulkParseLoad() {
+        const schemaPath = path.join(__dirname, 'schema.sql');
+        const schema = fs.readFileSync(schemaPath, 'utf-8');
+        for (const idx of DatabaseConnection.BULK_PARSE_INDEX_NAMES) {
+            const m = schema.match(new RegExp(`CREATE INDEX IF NOT EXISTS ${idx}\\b[^;]*;`));
+            if (!m)
+                throw new Error(`schema.sql: parse index ${idx} not found for bulk-load recreation`);
+            this.db.exec(m[0]);
+            await new Promise((resolve) => setImmediate(resolve));
+        }
+        await this.endBulkEdgeLoad();
+    }
+    /**
+     * unresolved_refs secondary indexes NOT read by the batched resolution
+     * loop. The loop pages pending refs by keyset (`status='pending' AND id>?`
+     * — the status index + PK), deletes resolved rows by id, and parks failures
+     * with a status UPDATE; every other ref index serves SYNC-time paths
+     * (per-file re-index deletes, name-keyed retry, failed-tail heal). Each
+     * per-batch DELETE maintains all of them — the biggest single main-thread
+     * stage on the dubbo profile (deletes 1.2s of a 5.4s resolution phase) —
+     * so the batched loop drops them and rebuilds at the end, where the table
+     * holds only the surviving FAILED refs (resolved rows are gone), making
+     * the recreate near-free.
+     */
+    static BULK_REF_INDEX_NAMES = [
+        'idx_unresolved_from_node',
+        'idx_unresolved_name',
+        'idx_unresolved_file_path',
+        'idx_unresolved_from_name',
+        'idx_unresolved_failed_tail',
+    ];
+    /**
+     * Enter bulk-ref mode for the batched resolution loop — see
+     * BULK_REF_INDEX_NAMES. MUST be paired with endBulkRefLoad(); a crash
+     * inside the window heals on the next open (schema.sql re-applies
+     * CREATE INDEX IF NOT EXISTS).
+     */
+    beginBulkRefLoad() {
+        for (const idx of DatabaseConnection.BULK_REF_INDEX_NAMES) {
+            this.db.exec(`DROP INDEX IF EXISTS ${idx}`);
+        }
+    }
+    /** Leave bulk-ref mode: recreate each index in one scan (yield between). */
+    async endBulkRefLoad() {
+        const schemaPath = path.join(__dirname, 'schema.sql');
+        const schema = fs.readFileSync(schemaPath, 'utf-8');
+        for (const idx of DatabaseConnection.BULK_REF_INDEX_NAMES) {
+            const m = schema.match(new RegExp(`CREATE INDEX IF NOT EXISTS ${idx}\\b[^;]*;`));
+            if (!m)
+                throw new Error(`schema.sql: ref index ${idx} not found for bulk-load recreation`);
+            this.db.exec(m[0]);
+            await new Promise((resolve) => setImmediate(resolve));
+        }
+    }
+    /**
+     * Names of the NON-UNIQUE edge indexes dropped for a bulk edge load.
+     * idx_edges_identity deliberately stays: INSERT OR IGNORE's dedup conflicts
+     * on it (#1034), and its leftmost column is `source`, so the source-keyed
+     * reads resolution makes mid-window (supertype walks over
+     * `implements`/`extends`) keep an index via its prefix — verified with
+     * EXPLAIN QUERY PLAN. Target-keyed and kind-keyed reads (traversal,
+     * synthesis) happen only after endBulkEdgeLoad().
+     */
+    static BULK_EDGE_INDEX_NAMES = [
+        'idx_edges_kind',
+        'idx_edges_source_kind',
+        'idx_edges_target_kind',
+        'idx_edges_provenance',
+    ];
+    /**
+     * Enter bulk-edge-load mode: drop the non-unique edge indexes so the mass
+     * INSERT OR IGNORE stream pays one B-tree (the identity index) instead of
+     * five — measured 2.8s → 1.1s inserting a 224k-edge resolution set, with
+     * recreation costing ~0.3s. MUST be paired with endBulkEdgeLoad(); a crash
+     * inside the window is healed on the next DatabaseConnection open (schema.sql
+     * re-applies CREATE INDEX IF NOT EXISTS).
