@jafreck/lore 0.2.4 → 0.3.0

package/dist/indexer/stages/import-resolution.js

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+/**
+ * @module indexer/stages/import-resolution
+ *
+ * Pipeline stage: resolve raw import strings to file IDs (internal) or
+ * external package names. Populates `file_imports.resolved_id` and
+ * `external_deps` rows.
+ */
+import { ImportResolver } from '../resolver.js';
+// ─── Stage ────────────────────────────────────────────────────────────────────
+/**
+ * Resolves raw imports in `file_imports` to internal file IDs (`resolved_id`)
+ * or external package names (`external_deps`).
+ */
+export class ImportResolutionStage {
+    name = 'import-resolution';
+    async execute(context, _mode) {
+        const { db, branch, walkerConfig } = context;
+        const rootDir = walkerConfig.rootDir;
+        const resolver = new ImportResolver();
+        // Fetch all unresolved imports with their file's path, language, and file_id
+        const rows = db
+            .prepare(`SELECT fi.id, fi.file_id, fi.raw_import, f.path, f.language
+         FROM file_imports fi
+         JOIN files f ON f.id = fi.file_id
+         WHERE fi.resolved_id IS NULL AND f.branch = ?`)
+            .all(branch);
+        // P5: Build a bulk path→id map so we don't do N individual SELECT lookups.
+        const fileIdByPath = new Map(db.prepare('SELECT id, path FROM files WHERE branch = ?').all(branch)
+            .map(r => [r.path, r.id]));
+        const updateResolved = db.prepare('UPDATE file_imports SET resolved_id = ? WHERE id = ?');
+        const insertExternalDep = db.prepare('INSERT OR IGNORE INTO external_deps (file_id, package) VALUES (?, ?)');
+        for (const row of rows) {
+            const resolved = resolver.resolve({ source: row.raw_import, importedNames: [] }, row.path, rootDir, row.language);
+            if (resolved.resolvedPath) {
+                const targetId = fileIdByPath.get(resolved.resolvedPath);
+                if (targetId !== undefined) {
+                    updateResolved.run(targetId, row.id);
+                }
+            }
+            else if (resolved.isExternal && resolved.externalName) {
+                insertExternalDep.run(row.file_id, resolved.externalName);
+            }
+        }
+        context.log.indexing('imports resolved', { totalUnresolved: rows.length });
+    }
+}
+//# sourceMappingURL=import-resolution.js.map

package/dist/indexer/stages/import-resolution.js.map

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package/dist/indexer/stages/index.d.ts

@@ -0,0 +1,12 @@
+/**
+ * @module indexer/stages
+ *
+ * Concrete pipeline stages with real implementations.
+ */
+export { SourceIndexStage } from './source-index.js';
+export { DocsIndexStage } from './docs-index.js';
+export { ImportResolutionStage } from './import-resolution.js';
+export { DependencyApiStage } from './dependency-api.js';
+export { LspEnrichmentStage } from './lsp-enrichment.js';
+export { EmbeddingStage } from './embedding.js';
+//# sourceMappingURL=index.d.ts.map

package/dist/indexer/stages/index.d.ts.map

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package/dist/indexer/stages/index.js

@@ -0,0 +1,12 @@
+/**
+ * @module indexer/stages
+ *
+ * Concrete pipeline stages with real implementations.
+ */
+export { SourceIndexStage } from './source-index.js';
+export { DocsIndexStage } from './docs-index.js';
+export { ImportResolutionStage } from './import-resolution.js';
+export { DependencyApiStage } from './dependency-api.js';
+export { LspEnrichmentStage } from './lsp-enrichment.js';
+export { EmbeddingStage } from './embedding.js';
+//# sourceMappingURL=index.js.map

package/dist/indexer/stages/index.js.map

@@ -0,0 +1 @@
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package/dist/indexer/stages/lsp-enrichment.d.ts

