@mcp-graph-workflow/mcp-graph 3.0.0

package/dist/core/search/tfidf.js

@@ -0,0 +1,67 @@
+/**
+ * Lightweight TF-IDF implementation for two-stage search reranking.
+ * No external dependencies — pure TypeScript.
+ */
+import { tokenize } from "./tokenizer.js";
+export class TfIdfIndex {
+    docs = [];
+    docFreq = new Map();
+    /**
+     * Add a document to the index.
+     */
+    addDocument(id, text) {
+        const tokens = tokenize(text);
+        const termFreq = new Map();
+        for (const token of tokens) {
+            termFreq.set(token, (termFreq.get(token) ?? 0) + 1);
+        }
+        // Update document frequency
+        for (const term of termFreq.keys()) {
+            this.docFreq.set(term, (this.docFreq.get(term) ?? 0) + 1);
+        }
+        this.docs.push({ id, tokens, termFreq });
+    }
+    /**
+     * Compute TF-IDF score for a query against all documents.
+     * Returns sorted results (highest score first).
+     */
+    search(query, limit = 20) {
+        const queryTokens = tokenize(query);
+        if (queryTokens.length === 0)
+            return [];
+        const n = this.docs.length;
+        if (n === 0)
+            return [];
+        const results = [];
+        for (const doc of this.docs) {
+            let score = 0;
+            const docLen = doc.tokens.length || 1;
+            for (const qt of queryTokens) {
+                const tf = (doc.termFreq.get(qt) ?? 0) / docLen;
+                const df = this.docFreq.get(qt) ?? 0;
+                if (df === 0)
+                    continue;
+                // IDF with smoothing: log(1 + N/df)
+                const idf = Math.log(1 + n / df);
+                score += tf * idf;
+            }
+            if (score > 0) {
+                results.push({ id: doc.id, score });
+            }
+        }
+        results.sort((a, b) => b.score - a.score);
+        return results.slice(0, limit);
+    }
+}
+/**
+ * Build a TF-IDF index from search result nodes and rerank them.
+ * Two-stage: FTS5 candidates → TF-IDF reranking.
+ */
+export function rerankWithTfIdf(candidates, query, limit = 20) {
+    const index = new TfIdfIndex();
+    for (const c of candidates) {
+        index.addDocument(c.id, c.text);
+    }
+    return index.search(query, limit);
+}
+//# sourceMappingURL=tfidf.js.map

package/dist/core/search/tfidf.js.map

@@ -0,0 +1 @@
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package/dist/core/search/tokenizer.d.ts

@@ -0,0 +1,9 @@
+/**
+ * Lightweight tokenizer for TF-IDF computation.
+ * Handles Portuguese and English text, strips accents and punctuation.
+ */
+/**
+ * Normalize and tokenize text into lowercase terms, stripping accents.
+ */
+export declare function tokenize(text: string): string[];
+//# sourceMappingURL=tokenizer.d.ts.map

package/dist/core/search/tokenizer.d.ts.map

@@ -0,0 +1 @@
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package/dist/core/search/tokenizer.js

@@ -0,0 +1,37 @@
+/**
+ * Lightweight tokenizer for TF-IDF computation.
+ * Handles Portuguese and English text, strips accents and punctuation.
+ */
+const STOPWORDS = new Set([
+    // Portuguese
+    "a", "o", "e", "é", "de", "do", "da", "dos", "das", "em", "no", "na",
+    "nos", "nas", "um", "uma", "uns", "umas", "por", "para", "com", "sem",
+    "que", "se", "ou", "ao", "aos", "como", "mais", "mas", "este", "esta",
+    "esse", "essa", "não", "nao", "ser", "ter", "foi", "são", "sao",
+    // English
+    "the", "a", "an", "is", "are", "was", "were", "be", "been", "being",
+    "have", "has", "had", "do", "does", "did", "will", "would", "could",
+    "should", "may", "might", "can", "shall", "of", "in", "to", "for",
+    "with", "on", "at", "by", "from", "as", "into", "through", "and",
+    "but", "or", "not", "no", "if", "it", "its", "this", "that", "they",
+    "we", "he", "she", "you", "i", "me", "my", "your", "his", "her",
+    "our", "their", "what", "which", "who", "when", "where", "how",
+]);
+/**
+ * Normalize and tokenize text into lowercase terms, stripping accents.
+ */
+export function tokenize(text) {
+    const normalized = text
+        .normalize("NFD")
+        .replace(/[\u0300-\u036f]/g, "") // strip accents
+        .toLowerCase()
+        .replace(/[^a-z0-9_\s]/g, " ") // keep only alphanumeric + underscore
+        .replace(/\s+/g, " ")
+        .trim();
+    if (!normalized)
+        return [];
+    return normalized
+        .split(" ")
+        .filter((t) => t.length >= 2 && !STOPWORDS.has(t));
+}
+//# sourceMappingURL=tokenizer.js.map

