cgraphx 1.1.0

package/dist/db/queries.js

@@ -0,0 +1,1591 @@
+"use strict";
+/**
+ * Database Queries
+ *
+ * Prepared statements for CRUD operations on the knowledge graph.
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.QueryBuilder = void 0;
+const utils_1 = require("../utils");
+const query_utils_1 = require("../search/query-utils");
+const query_parser_1 = require("../search/query-parser");
+const generated_detection_1 = require("../extraction/generated-detection");
+/**
+ * Path-only heuristic for files that should not be candidates for
+ * "dominant file" detection: test/spec files and tool-generated files.
+ * Generated files (`*.pb.go`, `*.pulsar.go`, mock outputs, …) often
+ * have huge in-file edge counts that dwarf the real source — etcd's
+ * `rpc.pb.go` has 4× the in-file edges of `server.go`.
+ */
+function isLowValueFile(filePath) {
+    const lp = filePath.toLowerCase();
+    return (/(?:^|\/)(tests?|__tests?__|spec)\//.test(lp) ||
+        /_test\.go$/.test(lp) ||
+        /(?:^|\/)test_[^/]+\.py$/.test(lp) ||
+        /_test\.py$/.test(lp) ||
+        /_spec\.rb$/.test(lp) ||
+        /_test\.rb$/.test(lp) ||
+        /\.(test|spec)\.[jt]sx?$/.test(lp) ||
+        /(test|spec|tests)\.(java|kt|scala)$/.test(lp) ||
+        /(tests?|spec)\.cs$/.test(lp) ||
+        /tests?\.swift$/.test(lp) ||
+        /_test\.dart$/.test(lp) ||
+        (0, generated_detection_1.isGeneratedFile)(filePath));
+}
+const SQLITE_PARAM_CHUNK_SIZE = 500;
+/**
+ * Convert database row to Node object
+ */
+function rowToNode(row) {
+    return {
+        id: row.id,
+        kind: row.kind,
+        name: row.name,
+        qualifiedName: row.qualified_name,
+        filePath: row.file_path,
+        language: row.language,
+        startLine: row.start_line,
+        endLine: row.end_line,
+        startColumn: row.start_column,
+        endColumn: row.end_column,
+        docstring: row.docstring ?? undefined,
+        signature: row.signature ?? undefined,
+        visibility: row.visibility,
+        isExported: row.is_exported === 1,
+        isAsync: row.is_async === 1,
+        isStatic: row.is_static === 1,
+        isAbstract: row.is_abstract === 1,
+        decorators: row.decorators ? (0, utils_1.safeJsonParse)(row.decorators, undefined) : undefined,
+        typeParameters: row.type_parameters ? (0, utils_1.safeJsonParse)(row.type_parameters, undefined) : undefined,
+        returnType: row.return_type ?? undefined,
+        updatedAt: row.updated_at,
+    };
+}
+/**
+ * Convert database row to Edge object
+ */
+function rowToEdge(row) {
+    return {
+        source: row.source,
+        target: row.target,
+        kind: row.kind,
+        metadata: row.metadata ? (0, utils_1.safeJsonParse)(row.metadata, undefined) : undefined,
+        line: row.line ?? undefined,
+        column: row.col ?? undefined,
+        provenance: row.provenance,
+    };
+}
+/**
+ * Convert database row to FileRecord object
+ */
+function rowToFileRecord(row) {
+    return {
+        path: row.path,
+        contentHash: row.content_hash,
+        language: row.language,
+        size: row.size,
+        modifiedAt: row.modified_at,
+        indexedAt: row.indexed_at,
+        nodeCount: row.node_count,
+        errors: row.errors ? (0, utils_1.safeJsonParse)(row.errors, undefined) : undefined,
+    };
+}
+/**
+ * Query builder for the knowledge graph database
+ */
+class QueryBuilder {
+    db;
+    // Project-name tokens (go.mod / package.json / repo dir), normalized. A query
+    // word matching one is dropped from path-relevance scoring — it names the
+    // whole project, not a symbol, so it carries no discriminative signal (#720).
+    // Set once by the CodeGraph instance; empty by default (no down-weighting).
+    projectNameTokens = new Set();
+    // Node cache for frequently accessed nodes (LRU-style, max 1000 entries)
+    nodeCache = new Map();
+    maxCacheSize = 1000;
+    // Prepared statements (lazily initialized)
+    stmts = {};
+    constructor(db) {
+        this.db = db;
+    }
+    /** Set the normalized project-name tokens used to down-weight non-discriminative
+     * query words in path scoring (#720). Called once when the project opens. */
+    setProjectNameTokens(tokens) {
+        this.projectNameTokens = tokens;
+    }
+    /** The normalized project-name tokens (#720); empty if none were derived. */
+    getProjectNameTokens() {
+        return this.projectNameTokens;
+    }
+    // ===========================================================================
+    // Node Operations
+    // ===========================================================================
+    /**
+     * Insert a new node
+     */
+    insertNode(node) {
+        if (!this.stmts.insertNode) {
+            this.stmts.insertNode = this.db.prepare(`
+        INSERT OR REPLACE INTO nodes (
+          id, kind, name, qualified_name, file_path, language,
+          start_line, end_line, start_column, end_column,
+          docstring, signature, visibility,
+          is_exported, is_async, is_static, is_abstract,
+          decorators, type_parameters, return_type, updated_at
+        ) VALUES (
+          @id, @kind, @name, @qualifiedName, @filePath, @language,
+          @startLine, @endLine, @startColumn, @endColumn,
+          @docstring, @signature, @visibility,
+          @isExported, @isAsync, @isStatic, @isAbstract,
+          @decorators, @typeParameters, @returnType, @updatedAt
+        )
+      `);
+        }
+        // Validate required fields to prevent SQLite bind errors
+        if (!node.id || !node.kind || !node.name || !node.filePath || !node.language) {
+            console.error('[cgraphx] Skipping node with missing required fields:', {
+                id: node.id,
+                kind: node.kind,
+                name: node.name,
+                filePath: node.filePath,
+                language: node.language,
+            });
+            return;
+        }
+        // INSERT OR REPLACE may overwrite a node we have cached. Drop the
+        // stale entry so the next getNodeById sees the new row, not the old
+        // one (matches the cache-invalidation pattern used by updateNode and
+        // deleteNode below).