@@ -0,0 +1,48 @@
+/**
+ * @module indexer/stages/lsp-enrichment
+ *
+ * Pipeline stage: enrich symbols, symbol_refs, type_refs, and
+ * symbol_relationships with LSP-derived metadata (definition_path,
+ * definition_line, resolved_type_signature, etc.).
+ *
+ * ## Data written
+ *
+ * - `symbols.resolved_type_signature`, `resolved_return_type`,
+ *   `definition_uri`, `definition_path`
+ * - `symbol_refs.resolved_type_signature`, `resolved_return_type`,
+ *   `definition_uri`, `definition_path`, `definition_line`, `definition_character`
+ * - `type_refs.resolved_type_signature`, `definition_uri`,
+ *   `definition_path`, `definition_line`, `definition_character`
+ * - `symbol_relationships.definition_uri`, `definition_path`,
+ *   `definition_line`, `definition_character`
+ *
+ * ## Data dependency
+ *
+ * **Must run before `ResolutionStage`.**  The resolution stage reads
+ * `definition_path` / `definition_line` columns populated here to perform
+ * LSP-based containment resolution.
+ */
+import type { PipelineContext, PipelineStage } from '../pipeline.js';
+import type { Database } from '../db.js';
+import { LspEnrichmentCoordinator } from '../lsp/enrichment.js';
+/**
+ * Enriches indexed artefacts with LSP-derived metadata.
+ *
+ * Manages the lifecycle of an `LspEnrichmentCoordinator` per pipeline run.
+ * The coordinator is started during `execute()` and disposed in `dispose()`.
+ */
+export declare class LspEnrichmentStage implements PipelineStage {
+    readonly name = "lsp-enrichment";
+    private coordinator;
+    execute(context: PipelineContext, _mode: 'build' | 'update'): Promise<void>;
+    dispose(): Promise<void>;
+}
+/**
+ * Enrich symbols, call refs, type refs, and relationships for every file in
+ * the context with LSP-derived metadata.
+ */
+export declare function enrichProjectRefs(db: Database.Database, branch: string, files: Array<{
+    path: string;
+    language: string;
+}>, coordinator: LspEnrichmentCoordinator): Promise<void>;
+//# sourceMappingURL=lsp-enrichment.d.ts.map

package/dist/indexer/stages/lsp-enrichment.d.ts.map

@@ -0,0 +1 @@
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package/dist/indexer/stages/lsp-enrichment.js