+     */
+    beginBulkEdgeLoad() {
+        for (const idx of DatabaseConnection.BULK_EDGE_INDEX_NAMES) {
+            this.db.exec(`DROP INDEX IF EXISTS ${idx}`);
+        }
+    }
+    /**
+     * Leave bulk-edge-load mode: recreate the dropped indexes in one pass each
+     * over the (now fully loaded) edges table — far cheaper than maintaining
+     * them per-insert. DDL is extracted from schema.sql so it cannot drift.
+     *
+     * Async with a yield BETWEEN the four CREATE INDEX statements: each build is
+     * a synchronous scan of the whole edges table (~20s apiece at Linux-kernel
+     * scale, 79s total measured), and running them back-to-back is a single
+     * event-loop stall longer than the #850 liveness watchdog's 60s window — a
+     * daemon-triggered re-index would be SIGKILLed right after doing the work.
+     * One yield per statement keeps every stall to a single index build, which
+     * stays inside the window.
+     */
+    async endBulkEdgeLoad() {
+        const schemaPath = path.join(__dirname, 'schema.sql');
+        const schema = fs.readFileSync(schemaPath, 'utf-8');
+        for (const idx of DatabaseConnection.BULK_EDGE_INDEX_NAMES) {
+            const m = schema.match(new RegExp(`CREATE INDEX IF NOT EXISTS ${idx}\\b[^;]*;`));
+            if (!m)
+                throw new Error(`schema.sql: edge index ${idx} not found for bulk-load recreation`);
+            this.db.exec(m[0]);
+            await new Promise((resolve) => setImmediate(resolve));
+        }
+    }
+    /** Recreate the FTS triggers + rebuild if a bulk-load window never closed. */
+    healBulkNodeLoad() {
+        const row = this.db
+            .prepare(`SELECT count(*) AS c FROM sqlite_master WHERE type = 'trigger' AND name IN ('nodes_ai','nodes_ad','nodes_au')`)
+            .get();
+        if ((row?.c ?? 0) >= DatabaseConnection.FTS_TRIGGER_NAMES.length)
+            return;
+        this.endBulkNodeLoad();
+    }
+    /**
+     * Recreate the FTS sync triggers from schema.sql — extracted from the file
+     * rather than duplicated here so the DDL cannot drift from the schema.
+     * (Re-execing the whole schema is not an option: it contains data INSERTs
+     * that are not idempotent, e.g. schema_versions.)
+     */
+    recreateFtsTriggers() {
+        const schemaPath = path.join(__dirname, 'schema.sql');
+        const schema = fs.readFileSync(schemaPath, 'utf-8');
+        const triggerDdls = schema.match(/CREATE TRIGGER IF NOT EXISTS nodes_a[idu]\b[\s\S]*?END;/g);
+        if (!triggerDdls || triggerDdls.length !== DatabaseConnection.FTS_TRIGGER_NAMES.length) {
+            throw new Error(`schema.sql: expected ${DatabaseConnection.FTS_TRIGGER_NAMES.length} nodes FTS triggers, found ${triggerDdls?.length ?? 0}`);
+        }
+        for (const ddl of triggerDdls) {
+            this.db.exec(ddl);
+        }
+    }
     /**
      * Get the underlying database instance
      */
@@ -217,6 +441,18 @@ class DatabaseConnection {
             return 0;
         }
     }
+    /** Size of the main DB file in bytes (0 for in-memory/unknown) — the WAL
+     * valve scales its fold caps with it (resolveWalValveMb). */
+    getDbFileSizeBytes() {
+        if (!this.dbPath || this.dbPath === ':memory:')
+            return 0;
+        try {
+            return fs.statSync(this.dbPath).size;
+        }
+        catch {
+            return 0;
+        }
+    }
     /** Current `wal_autocheckpoint` interval in pages (0 = disabled). */
     getWalAutocheckpoint() {
         const v = this.db.pragma('wal_autocheckpoint', { simple: true });
@@ -252,9 +488,27 @@ class DatabaseConnection {
      * never run inline on the main thread).