+        this.nodeCache.delete(node.id);
+        this.stmts.insertNode.run({
+            id: node.id,
+            kind: node.kind,
+            name: node.name,
+            qualifiedName: node.qualifiedName ?? node.name,
+            filePath: node.filePath,
+            language: node.language,
+            startLine: node.startLine ?? 0,
+            endLine: node.endLine ?? 0,
+            startColumn: node.startColumn ?? 0,
+            endColumn: node.endColumn ?? 0,
+            docstring: node.docstring ?? null,
+            signature: node.signature ?? null,
+            visibility: node.visibility ?? null,
+            isExported: node.isExported ? 1 : 0,
+            isAsync: node.isAsync ? 1 : 0,
+            isStatic: node.isStatic ? 1 : 0,
+            isAbstract: node.isAbstract ? 1 : 0,
+            decorators: node.decorators ? JSON.stringify(node.decorators) : null,
+            typeParameters: node.typeParameters ? JSON.stringify(node.typeParameters) : null,
+            returnType: node.returnType ?? null,
+            updatedAt: node.updatedAt ?? Date.now(),
+        });
+    }
+    /**
+     * Insert multiple nodes in a transaction
+     */
+    insertNodes(nodes) {
+        this.db.transaction(() => {
+            for (const node of nodes) {
+                this.insertNode(node);
+            }
+        })();
+    }
+    /**
+     * Update an existing node
+     */
+    updateNode(node) {
+        if (!this.stmts.updateNode) {
+            this.stmts.updateNode = this.db.prepare(`
+        UPDATE nodes SET
+          kind = @kind,
+          name = @name,
+          qualified_name = @qualifiedName,
+          file_path = @filePath,
+          language = @language,
+          start_line = @startLine,
+          end_line = @endLine,
+          start_column = @startColumn,
+          end_column = @endColumn,
+          docstring = @docstring,
+          signature = @signature,
+          visibility = @visibility,
+          is_exported = @isExported,
+          is_async = @isAsync,
+          is_static = @isStatic,
+          is_abstract = @isAbstract,
+          decorators = @decorators,
+          type_parameters = @typeParameters,
+          return_type = @returnType,
+          updated_at = @updatedAt
+        WHERE id = @id
+      `);
+        }
+        // Invalidate cache before update
+        this.nodeCache.delete(node.id);
+        // Validate required fields
+        if (!node.id || !node.kind || !node.name || !node.filePath || !node.language) {
+            console.error('[cgraphx] Skipping node update with missing required fields:', node.id);
+            return;
+        }
+        this.stmts.updateNode.run({
+            id: node.id,
+            kind: node.kind,
+            name: node.name,
+            qualifiedName: node.qualifiedName ?? node.name,
+            filePath: node.filePath,
+            language: node.language,
+            startLine: node.startLine ?? 0,
+            endLine: node.endLine ?? 0,
+            startColumn: node.startColumn ?? 0,
+            endColumn: node.endColumn ?? 0,
+            docstring: node.docstring ?? null,
+            signature: node.signature ?? null,
+            visibility: node.visibility ?? null,
+            isExported: node.isExported ? 1 : 0,
+            isAsync: node.isAsync ? 1 : 0,
+            isStatic: node.isStatic ? 1 : 0,
+            isAbstract: node.isAbstract ? 1 : 0,
+            decorators: node.decorators ? JSON.stringify(node.decorators) : null,
+            typeParameters: node.typeParameters ? JSON.stringify(node.typeParameters) : null,
+            returnType: node.returnType ?? null,
+            updatedAt: node.updatedAt ?? Date.now(),
+        });
+    }
+    /**
+     * Delete a node by ID
+     */
+    deleteNode(id) {
+        if (!this.stmts.deleteNode) {
+            this.stmts.deleteNode = this.db.prepare('DELETE FROM nodes WHERE id = ?');
+        }
+        // Invalidate cache
+        this.nodeCache.delete(id);
+        this.stmts.deleteNode.run(id);
+    }
+    /**
+     * Delete all nodes for a file
+     */
+    deleteNodesByFile(filePath) {
+        if (!this.stmts.deleteNodesByFile) {
+            this.stmts.deleteNodesByFile = this.db.prepare('DELETE FROM nodes WHERE file_path = ?');
+        }
+        // Invalidate cache for nodes in this file
+        for (const [id, node] of this.nodeCache) {
+            if (node.filePath === filePath) {
+                this.nodeCache.delete(id);
+            }
+        }
+        this.stmts.deleteNodesByFile.run(filePath);
+    }
+    /**
+     * Get a node by ID
+     */
+    getNodeById(id) {
+        // Check cache first
+        if (this.nodeCache.has(id)) {
+            const cached = this.nodeCache.get(id);
+            // Move to end to implement LRU (delete and re-add)
+            this.nodeCache.delete(id);
+            this.nodeCache.set(id, cached);
+            return cached;
+        }
+        if (!this.stmts.getNodeById) {
+            this.stmts.getNodeById = this.db.prepare('SELECT * FROM nodes WHERE id = ?');
+        }
+        const row = this.stmts.getNodeById.get(id);
+        if (!row) {
+            return null;
+        }
+        const node = rowToNode(row);
+        this.cacheNode(node);
+        return node;
+    }
+    /**
+     * Batch lookup: fetch many nodes by ID in a single SQL round-trip.
+     *
+     * Replaces the N+1 pattern in graph traversal where every edge would
+     * trigger its own `getNodeById` call. For a function with 50 callers
+     * this collapses 50 point reads into one IN-list query (~10-50x
+     * faster end-to-end).
+     *
+     * Returns a Map keyed by id so callers can preserve their own ordering
+     * (typically the order edges were returned from the graph). Missing IDs
+     * are simply absent from the map.
+     *
+     * Cache-aware: ids already in the LRU cache are served from memory and
+     * the SQL query only touches the misses.
+     */
+    getNodesByIds(ids) {
+        const out = new Map();
+        if (ids.length === 0)
+            return out;
+        // Serve cache hits first; build the miss list for SQL.
+        const misses = [];
+        for (const id of ids) {
+            const cached = this.nodeCache.get(id);
+            if (cached !== undefined) {
+                // LRU touch
+                this.nodeCache.delete(id);
+                this.nodeCache.set(id, cached);
+                out.set(id, cached);
+            }
+            else {
+                misses.push(id);
+            }
+        }
+        if (misses.length === 0)
+            return out;
+        // Chunk under SQLite's parameter limit (default 999, raised to 32766
+        // in better-sqlite3 builds — chunk at 500 for safety across both
+        // backends and to keep the query plan simple).
+        for (let i = 0; i < misses.length; i += SQLITE_PARAM_CHUNK_SIZE) {
+            const chunk = misses.slice(i, i + SQLITE_PARAM_CHUNK_SIZE);
+            const placeholders = chunk.map(() => '?').join(',');
+            const rows = this.db
+                .prepare(`SELECT * FROM nodes WHERE id IN (${placeholders})`)
+                .all(...chunk);
+            for (const row of rows) {
+                const node = rowToNode(row);
+                out.set(node.id, node);
+                this.cacheNode(node);
+            }
+        }
+        return out;
+    }
+    getExistingNodeIds(ids) {
+        const out = new Set();
+        if (ids.length === 0)
+            return out;
+        const uniqueIds = [...new Set(ids)];
+        for (let i = 0; i < uniqueIds.length; i += SQLITE_PARAM_CHUNK_SIZE) {
+            const chunk = uniqueIds.slice(i, i + SQLITE_PARAM_CHUNK_SIZE);
+            const placeholders = chunk.map(() => '?').join(',');
+            const rows = this.db
+                .prepare(`SELECT id FROM nodes WHERE id IN (${placeholders})`)
+                .all(...chunk);
+            for (const row of rows) {
+                out.add(row.id);
+            }
+        }
+        return out;
+    }
+    /**
+     * Add a node to the cache, evicting oldest if needed
+     */
+    cacheNode(node) {
+        if (this.nodeCache.size >= this.maxCacheSize) {
+            // Evict oldest (first) entry
+            const firstKey = this.nodeCache.keys().next().value;
+            if (firstKey) {
+                this.nodeCache.delete(firstKey);
+            }
+        }
+        this.nodeCache.set(node.id, node);
+    }
+    /**
+     * Clear the node cache
+     */
+    clearCache() {
+        this.nodeCache.clear();
+    }
+    /**
+     * Get all nodes in a file
+     */
+    getNodesByFile(filePath) {
+        if (!this.stmts.getNodesByFile) {
+            this.stmts.getNodesByFile = this.db.prepare('SELECT * FROM nodes WHERE file_path = ? ORDER BY start_line');
+        }
+        const rows = this.stmts.getNodesByFile.all(filePath);
+        return rows.map(rowToNode);
+    }
+    /**
+     * Find the file that holds the densest concentration of the project's
+     * internal call graph — the "core" file. Used by context-builder to
+     * boost ranking of symbols in that file's directory (so e.g. sinatra
+     * queries surface `lib/sinatra/base.rb`'s `route!` instead of
+     * `sinatra-contrib/lib/sinatra/multi_route.rb`'s `route` extension).
+     *
+     * Returns null if no file has a meaningful concentration (e.g. spread
+     * evenly across many files, or empty index).
+     *
+     * "Internal" = source and target are in the same file. Cross-file
+     * edges aren't useful here — they don't tell us which file is the
+     * functional center.
+     *
+     * Excludes test/spec files from candidacy via path-pattern. The agent's
+     * typical question is "how does X work", not "how is X tested", so
+     * boosting a test file's directory would be a misfire.
+     */
+    getDominantFile() {
+        if (!this.stmts.getDominantFile) {
+            // Pull top 20 candidates; we then filter out test/generated files
+            // in code (regex-grade matching that SQL LIKE can't express). The
+            // generated-file filter is critical — without it, etcd's
+            // `api/etcdserverpb/rpc.pb.go` (1916 in-file edges, generated
+            // protobuf stub) outranks the real `server/etcdserver/server.go`
+            // (470 edges) by 4×, and the boost would push the agent toward
+            // generated code.