@@ -0,0 +1,158 @@
+/**
+ * @module indexer/stages/lsp-enrichment
+ *
+ * Pipeline stage: enrich symbols, symbol_refs, type_refs, and
+ * symbol_relationships with LSP-derived metadata (definition_path,
+ * definition_line, resolved_type_signature, etc.).
+ *
+ * ## Data written
+ *
+ * - `symbols.resolved_type_signature`, `resolved_return_type`,
+ *   `definition_uri`, `definition_path`
+ * - `symbol_refs.resolved_type_signature`, `resolved_return_type`,
+ *   `definition_uri`, `definition_path`, `definition_line`, `definition_character`
+ * - `type_refs.resolved_type_signature`, `definition_uri`,
+ *   `definition_path`, `definition_line`, `definition_character`
+ * - `symbol_relationships.definition_uri`, `definition_path`,
+ *   `definition_line`, `definition_character`
+ *
+ * ## Data dependency
+ *
+ * **Must run before `ResolutionStage`.**  The resolution stage reads
+ * `definition_path` / `definition_line` columns populated here to perform
+ * LSP-based containment resolution.
+ */
+import * as fs from 'node:fs';
+import { LspEnrichmentCoordinator } from '../lsp/enrichment.js';
+import { buildStructuralEmbeddingText } from '../embedder.js';
+/**
+ * Enriches indexed artefacts with LSP-derived metadata.
+ *
+ * Manages the lifecycle of an `LspEnrichmentCoordinator` per pipeline run.
+ * The coordinator is started during `execute()` and disposed in `dispose()`.
+ */
+export class LspEnrichmentStage {
+    name = 'lsp-enrichment';
+    coordinator = null;
+    async execute(context, _mode) {
+        if (!context.lsp?.enabled || context.files.length === 0)
+            return;
+        this.coordinator = new LspEnrichmentCoordinator(context.lsp, context.walkerConfig.rootDir);
+        // Start language servers for all languages seen in the file list.
+        const languages = new Set(context.files.map(f => f.language));
+        if (context.indexDependencies)
+            languages.add('typescript');
+        await this.coordinator.start(languages);
+        await enrichProjectRefs(context.db, context.branch, context.files, this.coordinator);
+    }
+    async dispose() {
+        if (this.coordinator) {
+            await this.coordinator.dispose();
+            this.coordinator = null;
+        }
+    }
+}
+// ─── Enrichment logic ─────────────────────────────────────────────────────────────────
+/**
+ * Enrich symbols, call refs, type refs, and relationships for every file in
+ * the context with LSP-derived metadata.
+ */
+export async function enrichProjectRefs(db, branch, files, coordinator) {
+    const selectSymbols = db.prepare(`SELECT s.id, s.name, s.signature, s.start_line
+     FROM symbols s
+     JOIN files f ON f.id = s.file_id
+     WHERE f.path = ? AND f.branch = ?
+     ORDER BY s.id`);
+    const selectCallRefs = db.prepare(`SELECT sr.id, sr.call_line, sr.call_character
+     FROM symbol_refs sr
+     JOIN symbols s ON s.id = sr.caller_id
+     JOIN files f ON f.id = s.file_id
+     WHERE f.path = ? AND f.branch = ?
+     ORDER BY sr.id`);
+    const selectTypeRefs = db.prepare(`SELECT tr.id, tr.ref_line, tr.ref_character
+     FROM type_refs tr
+     JOIN files f ON f.id = tr.file_id
+     WHERE f.path = ? AND f.branch = ?
+     ORDER BY tr.id`);
+    const selectRelationships = db.prepare(`SELECT sr.id, sr.line, sr.character
+     FROM symbol_relationships sr
+     JOIN files f ON f.id = sr.file_id
+     WHERE f.path = ? AND f.branch = ? AND sr.line IS NOT NULL
+     ORDER BY sr.id`);
+    const updateSymbol = db.prepare(`UPDATE symbols
+     SET resolved_type_signature = ?, resolved_return_type = ?, definition_uri = ?, definition_path = ?
+     WHERE id = ?`);
+    const updateSymbolFts = db.prepare('UPDATE symbols_fts SET signature = ? WHERE rowid = ?');
+    const updateCallRef = db.prepare(`UPDATE symbol_refs
+     SET resolved_type_signature = ?, resolved_return_type = ?, definition_uri = ?, definition_path = ?, definition_line = ?, definition_character = ?
+     WHERE id = ?`);
+    const updateTypeRef = db.prepare(`UPDATE type_refs
+     SET resolved_type_signature = ?, definition_uri = ?, definition_path = ?, definition_line = ?, definition_character = ?
+     WHERE id = ?`);
+    const updateRelationship = db.prepare(`UPDATE symbol_relationships
+     SET definition_uri = ?, definition_path = ?, definition_line = ?, definition_character = ?
+     WHERE id = ?`);
+    for (const file of files) {
+        if (!file || !fs.existsSync(file.path))
+            continue;
+        let source;
+        try {
+            source = fs.readFileSync(file.path, 'utf8');
+        }
+        catch {
+            continue;
+        }
+        const tagged = [];
+        const symbols = selectSymbols.all(file.path, branch);
+        for (const s of symbols) {
+            tagged.push({ table: 'symbol', rowId: s.id, line: s.start_line, character: 0, name: s.name, signature: s.signature });
+        }
+        const callRefs = selectCallRefs.all(file.path, branch);
+        for (const cr of callRefs) {
+            tagged.push({ table: 'callRef', rowId: cr.id, line: cr.call_line, character: cr.call_character ?? 0 });
+        }
+        const typeRefs = selectTypeRefs.all(file.path, branch);
+        for (const tr of typeRefs) {
+            tagged.push({ table: 'typeRef', rowId: tr.id, line: tr.ref_line, character: tr.ref_character ?? 0 });
+        }
+        const relationships = selectRelationships.all(file.path, branch);
+        for (const r of relationships) {
+            tagged.push({ table: 'relationship', rowId: r.id, line: r.line, character: r.character ?? 0 });
+        }
+        if (tagged.length === 0)
+            continue;
+        const metadata = await coordinator.enrich({
+            filePath: file.path,
+            language: file.language,
+            source,
+            targets: tagged.map(t => ({ line: t.line, character: t.character })),
+        });
+        for (let i = 0; i < tagged.length; i++) {
+            const tag = tagged[i];
+            const m = metadata[i];
+            if (!m)
+                continue;
+            switch (tag.table) {
+                case 'symbol':
+                    updateSymbol.run(m.resolvedTypeSignature, m.resolvedReturnType, m.definitionUri, m.definitionPath, tag.rowId);
+                    updateSymbolFts.run(buildStructuralEmbeddingText({
+                        name: tag.name,
+                        signature: tag.signature ?? null,
+                        resolvedTypeSignature: m.resolvedTypeSignature,
+                        resolvedReturnType: m.resolvedReturnType,
+                    }), tag.rowId);
+                    break;
+                case 'callRef':
+                    updateCallRef.run(m.resolvedTypeSignature, m.resolvedReturnType, m.definitionUri, m.definitionPath, m.definitionLine, m.definitionCharacter, tag.rowId);
+                    break;
+                case 'typeRef':
+                    updateTypeRef.run(m.resolvedTypeSignature, m.definitionUri, m.definitionPath, m.definitionLine, m.definitionCharacter, tag.rowId);
+                    break;
+                case 'relationship':
+                    updateRelationship.run(m.definitionUri, m.definitionPath, m.definitionLine, m.definitionCharacter, tag.rowId);
+                    break;
+            }
+        }
+    }
+}
+//# sourceMappingURL=lsp-enrichment.js.map