      */
     async checkpointWalPassive() {
+        return this.checkpointWal('PASSIVE');
+    }
+    /**
+     * `PRAGMA wal_checkpoint(TRUNCATE)` — same off-thread pattern as PASSIVE,
+     * but on success the WAL FILE is chopped to zero. A completed passive
+     * backfill bounds the un-checkpointed backlog, yet the FILE only stops
+     * growing when a commit finds ZERO readers holding WAL marks — rare while
+     * pool workers cycle, so at kernel scale a fully-backfilled WAL still
+     * accreted the phase's whole write volume on disk (§7a.1: 22GB). The valve
+     * calls this exactly at a parked barrier (writer parked, pool drained,
+     * backfill complete) where the no-reader condition is guaranteed rather
+     * than lucky. The worker sets a short busy_timeout so a racing reader
+     * degrades this to a no-op (busy=1) instead of a stall.
+     */
+    async checkpointWalTruncate() {
+        return this.checkpointWal('TRUNCATE');
+    }
+    async checkpointWal(mode) {
         if (!this.dbPath || this.dbPath === ':memory:') {
             try {
-                const row = this.db.prepare('PRAGMA wal_checkpoint(PASSIVE)').get();
+                const row = this.db.prepare(`PRAGMA wal_checkpoint(${mode})`).get();
                 return row ? { busy: Number(row.busy), log: Number(row.log), checkpointed: Number(row.checkpointed) } : null;
             }
             catch {
@@ -263,16 +517,27 @@ class DatabaseConnection {
         }
         try {
             const { Worker } = await Promise.resolve().then(() => __importStar(require('node:worker_threads')));
-            const workerSource = `
-        const { workerData, parentPort } = require('node:worker_threads');
-        let row = null;
-        try {
-          const { DatabaseSync } = require('node:sqlite');
-          const db = new DatabaseSync(workerData.dbPath);
-          try { row = db.prepare('PRAGMA wal_checkpoint(PASSIVE)').get(); } catch {}
-          try { db.close(); } catch {}
-        } catch {}
-        parentPort.postMessage({ row });
+            const workerSource = `
+        const { workerData, parentPort } = require('node:worker_threads');
+        let row = null;
+        let err = null;
+        try {
+          let db = null;
+          try {
+            const { DatabaseSync } = require('node:sqlite');
+            db = new DatabaseSync(workerData.dbPath);
+          } catch {
+            const Database = require('better-sqlite3');
+            db = new Database(workerData.dbPath);
+          }
+          const mode = workerData.mode === 'TRUNCATE' ? 'TRUNCATE' : 'PASSIVE';
+          try {
+            if (mode === 'TRUNCATE') db.exec('PRAGMA busy_timeout = 2000');
+            row = db.prepare('PRAGMA wal_checkpoint(' + mode + ')').get();
+          } catch (e) { err = String(e && e.message || e); }
+          try { db.close(); } catch {}
+        } catch (e) { err = err || String(e && e.message || e); }
+        parentPort.postMessage({ row, err });
       `;
             return await new Promise((resolve) => {
                 let settled = false;
@@ -283,8 +548,14 @@ class DatabaseConnection {
                     resolve(row ? { busy: Number(row.busy), log: Number(row.log), checkpointed: Number(row.checkpointed) } : null);
                 };
                 try {
-                    const worker = new Worker(workerSource, { eval: true, workerData: { dbPath: this.dbPath } });
-                    worker.once('message', (m) => { void worker.terminate(); finish(m?.row ?? null); });
+                    const worker = new Worker(workerSource, { eval: true, workerData: { dbPath: this.dbPath, mode } });