+            this.stmts.getDominantFile = this.db.prepare(`
+        SELECT n.file_path AS file_path, COUNT(*) AS edge_count
+        FROM edges e
+        JOIN nodes n ON e.source = n.id
+        JOIN nodes m ON e.target = m.id
+        WHERE n.file_path = m.file_path
+        GROUP BY n.file_path
+        ORDER BY edge_count DESC
+        LIMIT 20
+      `);
+        }
+        const rows = this.stmts.getDominantFile.all();
+        const filtered = rows.filter(r => !isLowValueFile(r.file_path));
+        if (filtered.length === 0 || filtered[0].edge_count < 20)
+            return null;
+        return {
+            filePath: filtered[0].file_path,
+            edgeCount: filtered[0].edge_count,
+            nextEdgeCount: filtered[1]?.edge_count ?? 0,
+        };
+    }
+    /**
+     * Find the file that holds the densest concentration of the project's
+     * `route` nodes (framework-emitted: Express/Gin/Flask/Rails/Drupal/etc.).
+     * Used by handleContext on small repos to inline the project's routing
+     * config when the agent's query is about request flow — eliminating the
+     * "Glob + Read routes.rb" pattern that beats cgraphx on tiny realworld
+     * template repos.
+     *
+     * Excludes test/generated files from candidacy. Returns null if there
+     * are fewer than 3 non-test routes total, or if no file holds at least
+     * 30% of them (diffuse routing → no single answer file).
+     */
+    getTopRouteFile() {
+        if (!this.stmts.getTopRouteFile) {
+            this.stmts.getTopRouteFile = this.db.prepare(`
+        SELECT file_path, COUNT(*) AS cnt
+        FROM nodes
+        WHERE kind = 'route'
+        GROUP BY file_path
+        ORDER BY cnt DESC
+        LIMIT 20
+      `);
+        }
+        const rows = this.stmts.getTopRouteFile.all();
+        const filtered = rows.filter(r => !isLowValueFile(r.file_path));
+        if (filtered.length === 0)
+            return null;
+        const totalRoutes = filtered.reduce((sum, r) => sum + r.cnt, 0);
+        const top = filtered[0];
+        if (totalRoutes < 3 || top.cnt < 3)
+            return null;
+        if (top.cnt / totalRoutes < 0.30)
+            return null;
+        return { filePath: top.file_path, routeCount: top.cnt, totalRoutes };
+    }
+    /**
+     * Build a URL → handler manifest from the index. Each route node's
+     * `references` edge points at the function/method that handles the
+     * request. We join them in one pass; the agent gets the canonical
+     * routing answer ("POST /users/login → AuthController#login") without
+     * having to parse the framework's route DSL itself.
+     *
+     * Also returns the file with the most handler endpoints — used as the
+     * "top handler file" to inline source for, so the agent has both the
+     * mapping AND the handler implementations.
+     */
+    getRoutingManifest(limit = 40) {
+        if (!this.stmts.getRoutingManifest) {
+            // Edge kind varies across framework resolvers: Spring/Rails/
+            // Laravel/Drupal emit `references`, Express emits `calls`. Accept
+            // both — the semantic is the same (route → its handler).
+            this.stmts.getRoutingManifest = this.db.prepare(`
+        SELECT
+          r.name AS url,
+          h.name AS handler,
+          h.file_path AS handler_file,
+          h.start_line AS handler_line,
+          h.kind AS handler_kind
+        FROM nodes r
+        JOIN edges e ON e.source = r.id
+        JOIN nodes h ON e.target = h.id
+        WHERE r.kind = 'route'
+          AND e.kind IN ('references', 'calls')
+          AND h.kind IN ('function', 'method', 'class')
+        ORDER BY r.file_path, r.start_line
+        LIMIT ?
+      `);
+        }
+        const rows = this.stmts.getRoutingManifest.all(limit);
+        // Drop test/generated handlers — same hygiene as elsewhere.
+        const filtered = rows.filter(r => !isLowValueFile(r.handler_file));
+        if (filtered.length < 3)
+            return null;
+        // Identify the file holding the most handlers (the "primary handler file").
+        const fileCounts = new Map();
+        for (const r of filtered) {
+            fileCounts.set(r.handler_file, (fileCounts.get(r.handler_file) ?? 0) + 1);
+        }
+        let topHandlerFile = null;
+        let topHandlerFileCount = 0;
+        for (const [file, count] of fileCounts) {
+            if (count > topHandlerFileCount) {
+                topHandlerFile = file;
+                topHandlerFileCount = count;
+            }
+        }
+        return {
+            entries: filtered.map(r => ({
+                url: r.url,
+                handler: r.handler,
+                handlerFile: r.handler_file,
+                handlerLine: r.handler_line,
+                handlerKind: r.handler_kind,
+            })),
+            topHandlerFile,
+            topHandlerFileCount,
+            totalRoutes: filtered.length,
+        };
+    }
+    /**
+     * Get all nodes of a specific kind
+     */
+    getNodesByKind(kind) {
+        if (!this.stmts.getNodesByKind) {
+            this.stmts.getNodesByKind = this.db.prepare('SELECT * FROM nodes WHERE kind = ?');
+        }
+        const rows = this.stmts.getNodesByKind.all(kind);
+        return rows.map(rowToNode);
+    }
+    /**
+     * Stream every node of a kind one at a time (lazy) instead of materializing
+     * them all like {@link getNodesByKind}. For unbounded kinds (`function`,
+     * `method`) on a symbol-dense project the full array is gigabytes; the
+     * dynamic-edge synthesizers only scan-and-filter, so they iterate to keep
+     * memory O(1) in the node count rather than O(nodes) (#610).
+     */
+    *iterateNodesByKind(kind) {
+        // Fresh statement per call (not a cached one): an iterator holds an open
+        // cursor, so a shared statement would conflict across overlapping scans.
+        const stmt = this.db.prepare('SELECT * FROM nodes WHERE kind = ?');
+        for (const row of stmt.iterate(kind)) {
+            yield rowToNode(row);
+        }
+    }
+    /**
+     * Get all nodes in the database
+     */
+    getAllNodes() {
+        const rows = this.db.prepare('SELECT * FROM nodes').all();
+        return rows.map(rowToNode);
+    }
+    /**
+     * Get nodes by exact name match (uses idx_nodes_name index)
+     */
+    getNodesByName(name) {
+        if (!this.stmts.getNodesByName) {
+            this.stmts.getNodesByName = this.db.prepare('SELECT * FROM nodes WHERE name = ?');
+        }
+        const rows = this.stmts.getNodesByName.all(name);
+        return rows.map(rowToNode);
+    }
+    /**
+     * Get nodes by exact qualified name match (uses idx_nodes_qualified_name index)
+     */
+    getNodesByQualifiedNameExact(qualifiedName) {
+        if (!this.stmts.getNodesByQualifiedNameExact) {
+            this.stmts.getNodesByQualifiedNameExact = this.db.prepare('SELECT * FROM nodes WHERE qualified_name = ?');
+        }
+        const rows = this.stmts.getNodesByQualifiedNameExact.all(qualifiedName);
+        return rows.map(rowToNode);
+    }
+    /**
+     * Get nodes by lowercase name match (uses idx_nodes_lower_name expression index)
+     */
+    getNodesByLowerName(lowerName) {
+        if (!this.stmts.getNodesByLowerName) {
+            this.stmts.getNodesByLowerName = this.db.prepare('SELECT * FROM nodes WHERE lower(name) = ?');
+        }
+        const rows = this.stmts.getNodesByLowerName.all(lowerName);
+        return rows.map(rowToNode);
+    }
+    /**
+     * Search nodes by name using FTS with fallback to LIKE for better matching
+     *
+     * Search strategy:
+     * 1. Try FTS5 prefix match (query*) for word-start matching
+     * 2. If no results, try LIKE for substring matching (e.g., "signIn" finds "signInWithGoogle")
+     * 3. Score results based on match quality
+     */
+    searchNodes(query, options = {}) {
+        const { limit = 100, offset = 0 } = options;
+        // Parse field-qualified bits out of the raw query (kind:, lang:,
+        // path:, name:). Anything not recognised stays in `text` and goes
+        // to FTS unchanged. Filters compose with the SearchOptions arg —
+        // both are applied (intersection-style).