package/dist/core/search/tokenizer.js.map

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package/dist/core/store/knowledge-store.d.ts

@@ -0,0 +1,72 @@
+/**
+ * Knowledge Store — CRUD, FTS search, and dedup for knowledge_documents.
+ * Follows DocsCacheStore pattern. All sources (upload, serena, code_context,
+ * docs, web_capture) stored in a single table with source_type discriminator.
+ */
+import type Database from "better-sqlite3";
+import type { KnowledgeDocument, KnowledgeSourceType } from "../../schemas/knowledge.schema.js";
+export interface InsertKnowledgeDoc {
+    sourceType: KnowledgeSourceType;
+    sourceId: string;
+    title: string;
+    content: string;
+    chunkIndex?: number;
+    metadata?: Record<string, unknown>;
+}
+/**
+ * Compute SHA-256 hash of content for deduplication.
+ */
+export declare function contentHash(content: string): string;
+export declare class KnowledgeStore {
+    private db;
+    constructor(db: Database.Database);
+    /**
+     * Insert a knowledge document. Deduplicates by content_hash.
+     * Returns the existing doc if content already exists, or the new doc.
+     */
+    insert(doc: InsertKnowledgeDoc): KnowledgeDocument;
+    /**
+     * Insert multiple chunks from a single source document.
+     * Returns all inserted (or deduplicated) docs.
+     */
+    insertChunks(docs: InsertKnowledgeDoc[]): KnowledgeDocument[];
+    /**
+     * Get a knowledge document by ID.
+     */
+    getById(id: string): KnowledgeDocument | null;
+    /**
+     * List knowledge documents, optionally filtered by source type.
+     */
+    list(options?: {
+        sourceType?: KnowledgeSourceType;
+        limit?: number;
+        offset?: number;
+    }): KnowledgeDocument[];
+    /**
+     * Search knowledge documents via FTS5 with BM25 ranking.
+     */
+    search(query: string, limit?: number): Array<KnowledgeDocument & {
+        score: number;
+    }>;
+    /**
+     * Delete a knowledge document by ID.
+     */
+    delete(id: string): boolean;
+    /**
+     * Delete all documents from a specific source.
+     */
+    deleteBySource(sourceType: KnowledgeSourceType, sourceId: string): number;
+    /**
+     * Count documents, optionally filtered by source type.
+     */
+    count(sourceType?: KnowledgeSourceType): number;
+    /**
+     * Check if content already exists (by hash).
+     */
+    existsByHash(hash: string): boolean;
+    /**
+     * Get all documents for a given source ID (all chunks).
+     */
+    getBySourceId(sourceId: string): KnowledgeDocument[];
+}
+//# sourceMappingURL=knowledge-store.d.ts.map

package/dist/core/store/knowledge-store.d.ts.map

@@ -0,0 +1 @@
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package/dist/core/store/knowledge-store.js

