@selvakumaresra/specship 0.1.2 → 0.1.3

package/dist/db/queries.js

@@ -1,1504 +0,0 @@
-"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,
-        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;
-    // 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;
-    }
-    // ===========================================================================
-    // 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, updated_at
-        ) VALUES (
-          @id, @kind, @name, @qualifiedName, @filePath, @language,
-          @startLine, @endLine, @startColumn, @endColumn,
-          @docstring, @signature, @visibility,
-          @isExported, @isAsync, @isStatic, @isAbstract,
-          @decorators, @typeParameters, @updatedAt
-        )
-      `);
-        }
-        // Validate required fields to prevent SQLite bind errors
-        if (!node.id || !node.kind || !node.name || !node.filePath || !node.language) {
-            console.error('[SpecShip] 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,
-            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,
-          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('[SpecShip] 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,
-            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 specship 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)
-                    + (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);
-    }
-    // ===========================================================================
-    // 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