+        const parsed = (0, query_parser_1.parseQuery)(query);
+        const mergedKinds = parsed.kinds.length > 0
+            ? Array.from(new Set([...(options.kinds ?? []), ...parsed.kinds]))
+            : options.kinds;
+        const mergedLanguages = parsed.languages.length > 0
+            ? Array.from(new Set([...(options.languages ?? []), ...parsed.languages]))
+            : options.languages;
+        const pathFilters = parsed.pathFilters;
+        const nameFilters = parsed.nameFilters;
+        // The text portion drives FTS/LIKE; if all the user typed was
+        // filters (`kind:function`), we still need *some* candidate set,
+        // so synthesise an empty-text path that returns everything matching
+        // the filters.
+        const text = parsed.text;
+        const kinds = mergedKinds;
+        const languages = mergedLanguages;
+        // First try FTS5 with prefix matching
+        let results = text
+            ? this.searchNodesFTS(text, { kinds, languages, limit, offset })
+            // Over-fetch by 5× when running filter-only (no text). The
+            // post-scoring path: + name: filters can be very selective, so
+            // a smaller multiplier risks returning fewer than `limit`
+            // results despite the DB having plenty of matches.
+            : this.searchAllByFilters({ kinds, languages, limit: limit * 5 });
+        // If no FTS results, try LIKE-based substring search
+        if (results.length === 0 && text.length >= 2) {
+            results = this.searchNodesLike(text, { kinds, languages, limit, offset });
+        }
+        // Final fuzzy fallback: scan all known names and keep those within
+        // a tight Levenshtein distance. Only fires when both FTS and LIKE
+        // returned nothing AND there's a text portion long enough to be
+        // worth fuzzing (1-char queries would match too much).
+        if (results.length === 0 && text.length >= 3) {
+            results = this.searchNodesFuzzy(text, { kinds, languages, limit });
+        }
+        // Supplement: ensure exact name matches are always candidates.
+        // BM25 can bury short exact-match names (e.g. "getBean") under hundreds of
+        // compound names (e.g. "getBeanDescriptor") in large codebases,
+        // pushing them past the FTS fetch limit before post-hoc scoring can help.
+        // Use the max BM25 score as the base so the nameMatchBonus (exact=30 vs
+        // prefix=20) actually differentiates them after rescoring.
+        if (results.length > 0 && query) {
+            const existingIds = new Set(results.map(r => r.node.id));
+            const maxFtsScore = Math.max(...results.map(r => r.score));
+            const terms = query.split(/\s+/).filter(t => t.length >= 2);
+            for (const term of terms) {
+                let sql = 'SELECT * FROM nodes WHERE name = ? COLLATE NOCASE';
+                const params = [term];
+                if (kinds && kinds.length > 0) {
+                    sql += ` AND kind IN (${kinds.map(() => '?').join(',')})`;
+                    params.push(...kinds);
+                }
+                if (languages && languages.length > 0) {
+                    sql += ` AND language IN (${languages.map(() => '?').join(',')})`;
+                    params.push(...languages);
+                }
+                sql += ' LIMIT 20';
+                const rows = this.db.prepare(sql).all(...params);
+                for (const row of rows) {
+                    if (!existingIds.has(row.id)) {
+                        results.push({ node: rowToNode(row), score: maxFtsScore });
+                        existingIds.add(row.id);
+                    }
+                }
+            }
+        }
+        // Apply multi-signal scoring
+        if (results.length > 0 && (text || query)) {
+            const scoringQuery = text || query;
+            results = results.map(r => ({
+                ...r,
+                score: r.score
+                    + (0, query_utils_1.kindBonus)(r.node.kind)
+                    + (0, query_utils_1.scorePathRelevance)(r.node.filePath, scoringQuery, this.projectNameTokens)
+                    + (0, query_utils_1.nameMatchBonus)(r.node.name, scoringQuery),
+            }));
+            results.sort((a, b) => b.score - a.score);
+            // Trim to requested limit after rescoring
+            if (results.length > limit) {
+                results = results.slice(0, limit);
+            }
+        }
+        // Apply path: + name: filters AFTER scoring. Scoring already uses
+        // path/name as a soft signal; the explicit filters here are a hard
+        // gate. Done last so the FTS limit fetched plenty of candidates to
+        // narrow from.
+        if (pathFilters.length > 0) {
+            const lowered = pathFilters.map((p) => p.toLowerCase());
+            results = results.filter((r) => {
+                const fp = r.node.filePath.toLowerCase();
+                return lowered.some((p) => fp.includes(p));
+            });
+        }
+        if (nameFilters.length > 0) {
+            const lowered = nameFilters.map((n) => n.toLowerCase());
+            results = results.filter((r) => {
+                const nm = r.node.name.toLowerCase();
+                return lowered.some((n) => nm.includes(n));
+            });
+        }
+        return results;
+    }
+    /**
+     * Match-everything path used when the user supplied only field
+     * filters (`kind:function lang:typescript`) with no text. Returns
+     * candidates ordered by name; the caller's filter pass narrows to
+     * what was asked for.
+     */
+    searchAllByFilters(options) {
+        const { kinds, languages, limit } = options;
+        let sql = 'SELECT * FROM nodes WHERE 1=1';
+        const params = [];
+        if (kinds && kinds.length > 0) {
+            sql += ` AND kind IN (${kinds.map(() => '?').join(',')})`;
+            params.push(...kinds);
+        }
+        if (languages && languages.length > 0) {
+            sql += ` AND language IN (${languages.map(() => '?').join(',')})`;
+            params.push(...languages);
+        }
+        sql += ' ORDER BY name LIMIT ?';
+        params.push(limit);
+        const rows = this.db.prepare(sql).all(...params);
+        return rows.map((row) => ({ node: rowToNode(row), score: 1 }));
+    }
+    /**
+     * Fuzzy fallback: when zero FTS/LIKE hits, try an edit-distance
+     * sweep over the distinct symbol-name set. Caps `maxDist` at 2 so
+     * `getUssr` finds `getUser` but `process` doesn't match `prosody`.
+     * Bounded edit distance keeps each comparison cheap; the per-query
+     * scan is O(distinct-name-count) which is far smaller than total
+     * node count on any real codebase.
+     */
+    searchNodesFuzzy(text, options) {
+        const { kinds, languages, limit } = options;
+        const lowered = text.toLowerCase();
+        const maxDist = lowered.length <= 4 ? 1 : 2;
+        // Pull the distinct name list once. The set is cached on QueryBuilder
+        // by getAllNodeNames(); even on a 200k-node project the distinct
+        // name set is typically O(10k) because most names repeat. The
+        // candidate-cap below bounds memory regardless.
+        const allNames = this.getAllNodeNames();
+        const candidates = [];
+        for (const name of allNames) {
+            const dist = (0, query_parser_1.boundedEditDistance)(name.toLowerCase(), lowered, maxDist);
+            if (dist <= maxDist)
+                candidates.push({ name, dist });
+        }
+        candidates.sort((a, b) => a.dist - b.dist);
+        // Cap the per-name follow-up queries. Each survivor triggers a
+        // separate `SELECT * FROM nodes WHERE name = ?`; without this cap
+        // a project with many similar names (`getUser1`, `getUser2`...)
+        // could fan out far beyond `limit` queries before the inner-loop
+        // limit kicks in.