+                    worker.once('message', (m) => {
+                        if (m?.err && process.env.HOMEGRAPH_WAL_VALVE_DEBUG) {
+                            console.error(`[wal-valve] checkpoint worker (${mode}): ${m.err}`);
+                        }
+                        void worker.terminate();
+                        finish(m?.row ?? null);
+                    });
                     worker.once('error', () => { void worker.terminate(); finish(null); });
                     worker.once('exit', () => finish(null));
                 }
@@ -361,15 +632,21 @@ class DatabaseConnection {
     async runPragmasOffThread(pragmas, inlineFallback = []) {
         try {
             const { Worker } = await Promise.resolve().then(() => __importStar(require('node:worker_threads')));
-            const workerSource = `
-        const { workerData, parentPort } = require('node:worker_threads');
-        try {
-          const { DatabaseSync } = require('node:sqlite');
-          const db = new DatabaseSync(workerData.dbPath);
-          for (const p of workerData.pragmas) { try { db.exec(p); } catch {} }
-          try { db.close(); } catch {}
-        } catch {}
-        parentPort.postMessage('done');
+            const workerSource = `
+        const { workerData, parentPort } = require('node:worker_threads');
+        try {
+          let db = null;
+          try {
+            const { DatabaseSync } = require('node:sqlite');
+            db = new DatabaseSync(workerData.dbPath);
+          } catch {
+            const Database = require('better-sqlite3');
+            db = new Database(workerData.dbPath);
+          }
+          for (const p of workerData.pragmas) { try { db.exec(p); } catch {} }
+          try { db.close(); } catch {}
+        } catch {}
+        parentPort.postMessage('done');
       `;
             await new Promise((resolve) => {
                 let settled = false;

package/dist/db/index.js.map

@@ -1 +1 @@
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package/dist/db/migrations.js

@@ -26,17 +26,17 @@ const migrations = [
         version: 2,
         description: 'Add project metadata, provenance tracking, and unresolved ref context',
         up: (db) => {
-            db.exec(`
-        CREATE TABLE IF NOT EXISTS project_metadata (
-          key TEXT PRIMARY KEY,
-          value TEXT NOT NULL,
-          updated_at INTEGER NOT NULL
-        );
-        ALTER TABLE unresolved_refs ADD COLUMN file_path TEXT NOT NULL DEFAULT '';
-        ALTER TABLE unresolved_refs ADD COLUMN language TEXT NOT NULL DEFAULT 'unknown';
-        ALTER TABLE edges ADD COLUMN provenance TEXT DEFAULT NULL;
-        CREATE INDEX IF NOT EXISTS idx_unresolved_file_path ON unresolved_refs(file_path);
-        CREATE INDEX IF NOT EXISTS idx_edges_provenance ON edges(provenance);
+            db.exec(`
+        CREATE TABLE IF NOT EXISTS project_metadata (
+          key TEXT PRIMARY KEY,
+          value TEXT NOT NULL,
+          updated_at INTEGER NOT NULL
+        );
+        ALTER TABLE unresolved_refs ADD COLUMN file_path TEXT NOT NULL DEFAULT '';
+        ALTER TABLE unresolved_refs ADD COLUMN language TEXT NOT NULL DEFAULT 'unknown';
+        ALTER TABLE edges ADD COLUMN provenance TEXT DEFAULT NULL;
+        CREATE INDEX IF NOT EXISTS idx_unresolved_file_path ON unresolved_refs(file_path);
+        CREATE INDEX IF NOT EXISTS idx_edges_provenance ON edges(provenance);
       `);
         },
     },
@@ -44,8 +44,8 @@ const migrations = [
         version: 3,
         description: 'Add lower(name) expression index for memory-efficient case-insensitive lookups',
         up: (db) => {