package/dist/indexer/stages/lsp-enrichment.js.map

@@ -0,0 +1 @@
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package/dist/indexer/stages/source-index.d.ts

@@ -0,0 +1,31 @@
+/**
+ * @module indexer/stages/source-index
+ *
+ * Pipeline stage: walk, parse, extract, and insert symbols/imports/callRefs/
+ * typeRefs/relationships/routes/annotations for all source files.
+ *
+ * This is the first stage in the pipeline and populates `context.files`.
+ */
+import type { PipelineContext, PipelineStage } from '../pipeline.js';
+import type { Database } from '../db.js';
+import { ParserPool } from '../parser.js';
+/**
+ * Walk source files, parse with tree-sitter, extract symbols/imports/callRefs/
+ * typeRefs/relationships/routes/annotations, and persist to the database.
+ *
+ * Populates `context.files` for use by later stages.
+ */
+export declare class SourceIndexStage implements PipelineStage {
+    readonly name = "source-index";
+    private pool;
+    execute(context: PipelineContext, mode: 'build' | 'update'): Promise<void>;
+    dispose(): Promise<void>;
+    private processBuild;
+    private processUpdate;
+}
+/**
+ * Parse one file, extract symbols/imports/callRefs/typeRefs/relationships/
+ * routes/annotations, and insert into the DB.
+ */
+export declare function processFile(db: Database.Database, pool: ParserPool, filePath: string, language: string, branch: string): void;
+//# sourceMappingURL=source-index.d.ts.map

package/dist/indexer/stages/source-index.d.ts.map

@@ -0,0 +1 @@
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package/dist/indexer/stages/source-index.js