+        const FUZZY_FOLLOWUP_CAP = Math.max(limit * 2, 50);
+        const cappedCandidates = candidates.slice(0, FUZZY_FOLLOWUP_CAP);
+        const results = [];
+        const seen = new Set();
+        for (const c of cappedCandidates) {
+            if (results.length >= limit)
+                break;
+            let sql = 'SELECT * FROM nodes WHERE name = ?';
+            const params = [c.name];
+            if (kinds && kinds.length > 0) {
+                sql += ` AND kind IN (${kinds.map(() => '?').join(',')})`;
+                params.push(...kinds);
+            }
+            if (languages && languages.length > 0) {
+                sql += ` AND language IN (${languages.map(() => '?').join(',')})`;
+                params.push(...languages);
+            }
+            sql += ' LIMIT 5';
+            const rows = this.db.prepare(sql).all(...params);
+            for (const row of rows) {
+                if (seen.has(row.id))
+                    continue;
+                seen.add(row.id);
+                // Lower the score for each edit step away from the query so
+                // exact-match fallbacks (dist 0) outrank dist-2 typos.
+                results.push({ node: rowToNode(row), score: 1 / (1 + c.dist) });
+                if (results.length >= limit)
+                    break;
+            }
+        }
+        return results;
+    }
+    /**
+     * FTS5 search with prefix matching
+     */
+    searchNodesFTS(query, options) {
+        const { kinds, languages, limit = 100, offset = 0 } = options;
+        // Add prefix wildcard for better matching (e.g., "auth" matches "AuthService", "authenticate")
+        // Escape special FTS5 characters and add prefix wildcard.
+        //
+        // `::` is a qualifier separator in Rust/C++/Ruby, not a token char,
+        // so treat it as whitespace before the strip step. Otherwise queries
+        // like `stage_apply::run` collapse to `stage_applyrun` (the colons
+        // are stripped without splitting) and find nothing. See #173.
+        const ftsQuery = query
+            .replace(/::/g, ' ') // Rust/C++/Ruby qualifier separator
+            .replace(/['"*():^]/g, '') // Remove FTS5 special chars
+            .split(/\s+/)
+            .filter(term => term.length > 0)
+            // Strip FTS5 boolean operators to prevent query manipulation
+            .filter(term => !/^(AND|OR|NOT|NEAR)$/i.test(term))
+            .map(term => `"${term}"*`) // Prefix match each term
+            .join(' OR ');
+        if (!ftsQuery) {
+            return [];
+        }
+        // BM25 column weights: id=0, name=20, qualified_name=5, docstring=1, signature=2
+        // Heavy name weight ensures exact/prefix name matches rank above incidental
+        // mentions in long docstrings or qualified names of nested symbols.
+        // Fetch 5x requested limit so post-hoc rescoring (kindBonus, pathRelevance,
+        // nameMatchBonus) can promote results that BM25 alone undervalues.
+        const ftsLimit = Math.max(limit * 5, 100);
+        let sql = `
+      SELECT nodes.*, bm25(nodes_fts, 0, 20, 5, 1, 2) as score
+      FROM nodes_fts
+      JOIN nodes ON nodes_fts.id = nodes.id
+      WHERE nodes_fts MATCH ?
+    `;
+        const params = [ftsQuery];
+        if (kinds && kinds.length > 0) {
+            sql += ` AND nodes.kind IN (${kinds.map(() => '?').join(',')})`;
+            params.push(...kinds);
+        }
+        if (languages && languages.length > 0) {
+            sql += ` AND nodes.language IN (${languages.map(() => '?').join(',')})`;
+            params.push(...languages);
+        }
+        sql += ' ORDER BY score LIMIT ? OFFSET ?';
+        params.push(ftsLimit, offset);
+        try {
+            const rows = this.db.prepare(sql).all(...params);
+            return rows.map((row) => ({
+                node: rowToNode(row),
+                score: Math.abs(row.score), // bm25 returns negative scores
+            }));
+        }
+        catch {
+            // FTS query failed, return empty
+            return [];
+        }
+    }
+    /**
+     * LIKE-based substring search for cases where FTS doesn't match
+     * Useful for camelCase matching (e.g., "signIn" finds "signInWithGoogle")
+     */
+    searchNodesLike(query, options) {
+        const { kinds, languages, limit = 100, offset = 0 } = options;
+        let sql = `
+      SELECT nodes.*,
+        CASE
+          WHEN name = ? THEN 1.0
+          WHEN name LIKE ? THEN 0.9
+          WHEN name LIKE ? THEN 0.8
+          WHEN qualified_name LIKE ? THEN 0.7
+          ELSE 0.5
+        END as score
+      FROM nodes
+      WHERE (
+        name LIKE ? OR
+        qualified_name LIKE ? OR
+        name LIKE ?
+      )
+    `;
+        // Pattern variants for better matching
+        const exactMatch = query;
+        const startsWith = `${query}%`;
+        const contains = `%${query}%`;
+        const params = [
+            exactMatch, // Exact match score
+            startsWith, // Starts with score
+            contains, // Contains score
+            contains, // Qualified name score
+            contains, // WHERE: name contains
+            contains, // WHERE: qualified_name contains
+            startsWith, // WHERE: name starts with
+        ];
+        if (kinds && kinds.length > 0) {
+            sql += ` AND kind IN (${kinds.map(() => '?').join(',')})`;
+            params.push(...kinds);
+        }
+        if (languages && languages.length > 0) {
+            sql += ` AND language IN (${languages.map(() => '?').join(',')})`;
+            params.push(...languages);
+        }
+        sql += ' ORDER BY score DESC, length(name) ASC LIMIT ? OFFSET ?';
+        params.push(limit, offset);
+        const rows = this.db.prepare(sql).all(...params);
+        return rows.map((row) => ({
+            node: rowToNode(row),
+            score: row.score,
+        }));
+    }
+    /**
+     * Find nodes by exact name match
+     *
+     * Used for hybrid search - looks up symbols by exact name or case-insensitive match.
+     * Returns high-confidence matches for known symbol names extracted from query.
+     *
+     * @param names - Array of symbol names to look up
+     * @param options - Search options (kinds, languages, limit)
+     * @returns SearchResult array with exact matches scored at 1.0
+     */
+    findNodesByExactName(names, options = {}) {
+        if (names.length === 0)
+            return [];
+        const { kinds, languages, limit = 50 } = options;
+        // Two-pass approach to handle common names (e.g., "run" has 40+ matches):
+        // Pass 1: Find which files contain distinctive (rare) symbols from the query.
+        // Pass 2: Query each name, boosting results that co-locate with distinctive symbols.
+        // Pass 1: Find files containing each queried name, identify distinctive names
+        const nameToFiles = new Map();
+        for (const name of names) {
+            let sql = 'SELECT DISTINCT file_path FROM nodes WHERE name COLLATE NOCASE = ?';
+            const params = [name];
+            if (kinds && kinds.length > 0) {
+                sql += ` AND kind IN (${kinds.map(() => '?').join(',')})`;
+                params.push(...kinds);
+            }
+            sql += ' LIMIT 100';
+            const rows = this.db.prepare(sql).all(...params);
+            nameToFiles.set(name.toLowerCase(), new Set(rows.map(r => r.file_path)));
+        }
+        // Distinctive names are those with fewer than 10 file matches (e.g., "scrapeLoop" = 1 file)
+        const distinctiveFiles = new Set();
+        for (const [, files] of nameToFiles) {
+            if (files.size > 0 && files.size < 10) {
+                for (const f of files)
+                    distinctiveFiles.add(f);
+            }
+        }
+        // Pass 2: Query each name with per-name limit, scoring by co-location
+        const perNameLimit = Math.max(8, Math.ceil(limit / names.length));
+        const allResults = [];
+        const seenIds = new Set();
+        for (const name of names) {
+            let sql = `
+        SELECT nodes.*, 1.0 as score
+        FROM nodes
+        WHERE name COLLATE NOCASE = ?