-            db.exec(`
-        CREATE INDEX IF NOT EXISTS idx_nodes_lower_name ON nodes(lower(name));
+            db.exec(`
+        CREATE INDEX IF NOT EXISTS idx_nodes_lower_name ON nodes(lower(name));
       `);
         },
     },
@@ -53,9 +53,9 @@ const migrations = [
         version: 4,
         description: 'Drop redundant idx_edges_source / idx_edges_target (covered by source_kind / target_kind composites)',
         up: (db) => {
-            db.exec(`
-        DROP INDEX IF EXISTS idx_edges_source;
-        DROP INDEX IF EXISTS idx_edges_target;
+            db.exec(`
+        DROP INDEX IF EXISTS idx_edges_source;
+        DROP INDEX IF EXISTS idx_edges_target;
       `);
         },
     },
@@ -63,8 +63,8 @@ const migrations = [
         version: 5,
         description: 'Add nodes.return_type — normalized return/result type for receiver-type inference (C++ singletons/factories, #645)',
         up: (db) => {
-            db.exec(`
-        ALTER TABLE nodes ADD COLUMN return_type TEXT;
+            db.exec(`
+        ALTER TABLE nodes ADD COLUMN return_type TEXT;
       `);
         },
     },
@@ -81,14 +81,14 @@ const migrations = [
             // and it MUST match the GROUP BY exactly, or the index creation would
             // fail on a pair the DELETE left behind. Idempotent: the index is
             // `IF NOT EXISTS` and the DELETE is a no-op once the table is unique.
-            db.exec(`
-        DELETE FROM edges
-        WHERE id NOT IN (
-          SELECT MIN(id) FROM edges
-          GROUP BY source, target, kind, IFNULL(line, -1), IFNULL(col, -1)
-        );
-        CREATE UNIQUE INDEX IF NOT EXISTS idx_edges_identity
-          ON edges(source, target, kind, IFNULL(line, -1), IFNULL(col, -1));
+            db.exec(`
+        DELETE FROM edges
+        WHERE id NOT IN (
+          SELECT MIN(id) FROM edges
+          GROUP BY source, target, kind, IFNULL(line, -1), IFNULL(col, -1)
+        );
+        CREATE UNIQUE INDEX IF NOT EXISTS idx_edges_identity
+          ON edges(source, target, kind, IFNULL(line, -1), IFNULL(col, -1));
       `);
         },
     },
@@ -96,14 +96,14 @@ const migrations = [
         version: 7,
         description: 'Add mcp_query_cache table for MCP tool response caching',
         up: (db) => {
-            db.exec(`
-        CREATE TABLE IF NOT EXISTS mcp_query_cache (
-          cache_key   TEXT PRIMARY KEY,
-          tool        TEXT NOT NULL,
-          response    TEXT NOT NULL,
-          created_at  INTEGER NOT NULL
-        );
-        CREATE INDEX IF NOT EXISTS idx_mcp_query_cache_tool ON mcp_query_cache(tool);
+            db.exec(`
+        CREATE TABLE IF NOT EXISTS mcp_query_cache (
+          cache_key   TEXT PRIMARY KEY,
+          tool        TEXT NOT NULL,
+          response    TEXT NOT NULL,
+          created_at  INTEGER NOT NULL
+        );
+        CREATE INDEX IF NOT EXISTS idx_mcp_query_cache_tool ON mcp_query_cache(tool);
       `);
         },
     },
@@ -119,9 +119,9 @@ const migrations = [
             if (!hasColumn('name_tail')) {
                 db.exec("ALTER TABLE unresolved_refs ADD COLUMN name_tail TEXT NOT NULL DEFAULT ''");
             }
-            db.exec(`
-        CREATE INDEX IF NOT EXISTS idx_unresolved_status ON unresolved_refs(status);
-        CREATE INDEX IF NOT EXISTS idx_unresolved_failed_tail ON unresolved_refs(name_tail) WHERE status = 'failed';
+            db.exec(`
+        CREATE INDEX IF NOT EXISTS idx_unresolved_status ON unresolved_refs(status);
+        CREATE INDEX IF NOT EXISTS idx_unresolved_failed_tail ON unresolved_refs(name_tail) WHERE status = 'failed';
       `);
         },
     },