@@ -0,0 +1,314 @@
+/**
+ * @module indexer/stages/source-index
+ *
+ * Pipeline stage: walk, parse, extract, and insert symbols/imports/callRefs/
+ * typeRefs/relationships/routes/annotations for all source files.
+ *
+ * This is the first stage in the pipeline and populates `context.files`.
+ */
+import * as fs from 'node:fs';
+import * as crypto from 'node:crypto';
+import { setLoreMeta, getLoreMeta, LORE_META_INDEX_CHECKPOINT, } from '../db.js';
+import { walkFiles, detectLanguageForPath } from '../walker.js';
+import { ParserPool } from '../parser.js';
+import { buildStructuralEmbeddingText } from '../embedder.js';
+import { normalizeTypeName } from '../call-graph.js';
+import { CExtractor } from '../extractors/c.js';
+import { RustExtractor } from '../extractors/rust.js';
+import { PythonExtractor } from '../extractors/python.js';
+import { CppExtractor } from '../extractors/cpp.js';
+import { TypeScriptExtractor } from '../extractors/typescript.js';
+import { JavaScriptExtractor } from '../extractors/javascript.js';
+import { GoExtractor } from '../extractors/go.js';
+import { JavaExtractor } from '../extractors/java.js';
+import { CSharpExtractor } from '../extractors/csharp.js';
+import { RubyExtractor } from '../extractors/ruby.js';
+import { PhpExtractor } from '../extractors/php.js';
+import { SwiftExtractor } from '../extractors/swift.js';
+import { KotlinExtractor } from '../extractors/kotlin.js';
+import { ScalaExtractor } from '../extractors/scala.js';
+import { LuaExtractor } from '../extractors/lua.js';
+import { BashExtractor } from '../extractors/bash.js';
+import { ElixirExtractor } from '../extractors/elixir.js';
+import { ZigExtractor } from '../extractors/zig.js';
+import { DartExtractor } from '../extractors/dart.js';
+import { OcamlExtractor } from '../extractors/ocaml.js';
+import { HaskellExtractor } from '../extractors/haskell.js';
+import { JuliaExtractor } from '../extractors/julia.js';
+import { ElmExtractor } from '../extractors/elm.js';
+import { ObjcExtractor } from '../extractors/objc.js';
+// ─── Extractor registry ───────────────────────────────────────────────────────
+const EXTRACTORS = {
+    c: new CExtractor(),
+    rust: new RustExtractor(),
+    python: new PythonExtractor(),
+    cpp: new CppExtractor(),
+    typescript: new TypeScriptExtractor(),
+    javascript: new JavaScriptExtractor(),
+    go: new GoExtractor(),
+    java: new JavaExtractor(),
+    csharp: new CSharpExtractor(),
+    ruby: new RubyExtractor(),
+    php: new PhpExtractor(),
+    swift: new SwiftExtractor(),
+    kotlin: new KotlinExtractor(),
+    scala: new ScalaExtractor(),
+    lua: new LuaExtractor(),
+    bash: new BashExtractor(),
+    elixir: new ElixirExtractor(),
+    zig: new ZigExtractor(),
+    dart: new DartExtractor(),
+    ocaml: new OcamlExtractor(),
+    haskell: new HaskellExtractor(),
+    julia: new JuliaExtractor(),
+    elm: new ElmExtractor(),
+    objc: new ObjcExtractor(),
+};
+// ─── Stage ────────────────────────────────────────────────────────────────────
+/**
+ * Walk source files, parse with tree-sitter, extract symbols/imports/callRefs/
+ * typeRefs/relationships/routes/annotations, and persist to the database.
+ *
+ * Populates `context.files` for use by later stages.
+ */
+export class SourceIndexStage {
+    name = 'source-index';
+    pool = null;
+    async execute(context, mode) {
+        this.pool = new ParserPool();
+        // Save docs auto-notes setting.
+        setLoreMeta(context.db, 'docs_auto_notes', context.docsAutoNotes ? '1' : '0');
+        if (mode === 'build') {
+            const files = await walkFiles(context.walkerConfig);
+            context.files = files;
+            context.log.indexing('walk complete', { fileCount: files.length });
+            await this.processBuild(context, files);
+        }
+        else {
+            await this.processUpdate(context);
+        }
+    }
+    async dispose() {