@@ -0,0 +1,166 @@
+/**
+ * Knowledge Store — CRUD, FTS search, and dedup for knowledge_documents.
+ * Follows DocsCacheStore pattern. All sources (upload, serena, code_context,
+ * docs, web_capture) stored in a single table with source_type discriminator.
+ */
+import { createHash } from "node:crypto";
+import { generateId } from "../utils/id.js";
+import { now } from "../utils/time.js";
+import { logger } from "../utils/logger.js";
+function rowToDoc(row) {
+    return {
+        id: row.id,
+        sourceType: row.source_type,
+        sourceId: row.source_id,
+        title: row.title,
+        content: row.content,
+        contentHash: row.content_hash,
+        chunkIndex: row.chunk_index,
+        metadata: row.metadata ? JSON.parse(row.metadata) : undefined,
+        createdAt: row.created_at,
+        updatedAt: row.updated_at,
+    };
+}
+/**
+ * Compute SHA-256 hash of content for deduplication.
+ */
+export function contentHash(content) {
+    return createHash("sha256").update(content).digest("hex");
+}
+export class KnowledgeStore {
+    db;
+    constructor(db) {
+        this.db = db;
+    }
+    /**
+     * Insert a knowledge document. Deduplicates by content_hash.
+     * Returns the existing doc if content already exists, or the new doc.
+     */
+    insert(doc) {
+        const hash = contentHash(doc.content);
+        // Check for duplicate content
+        const existing = this.db
+            .prepare("SELECT * FROM knowledge_documents WHERE content_hash = ? AND source_id = ?")
+            .get(hash, doc.sourceId);
+        if (existing) {
+            logger.debug("Knowledge doc dedup hit", { hash: hash.slice(0, 8), sourceId: doc.sourceId });
+            return rowToDoc(existing);
+        }
+        const id = generateId("kdoc");
+        const timestamp = now();
+        this.db.prepare(`INSERT INTO knowledge_documents
+        (id, source_type, source_id, title, content, content_hash, chunk_index, metadata, created_at, updated_at)
+       VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)`).run(id, doc.sourceType, doc.sourceId, doc.title, doc.content, hash, doc.chunkIndex ?? 0, doc.metadata ? JSON.stringify(doc.metadata) : null, timestamp, timestamp);
+        logger.info("Knowledge doc inserted", { id, sourceType: doc.sourceType, title: doc.title });
+        return this.getById(id);
+    }
+    /**
+     * Insert multiple chunks from a single source document.
+     * Returns all inserted (or deduplicated) docs.
+     */
+    insertChunks(docs) {
+        const results = [];
+        this.db.transaction(() => {
+            for (const doc of docs) {
+                results.push(this.insert(doc));
+            }
+        })();
+        return results;
+    }
+    /**
+     * Get a knowledge document by ID.
+     */
+    getById(id) {
+        const row = this.db
+            .prepare("SELECT * FROM knowledge_documents WHERE id = ?")
+            .get(id);
+        return row ? rowToDoc(row) : null;
+    }
+    /**
+     * List knowledge documents, optionally filtered by source type.
+     */
+    list(options) {
+        const limit = options?.limit ?? 100;
+        const offset = options?.offset ?? 0;
+        if (options?.sourceType) {
+            const rows = this.db
+                .prepare("SELECT * FROM knowledge_documents WHERE source_type = ? ORDER BY created_at DESC LIMIT ? OFFSET ?")
+                .all(options.sourceType, limit, offset);
+            return rows.map(rowToDoc);
+        }
+        const rows = this.db
+            .prepare("SELECT * FROM knowledge_documents ORDER BY created_at DESC LIMIT ? OFFSET ?")
+            .all(limit, offset);
+        return rows.map(rowToDoc);
+    }
+    /**
+     * Search knowledge documents via FTS5 with BM25 ranking.
+     */
+    search(query, limit = 20) {
+        const rows = this.db
+            .prepare(`SELECT kd.*, bm25(knowledge_fts) AS score
+         FROM knowledge_fts fts
+         JOIN knowledge_documents kd ON kd.rowid = fts.rowid
+         WHERE knowledge_fts MATCH ?
+         ORDER BY score
+         LIMIT ?`)
+            .all(query, limit);
+        return rows.map((row) => ({
+            ...rowToDoc(row),
+            score: row.score,
+        }));
+    }
+    /**
+     * Delete a knowledge document by ID.
+     */
+    delete(id) {
+        const result = this.db
+            .prepare("DELETE FROM knowledge_documents WHERE id = ?")
+            .run(id);
+        return result.changes > 0;
+    }
+    /**
+     * Delete all documents from a specific source.
+     */
+    deleteBySource(sourceType, sourceId) {
+        const result = this.db
+            .prepare("DELETE FROM knowledge_documents WHERE source_type = ? AND source_id = ?")
+            .run(sourceType, sourceId);
+        logger.info("Knowledge docs deleted by source", { sourceType, sourceId, count: result.changes });
+        return result.changes;
+    }
+    /**
+     * Count documents, optionally filtered by source type.
+     */
+    count(sourceType) {
+        if (sourceType) {
+            const row = this.db
+                .prepare("SELECT COUNT(*) as cnt FROM knowledge_documents WHERE source_type = ?")
+                .get(sourceType);
+            return row.cnt;
+        }
+        const row = this.db
+            .prepare("SELECT COUNT(*) as cnt FROM knowledge_documents")
+            .get();
+        return row.cnt;
+    }
+    /**
+     * Check if content already exists (by hash).
+     */
+    existsByHash(hash) {
+        const row = this.db
+            .prepare("SELECT 1 FROM knowledge_documents WHERE content_hash = ? LIMIT 1")
+            .get(hash);
+        return row !== undefined;
+    }
+    /**
+     * Get all documents for a given source ID (all chunks).
+     */
+    getBySourceId(sourceId) {
+        const rows = this.db
+            .prepare("SELECT * FROM knowledge_documents WHERE source_id = ? ORDER BY chunk_index")
+            .all(sourceId);
+        return rows.map(rowToDoc);
+    }
+}
+//# sourceMappingURL=knowledge-store.js.map