+      `;
+            const params = [name];
+            if (kinds && kinds.length > 0) {
+                sql += ` AND kind IN (${kinds.map(() => '?').join(',')})`;
+                params.push(...kinds);
+            }
+            if (languages && languages.length > 0) {
+                sql += ` AND language IN (${languages.map(() => '?').join(',')})`;
+                params.push(...languages);
+            }
+            // Fetch enough to find co-located results among common names
+            sql += ' LIMIT ?';
+            params.push(Math.max(perNameLimit * 3, 50));
+            const rows = this.db.prepare(sql).all(...params);
+            const nameResults = [];
+            for (const row of rows) {
+                const node = rowToNode(row);
+                if (seenIds.has(node.id))
+                    continue;
+                // Boost results in files that also contain distinctive symbols
+                const coLocationBoost = distinctiveFiles.has(node.filePath) ? 20 : 0;
+                nameResults.push({ node, score: row.score + coLocationBoost });
+            }
+            // Sort by score (co-located first), take per-name limit
+            nameResults.sort((a, b) => b.score - a.score);
+            for (const r of nameResults.slice(0, perNameLimit)) {
+                seenIds.add(r.node.id);
+                allResults.push(r);
+            }
+        }
+        // Sort all results by score so co-located results bubble up
+        allResults.sort((a, b) => b.score - a.score);
+        return allResults.slice(0, limit);
+    }
+    /**
+     * Find nodes whose name contains a substring (LIKE-based).
+     * Useful for CamelCase-part matching where FTS fails because
+     * e.g. "TransportSearchAction" is one FTS token, not matchable by "Search"*.
+     *
+     * Results are ordered by name length (shorter = more likely to be the core type).
+     */
+    findNodesByNameSubstring(substring, options = {}) {
+        const { kinds, languages, limit = 30, excludePrefix } = options;
+        let sql = `
+      SELECT nodes.*, 1.0 as score
+      FROM nodes
+      WHERE name LIKE ?
+    `;
+        const params = [`%${substring}%`];
+        // Exclude prefix matches (handled by FTS-based prefix search in Step 2b)
+        if (excludePrefix) {
+            sql += ` AND name NOT LIKE ?`;
+            params.push(`${substring}%`);
+        }
+        if (kinds && kinds.length > 0) {
+            sql += ` AND kind IN (${kinds.map(() => '?').join(',')})`;
+            params.push(...kinds);
+        }
+        if (languages && languages.length > 0) {
+            sql += ` AND language IN (${languages.map(() => '?').join(',')})`;
+            params.push(...languages);
+        }
+        sql += ' ORDER BY length(name) ASC LIMIT ?';
+        params.push(limit);
+        const rows = this.db.prepare(sql).all(...params);
+        return rows.map((row) => ({
+            node: rowToNode(row),
+            score: row.score,
+        }));
+    }
+    // ===========================================================================
+    // Edge Operations
+    // ===========================================================================
+    /**
+     * Insert a new edge
+     */
+    insertEdge(edge) {
+        if (!this.stmts.insertEdge) {
+            this.stmts.insertEdge = this.db.prepare(`
+        INSERT OR IGNORE INTO edges (source, target, kind, metadata, line, col, provenance)
+        VALUES (@source, @target, @kind, @metadata, @line, @col, @provenance)
+      `);
+        }
+        this.stmts.insertEdge.run({
+            source: edge.source,
+            target: edge.target,
+            kind: edge.kind,
+            metadata: edge.metadata ? JSON.stringify(edge.metadata) : null,
+            line: edge.line ?? null,
+            col: edge.column ?? null,
+            provenance: edge.provenance ?? null,
+        });
+    }
+    /**
+     * Insert multiple edges in a transaction
+     */
+    insertEdges(edges) {
+        if (edges.length === 0)
+            return;
+        this.db.transaction(() => {
+            const endpointIds = new Set();
+            for (const edge of edges) {
+                endpointIds.add(edge.source);
+                endpointIds.add(edge.target);
+            }
+            const existingNodeIds = this.getExistingNodeIds([...endpointIds]);
+            for (const edge of edges) {
+                if (!existingNodeIds.has(edge.source) || !existingNodeIds.has(edge.target)) {
+                    continue;
+                }
+                this.insertEdge(edge);
+            }
+        })();
+    }
+    /**
+     * Delete all edges from a source node
+     */
+    deleteEdgesBySource(sourceId) {
+        if (!this.stmts.deleteEdgesBySource) {
+            this.stmts.deleteEdgesBySource = this.db.prepare('DELETE FROM edges WHERE source = ?');
+        }
+        this.stmts.deleteEdgesBySource.run(sourceId);
+    }
+    /**
+     * Get outgoing edges from a node
+     */
+    getOutgoingEdges(sourceId, kinds, provenance) {
+        if ((kinds && kinds.length > 0) || provenance) {
+            let sql = 'SELECT * FROM edges WHERE source = ?';
+            const params = [sourceId];
+            if (kinds && kinds.length > 0) {
+                sql += ` AND kind IN (${kinds.map(() => '?').join(',')})`;
+                params.push(...kinds);
+            }
+            if (provenance) {
+                sql += ' AND provenance = ?';
+                params.push(provenance);
+            }
+            const rows = this.db.prepare(sql).all(...params);
+            return rows.map(rowToEdge);
+        }
+        if (!this.stmts.getEdgesBySource) {
+            this.stmts.getEdgesBySource = this.db.prepare('SELECT * FROM edges WHERE source = ?');
+        }
+        const rows = this.stmts.getEdgesBySource.all(sourceId);
+        return rows.map(rowToEdge);
+    }
+    /**
+     * Get incoming edges to a node
+     */
+    getIncomingEdges(targetId, kinds) {
+        if (kinds && kinds.length > 0) {
+            const sql = `SELECT * FROM edges WHERE target = ? AND kind IN (${kinds.map(() => '?').join(',')})`;
+            const rows = this.db.prepare(sql).all(targetId, ...kinds);
+            return rows.map(rowToEdge);
+        }
+        if (!this.stmts.getEdgesByTarget) {
+            this.stmts.getEdgesByTarget = this.db.prepare('SELECT * FROM edges WHERE target = ?');
+        }
+        const rows = this.stmts.getEdgesByTarget.all(targetId);
+        return rows.map(rowToEdge);
+    }
+    /**
+     * Find all edges where both source and target are in the given node set.
+     * Useful for recovering inter-node connectivity after BFS.
+     */
+    findEdgesBetweenNodes(nodeIds, kinds) {
+        if (nodeIds.length === 0)
+            return [];
+        const idsJson = JSON.stringify(nodeIds);
+        let sql = `SELECT * FROM edges WHERE source IN (SELECT value FROM json_each(?)) AND target IN (SELECT value FROM json_each(?))`;
+        const params = [idsJson, idsJson];
+        if (kinds && kinds.length > 0) {
+            sql += ` AND kind IN (${kinds.map(() => '?').join(',')})`;
+            params.push(...kinds);
+        }
+        const rows = this.db.prepare(sql).all(...params);
+        return rows.map(rowToEdge);
+    }
+    /**
+     * Distinct file paths that DEPEND ON `filePath`: every file containing a
+     * symbol with a cross-file edge (any kind except `contains`) into a symbol
+     * of this file. This is the file-level projection of the symbol dependency
+     * graph and the basis for blast-radius / `affected` test selection.
+     *
+     * It deliberately does NOT restrict to `imports` edges. In this graph an
+     * `imports` edge connects a file to its own local import declarations
+     * (it is always same-file), so an imports-only lookup returns zero
+     * cross-file dependents for every file. The real cross-file dependency
+     * signal is the resolved call/reference graph — calls, references,
+     * instantiates, extends, implements, overrides, type_of, returns,
+     * decorates — exactly what {@link GraphTraverser.getImpactRadius} traverses.
+     * `contains` is excluded: a parent containing a symbol does not *depend* on
+     * it. One indexed query (idx_nodes_file_path + idx_edges_target_kind).
+     */
+    getDependentFilePaths(filePath) {
+        const sql = `SELECT DISTINCT src.file_path AS fp
+      FROM edges e
+      JOIN nodes tgt ON tgt.id = e.target
+      JOIN nodes src ON src.id = e.source
+      WHERE tgt.file_path = ?
+        AND e.kind != 'contains'
+        AND src.file_path != ?`;
+        const rows = this.db.prepare(sql).all(filePath, filePath);
+        return rows.map((r) => r.fp);
+    }
+    /**
+     * Distinct file paths that `filePath` DEPENDS ON — the inverse of
+     * {@link getDependentFilePaths}: every file containing a symbol that a
+     * symbol of this file has a cross-file edge into. Same edge-kind rules
+     * (all kinds except `contains`); same reason imports-only is insufficient.