+        this.pool = null;
+    }
+    // ─── Build mode ──────────────────────────────────────────────────────────
+    async processBuild(context, files) {
+        const { db, branch } = context;
+        const pool = this.pool;
+        const resumeAt = loadBuildCheckpoint(db, branch, context.walkerConfig.rootDir, files.length);
+        if (resumeAt > 0) {
+            context.log.indexing('resuming from checkpoint', { resumeAt, totalFiles: files.length });
+        }
+        db.transaction(() => {
+            for (let i = resumeAt; i < files.length; i++) {
+                const file = files[i];
+                if (!file)
+                    continue;
+                processFile(db, pool, file.path, file.language, branch);
+                saveBuildCheckpoint(db, branch, context.walkerConfig.rootDir, i + 1, files.length);
+            }
+        })();
+        saveBuildCheckpoint(db, branch, context.walkerConfig.rootDir, files.length, files.length);
+    }
+    // ─── Update mode ─────────────────────────────────────────────────────────
+    async processUpdate(context) {
+        const { db, branch, walkerConfig } = context;
+        const changedFiles = context.changedFiles ?? [];
+        const pool = this.pool;
+        const enrichedFiles = [];
+        db.transaction(() => {
+            for (const filePath of changedFiles) {
+                // If the file no longer exists, remove it from the DB
+                if (!fs.existsSync(filePath)) {
+                    const row = db.prepare('SELECT id FROM files WHERE path = ? AND branch = ?').get(filePath, branch);
+                    if (row) {
+                        const symRows = db.prepare('SELECT id FROM symbols WHERE file_id = ?').all(row.id);
+                        for (const s of symRows)
+                            context.staleSymbolIds.push(s.id);
+                        db.prepare('UPDATE file_imports SET resolved_id = NULL WHERE resolved_id = ?').run(row.id);
+                        db.prepare('DELETE FROM symbols_fts WHERE rowid IN (SELECT id FROM symbols WHERE file_id = ?)').run(row.id);
+                        db.prepare('DELETE FROM files WHERE id = ?').run(row.id);
+                    }
+                    continue;
+                }
+                const language = detectLanguageForPath(filePath, walkerConfig);
+                if (language) {
+                    enrichedFiles.push({ path: filePath, language });
+                    context.changedSourcePaths.push(filePath);
+                    const existingRow = db.prepare('SELECT id FROM files WHERE path = ? AND branch = ?').get(filePath, branch);
+                    if (existingRow) {
+                        const symRows = db.prepare('SELECT id FROM symbols WHERE file_id = ?').all(existingRow.id);
+                        for (const s of symRows)
+                            context.staleSymbolIds.push(s.id);
+                        db.prepare('UPDATE file_imports SET resolved_id = NULL WHERE resolved_id = ?').run(existingRow.id);
+                        db.prepare('UPDATE symbol_refs SET callee_id = NULL WHERE callee_id IN (SELECT id FROM symbols WHERE file_id = ?)').run(existingRow.id);
+                        db.prepare('UPDATE type_refs SET type_id = NULL WHERE type_id IN (SELECT id FROM symbols WHERE file_id = ?)').run(existingRow.id);
+                        db.prepare('UPDATE symbol_relationships SET target_symbol_id = NULL WHERE target_symbol_id IN (SELECT id FROM symbols WHERE file_id = ?)').run(existingRow.id);
+                        db.prepare('DELETE FROM symbols_fts WHERE rowid IN (SELECT id FROM symbols WHERE file_id = ?)').run(existingRow.id);
+                    }
+                    db.prepare('DELETE FROM files WHERE path = ? AND branch = ?').run(filePath, branch);
+                    processFile(db, pool, filePath, language, branch);
+                }
+            }
+        })();