package/dist/core/store/knowledge-store.js.map

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package/dist/core/store/migrations.d.ts

@@ -0,0 +1,4 @@
+import type Database from "better-sqlite3";
+export declare function runMigrations(db: Database.Database): void;
+export declare function configureDb(db: Database.Database): void;
+//# sourceMappingURL=migrations.d.ts.map

package/dist/core/store/migrations.d.ts.map

@@ -0,0 +1 @@
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package/dist/core/store/migrations.js

@@ -0,0 +1,223 @@
+import { logger } from "../utils/logger.js";
+const migrations = [
+    {
+        version: 1,
+        description: "Initial schema — projects, nodes, edges, snapshots, import_history",
+        sql: `
+      CREATE TABLE IF NOT EXISTS projects (
+        id          TEXT PRIMARY KEY,
+        name        TEXT NOT NULL,
+        created_at  TEXT NOT NULL,
+        updated_at  TEXT NOT NULL
+      );
+
+      CREATE TABLE IF NOT EXISTS nodes (
+        id                  TEXT PRIMARY KEY,
+        project_id          TEXT NOT NULL REFERENCES projects(id),
+        type                TEXT NOT NULL,
+        title               TEXT NOT NULL,
+        description         TEXT,
+        status              TEXT NOT NULL DEFAULT 'backlog',
+        priority            INTEGER NOT NULL DEFAULT 3,
+        xp_size             TEXT,
+        estimate_minutes    INTEGER,
+        tags                TEXT, -- JSON array
+        parent_id           TEXT,
+        sprint              TEXT,
+        source_file         TEXT,
+        source_start_line   INTEGER,
+        source_end_line     INTEGER,
+        source_confidence   REAL,
+        acceptance_criteria TEXT, -- JSON array
+        blocked             INTEGER NOT NULL DEFAULT 0,
+        metadata            TEXT, -- JSON object
+        created_at          TEXT NOT NULL,
+        updated_at          TEXT NOT NULL
+      );
+
+      CREATE TABLE IF NOT EXISTS edges (
+        id            TEXT PRIMARY KEY,
+        project_id    TEXT NOT NULL REFERENCES projects(id),
+        from_node     TEXT NOT NULL REFERENCES nodes(id),
+        to_node       TEXT NOT NULL REFERENCES nodes(id),
+        relation_type TEXT NOT NULL,
+        weight        REAL,
+        reason        TEXT,
+        metadata      TEXT, -- JSON object
+        created_at    TEXT NOT NULL
+      );
+
+      CREATE TABLE IF NOT EXISTS snapshots (
+        id          INTEGER PRIMARY KEY AUTOINCREMENT,
+        project_id  TEXT NOT NULL REFERENCES projects(id),
+        data        TEXT NOT NULL, -- JSON dump of GraphDocument
+        created_at  TEXT NOT NULL
+      );
+
+      CREATE TABLE IF NOT EXISTS import_history (
+        id             INTEGER PRIMARY KEY AUTOINCREMENT,
+        project_id     TEXT NOT NULL REFERENCES projects(id),
+        source_file    TEXT NOT NULL,
+        nodes_created  INTEGER NOT NULL DEFAULT 0,
+        edges_created  INTEGER NOT NULL DEFAULT 0,
+        imported_at    TEXT NOT NULL
+      );
+
+      -- Indexes for common query patterns