+     */
+    getDependencyFilePaths(filePath) {
+        const sql = `SELECT DISTINCT tgt.file_path AS fp
+      FROM edges e
+      JOIN nodes src ON src.id = e.source
+      JOIN nodes tgt ON tgt.id = e.target
+      WHERE src.file_path = ?
+        AND e.kind != 'contains'
+        AND tgt.file_path != ?`;
+        const rows = this.db.prepare(sql).all(filePath, filePath);
+        return rows.map((r) => r.fp);
+    }
+    /**
+     * Cross-file edges whose TARGET is a node in `filePath` and whose SOURCE is a
+     * node in a *different* file, paired with the target node's (name, kind) so a
+     * caller can re-resolve the edge to the re-indexed target's new ID (node IDs
+     * are `sha256(filePath:kind:name:line)`, so any line shift in the callee file
+     * changes target IDs and a naive re-insert by old ID silently drops them).
+     * Used by `storeExtractionResult` to preserve incoming edges across a file
+     * re-index (issue #899). Same edge-kind rules as
+     * {@link getDependentFilePaths}: all kinds except `contains`.
+     */
+    getCrossFileIncomingEdgesWithTarget(filePath) {
+        const sql = `SELECT e.*, tgt.name AS target_name, tgt.kind AS target_kind
+      FROM edges e
+      JOIN nodes tgt ON tgt.id = e.target
+      JOIN nodes src ON src.id = e.source
+      WHERE tgt.file_path = ?
+        AND e.kind != 'contains'
+        AND src.file_path != ?`;
+        const rows = this.db.prepare(sql).all(filePath, filePath);
+        return rows.map(row => ({
+            ...rowToEdge(row),
+            targetName: row.target_name,
+            targetKind: row.target_kind,
+        }));
+    }
+    // ===========================================================================
+    // File Operations
+    // ===========================================================================
+    /**
+     * Insert or update a file record
+     */
+    upsertFile(file) {
+        if (!this.stmts.upsertFile) {
+            this.stmts.upsertFile = this.db.prepare(`
+        INSERT INTO files (path, content_hash, language, size, modified_at, indexed_at, node_count, errors)
+        VALUES (@path, @contentHash, @language, @size, @modifiedAt, @indexedAt, @nodeCount, @errors)
+        ON CONFLICT(path) DO UPDATE SET
+          content_hash = @contentHash,
+          language = @language,
+          size = @size,
+          modified_at = @modifiedAt,
+          indexed_at = @indexedAt,
+          node_count = @nodeCount,
+          errors = @errors
+      `);
+        }
+        this.stmts.upsertFile.run({
+            path: file.path,
+            contentHash: file.contentHash,
+            language: file.language,
+            size: file.size,
+            modifiedAt: file.modifiedAt,
+            indexedAt: file.indexedAt,
+            nodeCount: file.nodeCount,
+            errors: file.errors ? JSON.stringify(file.errors) : null,
+        });
+    }
+    /**
+     * Delete a file record and its nodes
+     */
+    deleteFile(filePath) {
+        this.db.transaction(() => {
+            this.deleteNodesByFile(filePath);
+            if (!this.stmts.deleteFile) {
+                this.stmts.deleteFile = this.db.prepare('DELETE FROM files WHERE path = ?');
+            }
+            this.stmts.deleteFile.run(filePath);
+        })();
+    }
+    /**
+     * Get a file record by path
+     */
+    getFileByPath(filePath) {
+        if (!this.stmts.getFileByPath) {
+            this.stmts.getFileByPath = this.db.prepare('SELECT * FROM files WHERE path = ?');
+        }
+        const row = this.stmts.getFileByPath.get(filePath);
+        return row ? rowToFileRecord(row) : null;
+    }
+    /**
+     * Get all tracked files
+     */
+    getAllFiles() {
+        if (!this.stmts.getAllFiles) {
+            this.stmts.getAllFiles = this.db.prepare('SELECT * FROM files ORDER BY path');
+        }
+        const rows = this.stmts.getAllFiles.all();
+        return rows.map(rowToFileRecord);
+    }
+    /**
+     * Most recent index timestamp (ms since epoch) across all tracked files, or
+     * null when nothing is indexed yet. One indexed aggregate, no per-row scan. (#329)
+     */
+    getLastIndexedAt() {
+        const row = this.db
+            .prepare('SELECT MAX(indexed_at) AS last FROM files')
+            .get();
+        return row?.last ?? null;
+    }
+    /**
+     * Get files that need re-indexing (hash changed)
+     */
+    getStaleFiles(currentHashes) {
+        const files = this.getAllFiles();
+        return files.filter((f) => {
+            const currentHash = currentHashes.get(f.path);
+            return currentHash && currentHash !== f.contentHash;
+        });
+    }
+    // ===========================================================================
+    // Unresolved References
+    // ===========================================================================
+    /**
+     * Insert an unresolved reference
+     */
+    insertUnresolvedRef(ref) {
+        if (!this.stmts.insertUnresolved) {
+            this.stmts.insertUnresolved = this.db.prepare(`
+        INSERT INTO unresolved_refs (from_node_id, reference_name, reference_kind, line, col, candidates, file_path, language)
+        VALUES (@fromNodeId, @referenceName, @referenceKind, @line, @col, @candidates, @filePath, @language)
+      `);
+        }
+        this.stmts.insertUnresolved.run({
+            fromNodeId: ref.fromNodeId,
+            referenceName: ref.referenceName,
+            referenceKind: ref.referenceKind,
+            line: ref.line,
+            col: ref.column,
+            candidates: ref.candidates ? JSON.stringify(ref.candidates) : null,
+            filePath: ref.filePath ?? '',
+            language: ref.language ?? 'unknown',
+        });
+    }
+    /**
+     * Insert multiple unresolved references in a transaction
+     */
+    insertUnresolvedRefsBatch(refs) {
+        if (refs.length === 0)
+            return;
+        const insert = this.db.transaction(() => {
+            for (const ref of refs) {
+                this.insertUnresolvedRef(ref);
+            }
+        });
+        insert();
+    }
+    /**
+     * Delete unresolved references from a node
+     */
+    deleteUnresolvedByNode(nodeId) {
+        if (!this.stmts.deleteUnresolvedByNode) {
+            this.stmts.deleteUnresolvedByNode = this.db.prepare('DELETE FROM unresolved_refs WHERE from_node_id = ?');
+        }
+        this.stmts.deleteUnresolvedByNode.run(nodeId);
+    }
+    /**
+     * Get unresolved references by name (for resolution)
+     */
+    getUnresolvedByName(name) {
+        if (!this.stmts.getUnresolvedByName) {
+            this.stmts.getUnresolvedByName = this.db.prepare('SELECT * FROM unresolved_refs WHERE reference_name = ?');
+        }
+        const rows = this.stmts.getUnresolvedByName.all(name);
+        return rows.map((row) => ({
+            fromNodeId: row.from_node_id,
+            referenceName: row.reference_name,
+            referenceKind: row.reference_kind,
+            line: row.line,
+            column: row.col,
+            candidates: row.candidates ? (0, utils_1.safeJsonParse)(row.candidates, undefined) : undefined,
+            filePath: row.file_path,
+            language: row.language,
+        }));
+    }
+    /**
+     * Get all unresolved references
+     */
+    getUnresolvedReferences() {
+        const rows = this.db.prepare('SELECT * FROM unresolved_refs').all();
+        return rows.map((row) => ({
+            fromNodeId: row.from_node_id,
+            referenceName: row.reference_name,
+            referenceKind: row.reference_kind,
+            line: row.line,
+            column: row.col,
+            candidates: row.candidates ? (0, utils_1.safeJsonParse)(row.candidates, undefined) : undefined,
+            filePath: row.file_path,
+            language: row.language,
+        }));
+    }
+    /**
+     * Get the count of unresolved references without loading them into memory
+     */
+    getUnresolvedReferencesCount() {
+        if (!this.stmts.getUnresolvedCount) {
+            this.stmts.getUnresolvedCount = this.db.prepare('SELECT COUNT(*) as count FROM unresolved_refs');
+        }
+        const row = this.stmts.getUnresolvedCount.get();
+        return row.count;
+    }
+    /**
+     * Get a batch of unresolved references using LIMIT/OFFSET pagination.