+        // In update mode, context.files = only the changed/enriched files
+        context.files = enrichedFiles;
+    }
+}
+// ─── File processing (extracted from IndexBuilder.processFile) ────────────────
+/**
+ * Parse one file, extract symbols/imports/callRefs/typeRefs/relationships/
+ * routes/annotations, and insert into the DB.
+ */
+export function processFile(db, pool, filePath, language, branch) {
+    // P3: fast-path — check file size via stat before reading+hashing.
+    const existing = db.prepare('SELECT id, last_hash, size_bytes FROM files WHERE path = ? AND branch = ?').get(filePath, branch);
+    if (existing) {
+        try {
+            const stat = fs.statSync(filePath);
+            if (stat.size === existing.size_bytes && existing.last_hash !== null) {
+                // Size matches — read and hash to confirm.
+                let source;
+                try {
+                    source = fs.readFileSync(filePath, 'utf8');
+                }
+                catch {
+                    return;
+                }
+                const hash = crypto.createHash('sha256').update(source).digest('hex');
+                if (existing.last_hash === hash)
+                    return;
+                processFileWithSource(db, pool, filePath, language, branch, source, hash, existing);
+                return;
+            }
+        }
+        catch {
+            return;
+        }
+    }
+    let source;
+    try {
+        source = fs.readFileSync(filePath, 'utf8');
+    }
+    catch {
+        return;
+    }
+    const hash = crypto.createHash('sha256').update(source).digest('hex');
+    if (existing?.last_hash === hash)
+        return;
+    processFileWithSource(db, pool, filePath, language, branch, source, hash, existing);
+}
+/** Core file processing after source has been read and hashed. */
+function processFileWithSource(db, pool, filePath, language, branch, source, hash, existing) {
+    const sizeBytes = Buffer.byteLength(source, 'utf8');
+    // Upsert the file row
+    let fileId;
+    if (existing) {
+        db.prepare(`UPDATE files SET language = ?, size_bytes = ?, last_hash = ?, source = ?, indexed_at = unixepoch()
+        WHERE id = ?`).run(language, sizeBytes, hash, source, existing.id);
+        fileId = existing.id;
+        // Remove stale symbols / imports / external deps (also clean up FTS5 index)
+        db.prepare('DELETE FROM symbols_fts WHERE rowid IN (SELECT id FROM symbols WHERE file_id = ?)').run(fileId);
+        db.prepare('DELETE FROM symbol_relationships WHERE file_id = ?').run(fileId);
+        db.prepare('DELETE FROM type_refs WHERE file_id = ?').run(fileId);
+        // NULL out cross-file FK references that point to symbols in this file
+        db.prepare('UPDATE symbol_refs SET callee_id = NULL WHERE callee_id IN (SELECT id FROM symbols WHERE file_id = ?)').run(fileId);
+        db.prepare('UPDATE type_refs SET type_id = NULL WHERE type_id IN (SELECT id FROM symbols WHERE file_id = ?)').run(fileId);
+        db.prepare('UPDATE symbol_relationships SET target_symbol_id = NULL WHERE target_symbol_id IN (SELECT id FROM symbols WHERE file_id = ?)').run(fileId);
+        db.prepare('DELETE FROM symbols WHERE file_id = ?').run(fileId);
+        db.prepare('DELETE FROM file_imports WHERE file_id = ?').run(fileId);
+        db.prepare('DELETE FROM external_deps WHERE file_id = ?').run(fileId);
+        db.prepare('DELETE FROM api_routes WHERE file_id = ?').run(fileId);
+        db.prepare('DELETE FROM annotations WHERE file_id = ?').run(fileId);
+    }
+    else {
+        const info = db
+            .prepare(`INSERT INTO files (path, branch, language, size_bytes, last_hash, source)
+         VALUES (?, ?, ?, ?, ?, ?)`)
+            .run(filePath, branch, language, sizeBytes, hash, source);
+        fileId = Number(info.lastInsertRowid);
+    }
+    // Parse the source
+    const tree = pool.parse(language, source);
+    if (!tree)
+        return;