+      CREATE INDEX IF NOT EXISTS idx_nodes_project     ON nodes(project_id);
+      CREATE INDEX IF NOT EXISTS idx_nodes_type        ON nodes(project_id, type);
+      CREATE INDEX IF NOT EXISTS idx_nodes_status      ON nodes(project_id, status);
+      CREATE INDEX IF NOT EXISTS idx_nodes_parent      ON nodes(parent_id);
+      CREATE INDEX IF NOT EXISTS idx_edges_project     ON edges(project_id);
+      CREATE INDEX IF NOT EXISTS idx_edges_from        ON edges(from_node);
+      CREATE INDEX IF NOT EXISTS idx_edges_to          ON edges(to_node);
+      CREATE INDEX IF NOT EXISTS idx_snapshots_project ON snapshots(project_id);
+      CREATE INDEX IF NOT EXISTS idx_imports_project   ON import_history(project_id);
+    `,
+    },
+    {
+        version: 2,
+        description: "FTS5 full-text search index on nodes",
+        sql: `
+      CREATE VIRTUAL TABLE IF NOT EXISTS nodes_fts USING fts5(
+        title, description, tags,
+        content='nodes', content_rowid='rowid'
+      );
+
+      -- Populate FTS from existing nodes
+      INSERT INTO nodes_fts(rowid, title, description, tags)
+        SELECT rowid, title, COALESCE(description, ''), COALESCE(tags, '')
+        FROM nodes;
+
+      -- Sync triggers: keep FTS in sync with nodes table
+      CREATE TRIGGER IF NOT EXISTS nodes_fts_insert AFTER INSERT ON nodes BEGIN
+        INSERT INTO nodes_fts(rowid, title, description, tags)
+          VALUES (NEW.rowid, NEW.title, COALESCE(NEW.description, ''), COALESCE(NEW.tags, ''));
+      END;
+
+      CREATE TRIGGER IF NOT EXISTS nodes_fts_delete AFTER DELETE ON nodes BEGIN
+        INSERT INTO nodes_fts(nodes_fts, rowid, title, description, tags)
+          VALUES ('delete', OLD.rowid, OLD.title, COALESCE(OLD.description, ''), COALESCE(OLD.tags, ''));
+      END;
+
+      CREATE TRIGGER IF NOT EXISTS nodes_fts_update AFTER UPDATE ON nodes BEGIN
+        INSERT INTO nodes_fts(nodes_fts, rowid, title, description, tags)
+          VALUES ('delete', OLD.rowid, OLD.title, COALESCE(OLD.description, ''), COALESCE(OLD.tags, ''));
+        INSERT INTO nodes_fts(rowid, title, description, tags)
+          VALUES (NEW.rowid, NEW.title, COALESCE(NEW.description, ''), COALESCE(NEW.tags, ''));
+      END;
+    `,
+    },
+    {
+        version: 3,
+        description: "Docs cache table with FTS5 index for Context7 documentation",
+        sql: `
+      CREATE TABLE IF NOT EXISTS docs_cache (
+        id           INTEGER PRIMARY KEY AUTOINCREMENT,
+        lib_id       TEXT NOT NULL,
+        lib_name     TEXT NOT NULL,
+        version      TEXT,
+        content      TEXT NOT NULL,
+        fetched_at   TEXT NOT NULL,
+        UNIQUE(lib_id)
+      );
+
+      CREATE VIRTUAL TABLE IF NOT EXISTS docs_fts USING fts5(
+        lib_name, content,
+        content='docs_cache', content_rowid='id'
+      );
+
+      -- Sync triggers: keep FTS in sync with docs_cache table
+      CREATE TRIGGER IF NOT EXISTS docs_fts_insert AFTER INSERT ON docs_cache BEGIN
+        INSERT INTO docs_fts(rowid, lib_name, content)