+     * Used to process references in bounded memory chunks.
+     */
+    getUnresolvedReferencesBatch(offset, limit) {
+        if (!this.stmts.getUnresolvedBatch) {
+            this.stmts.getUnresolvedBatch = this.db.prepare('SELECT * FROM unresolved_refs LIMIT ? OFFSET ?');
+        }
+        const rows = this.stmts.getUnresolvedBatch.all(limit, offset);
+        return rows.map((row) => ({
+            fromNodeId: row.from_node_id,
+            referenceName: row.reference_name,
+            referenceKind: row.reference_kind,
+            line: row.line,
+            column: row.col,
+            candidates: row.candidates ? (0, utils_1.safeJsonParse)(row.candidates, undefined) : undefined,
+            filePath: row.file_path,
+            language: row.language,
+        }));
+    }
+    /**
+     * Get all tracked file paths (lightweight — no full FileRecord objects)
+     */
+    getAllFilePaths() {
+        if (!this.stmts.getAllFilePaths) {
+            this.stmts.getAllFilePaths = this.db.prepare('SELECT path FROM files ORDER BY path');
+        }
+        const rows = this.stmts.getAllFilePaths.all();
+        return rows.map((r) => r.path);
+    }
+    /**
+     * Get all distinct node names (lightweight — just name strings for pre-filtering)
+     */
+    getAllNodeNames() {
+        if (!this.stmts.getAllNodeNames) {
+            this.stmts.getAllNodeNames = this.db.prepare('SELECT DISTINCT name FROM nodes');
+        }
+        const rows = this.stmts.getAllNodeNames.all();
+        return rows.map((r) => r.name);
+    }
+    /**
+     * Get unresolved references scoped to specific file paths.
+     * Uses the idx_unresolved_file_path index for efficient lookup.
+     */
+    getUnresolvedReferencesByFiles(filePaths) {
+        if (filePaths.length === 0)
+            return [];
+        // Chunk under SQLite's parameter limit: the first sync of a very large repo
+        // passes every changed file here, which an unbounded `IN (...)` would bind
+        // as one parameter each — exceeding MAX_VARIABLE_NUMBER and aborting with
+        // "too many SQL variables". (#540)
+        const rows = [];
+        for (let i = 0; i < filePaths.length; i += SQLITE_PARAM_CHUNK_SIZE) {
+            const chunk = filePaths.slice(i, i + SQLITE_PARAM_CHUNK_SIZE);
+            const placeholders = chunk.map(() => '?').join(',');
+            const chunkRows = this.db
+                .prepare(`SELECT * FROM unresolved_refs WHERE file_path IN (${placeholders})`)
+                .all(...chunk);
+            rows.push(...chunkRows);
+        }
+        return rows.map((row) => ({
+            fromNodeId: row.from_node_id,
+            referenceName: row.reference_name,
+            referenceKind: row.reference_kind,
+            line: row.line,
+            column: row.col,
+            candidates: row.candidates ? (0, utils_1.safeJsonParse)(row.candidates, undefined) : undefined,
+            filePath: row.file_path,
+            language: row.language,
+        }));
+    }
+    /**
+     * Delete all unresolved references (after resolution)
+     */
+    clearUnresolvedReferences() {
+        this.db.exec('DELETE FROM unresolved_refs');
+    }
+    /**
+     * Delete resolved references by their IDs
+     */
+    deleteResolvedReferences(fromNodeIds) {
+        if (fromNodeIds.length === 0)
+            return;
+        const placeholders = fromNodeIds.map(() => '?').join(',');
+        this.db.prepare(`DELETE FROM unresolved_refs WHERE from_node_id IN (${placeholders})`).run(...fromNodeIds);
+    }
+    /**
+     * Delete specific resolved references by (fromNodeId, referenceName, referenceKind) tuples.
+     * More precise than deleteResolvedReferences — only removes refs that were actually resolved.
+     */
+    deleteSpecificResolvedReferences(refs) {
+        if (refs.length === 0)
+            return;
+        const stmt = this.db.prepare('DELETE FROM unresolved_refs WHERE from_node_id = ? AND reference_name = ? AND reference_kind = ?');
+        const deleteMany = this.db.transaction((items) => {
+            for (const ref of items) {
+                stmt.run(ref.fromNodeId, ref.referenceName, ref.referenceKind);
+            }
+        });
+        deleteMany(refs);
+    }
+    // ===========================================================================
+    // Statistics
+    // ===========================================================================
+    /**
+     * Lightweight (nodes, edges) count snapshot. Used around an index/sync
+     * run to compute true additions across extraction + resolution +
+     * synthesis — the per-phase counter in the orchestrator only sees
+     * extraction's contribution, which is why the CLI summary under-reported
+     * the edge count (resolution + synthesizer edges were invisible).
+     */
+    getNodeAndEdgeCount() {
+        return this.db
+            .prepare('SELECT (SELECT COUNT(*) FROM nodes) AS nodes, (SELECT COUNT(*) FROM edges) AS edges')
+            .get();
+    }
+    /**
+     * Get graph statistics
+     */
+    getStats() {
+        // Single query for all three aggregate counts
+        const counts = this.db.prepare(`
+      SELECT
+        (SELECT COUNT(*) FROM nodes) AS node_count,
+        (SELECT COUNT(*) FROM edges) AS edge_count,
+        (SELECT COUNT(*) FROM files) AS file_count
+    `).get();
+        const nodesByKind = {};
+        const nodeKindRows = this.db
+            .prepare('SELECT kind, COUNT(*) as count FROM nodes GROUP BY kind')
+            .all();
+        for (const row of nodeKindRows) {
+            nodesByKind[row.kind] = row.count;
+        }
+        const edgesByKind = {};
+        const edgeKindRows = this.db
+            .prepare('SELECT kind, COUNT(*) as count FROM edges GROUP BY kind')
+            .all();
+        for (const row of edgeKindRows) {
+            edgesByKind[row.kind] = row.count;
+        }
+        const filesByLanguage = {};
+        const languageRows = this.db
+            .prepare('SELECT language, COUNT(*) as count FROM files GROUP BY language')
+            .all();
+        for (const row of languageRows) {
+            filesByLanguage[row.language] = row.count;
+        }
+        return {
+            nodeCount: counts.node_count,
+            edgeCount: counts.edge_count,
+            fileCount: counts.file_count,
+            nodesByKind,
+            edgesByKind,
+            filesByLanguage,
+            dbSizeBytes: 0, // Set by caller using DatabaseConnection.getSize()
+            lastUpdated: Date.now(),
+        };
+    }
+    // ===========================================================================
+    // Project Metadata
+    // ===========================================================================
+    /**
+     * Get a metadata value by key
+     */
+    getMetadata(key) {
+        const row = this.db.prepare('SELECT value FROM project_metadata WHERE key = ?').get(key);
+        return row?.value ?? null;
+    }
+    /**
+     * Set a metadata key-value pair (upsert)
+     */
+    setMetadata(key, value) {
+        this.db.prepare('INSERT INTO project_metadata (key, value, updated_at) VALUES (?, ?, ?) ON CONFLICT(key) DO UPDATE SET value = excluded.value, updated_at = excluded.updated_at').run(key, value, Date.now());
+    }
+    /**
+     * Get all metadata as a key-value record
+     */
+    getAllMetadata() {
+        const rows = this.db.prepare('SELECT key, value FROM project_metadata').all();
+        const result = {};
+        for (const row of rows) {
+            result[row.key] = row.value;
+        }
+        return result;
+    }
+    /**
+     * Clear all data from the database
+     */
+    clear() {
+        this.nodeCache.clear();
+        this.db.transaction(() => {
+            this.db.exec('DELETE FROM unresolved_refs');
+            this.db.exec('DELETE FROM edges');
+            this.db.exec('DELETE FROM nodes');
+            this.db.exec('DELETE FROM files');
+        })();
+    }
+}
+exports.QueryBuilder = QueryBuilder;
+//# sourceMappingURL=queries.js.map