+    const extractor = EXTRACTORS[language];
+    if (!extractor)
+        return;
+    const result = extractor.extract(tree, source, filePath);
+    // Insert symbols and keep FTS5 index in sync
+    const insertSymbol = db.prepare(`INSERT INTO symbols (file_id, name, kind, start_line, end_line, signature, doc_comment)
+     VALUES (?, ?, ?, ?, ?, ?, ?)`);
+    const insertFts = db.prepare('INSERT INTO symbols_fts(rowid, name, signature, kind) VALUES (?, ?, ?, ?)');
+    const symbolIdMap = new Map();
+    for (const sym of result.symbols) {
+        const info = insertSymbol.run(fileId, sym.name, sym.kind, sym.startLine, sym.endLine, sym.signature ?? null, sym.docComment ?? null);
+        const symId = Number(info.lastInsertRowid);
+        symbolIdMap.set(sym.name, symId);
+        insertFts.run(symId, sym.name, buildStructuralEmbeddingText({
+            name: sym.name,
+            signature: sym.signature ?? null,
+        }), sym.kind);
+    }
+    // Insert API routes
+    const insertRoute = db.prepare(`INSERT INTO api_routes (file_id, method, path, handler_id, handler_name, framework, line, middleware)
+     VALUES (?, ?, ?, ?, ?, ?, ?, ?)`);
+    for (const route of result.routes) {
+        insertRoute.run(fileId, route.method, route.path, symbolIdMap.get(route.handler) ?? null, route.handler, route.framework, route.line, route.middleware ? JSON.stringify(route.middleware) : null);
+    }
+    // Insert raw imports
+    const insertImport = db.prepare('INSERT INTO file_imports (file_id, raw_import) VALUES (?, ?)');
+    for (const imp of result.imports) {
+        insertImport.run(fileId, imp.source);
+    }
+    // Insert call refs
+    const insertCallRef = db.prepare(`INSERT INTO symbol_refs (caller_id, file_id, callee_name, call_line, call_character, call_kind)
+     VALUES (?, ?, ?, ?, ?, ?)`);
+    for (const ref of result.callRefs) {
+        const callerId = symbolIdMap.get(ref.callerSymbol);
+        if (callerId !== undefined) {
+            insertCallRef.run(callerId, fileId, ref.calleeRaw, ref.line, ref.character ?? null, ref.callKind ?? 'direct');
+        }
+    }
+    // Insert relationships
+    const insertRelationship = db.prepare(`INSERT INTO symbol_relationships (file_id, source_symbol_id, target_symbol_name, relationship_type, line, character)
+     VALUES (?, ?, ?, ?, ?, ?)`);
+    for (const rel of result.relationships) {
+        const sourceId = symbolIdMap.get(rel.fromSymbol) ?? null;
+        insertRelationship.run(fileId, sourceId, rel.toSymbol, rel.kind, rel.line, rel.character ?? null);
+    }
+    // Insert type refs
+    const insertTypeRef = db.prepare(`INSERT INTO type_refs (file_id, symbol_id, type_name, type_name_bare, ref_kind, ref_line, ref_character)
+     VALUES (?, ?, ?, ?, ?, ?, ?)`);
+    for (const ref of result.typeRefs) {
+        const symId = symbolIdMap.get(ref.enclosingSymbol) ?? null;
+        insertTypeRef.run(fileId, symId, ref.typeRaw, normalizeTypeName(ref.typeRaw), ref.refKind, ref.line, ref.character ?? null);
+    }
+}
+// ─── Checkpoint helpers ───────────────────────────────────────────────────────
+function loadBuildCheckpoint(db, branch, rootDir, totalFiles) {
+    const raw = getLoreMeta(db, LORE_META_INDEX_CHECKPOINT);
+    if (!raw)
+        return 0;
+    try {
+        const parsed = JSON.parse(raw);
+        if (parsed.branch !== branch || parsed.rootDir !== rootDir)
+            return 0;
+        const nextFileIndex = parsed.nextFileIndex ?? 0;
+        return Math.max(0, Math.min(totalFiles, nextFileIndex));
+    }
+    catch {
+        return 0;
+    }
+}
+function saveBuildCheckpoint(db, branch, rootDir, nextFileIndex, totalFiles) {
+    const checkpoint = {
+        branch,
+        rootDir,
+        totalFiles,
+        nextFileIndex,
+        updatedAt: Math.floor(Date.now() / 1000),
+    };
+    setLoreMeta(db, LORE_META_INDEX_CHECKPOINT, JSON.stringify(checkpoint));
+}
+//# sourceMappingURL=source-index.js.map