+          VALUES (NEW.id, NEW.lib_name, NEW.content);
+      END;
+
+      CREATE TRIGGER IF NOT EXISTS docs_fts_delete AFTER DELETE ON docs_cache BEGIN
+        INSERT INTO docs_fts(docs_fts, rowid, lib_name, content)
+          VALUES ('delete', OLD.id, OLD.lib_name, OLD.content);
+      END;
+
+      CREATE TRIGGER IF NOT EXISTS docs_fts_update AFTER UPDATE ON docs_cache BEGIN
+        INSERT INTO docs_fts(docs_fts, rowid, lib_name, content)
+          VALUES ('delete', OLD.id, OLD.lib_name, OLD.content);
+        INSERT INTO docs_fts(rowid, lib_name, content)
+          VALUES (NEW.id, NEW.lib_name, NEW.content);
+      END;
+    `,
+    },
+    {
+        version: 4,
+        description: "Knowledge documents table with FTS5 index for unified knowledge store",
+        sql: `
+      CREATE TABLE IF NOT EXISTS knowledge_documents (
+        id            TEXT PRIMARY KEY,
+        source_type   TEXT NOT NULL,
+        source_id     TEXT NOT NULL,
+        title         TEXT NOT NULL,
+        content       TEXT NOT NULL,
+        content_hash  TEXT NOT NULL,
+        chunk_index   INTEGER NOT NULL DEFAULT 0,
+        metadata      TEXT, -- JSON object
+        created_at    TEXT NOT NULL,
+        updated_at    TEXT NOT NULL
+      );
+
+      CREATE INDEX IF NOT EXISTS idx_knowledge_source_type ON knowledge_documents(source_type);
+      CREATE INDEX IF NOT EXISTS idx_knowledge_source_id ON knowledge_documents(source_id);
+      CREATE INDEX IF NOT EXISTS idx_knowledge_content_hash ON knowledge_documents(content_hash);
+
+      CREATE VIRTUAL TABLE IF NOT EXISTS knowledge_fts USING fts5(
+        title, content,
+        content='knowledge_documents', content_rowid='rowid'
+      );
+
+      -- Sync triggers: keep FTS in sync with knowledge_documents table
+      CREATE TRIGGER IF NOT EXISTS knowledge_fts_insert AFTER INSERT ON knowledge_documents BEGIN
+        INSERT INTO knowledge_fts(rowid, title, content)
+          VALUES (NEW.rowid, NEW.title, NEW.content);
+      END;
+
+      CREATE TRIGGER IF NOT EXISTS knowledge_fts_delete AFTER DELETE ON knowledge_documents BEGIN
+        INSERT INTO knowledge_fts(knowledge_fts, rowid, title, content)
+          VALUES ('delete', OLD.rowid, OLD.title, OLD.content);
+      END;
+
+      CREATE TRIGGER IF NOT EXISTS knowledge_fts_update AFTER UPDATE ON knowledge_documents BEGIN
+        INSERT INTO knowledge_fts(knowledge_fts, rowid, title, content)
+          VALUES ('delete', OLD.rowid, OLD.title, OLD.content);
+        INSERT INTO knowledge_fts(rowid, title, content)
+          VALUES (NEW.rowid, NEW.title, NEW.content);
+      END;
+    `,
+    },
+];
+export function runMigrations(db) {
+    // Create migrations tracking table
+    db.exec(`
+    CREATE TABLE IF NOT EXISTS _migrations (
+      version     INTEGER PRIMARY KEY,
+      description TEXT NOT NULL,
+      applied_at  TEXT NOT NULL
+    );
+  `);
+    const applied = new Set(db
+        .prepare("SELECT version FROM _migrations")
+        .all()
+        .map((row) => row.version));
+    for (const migration of migrations) {
+        if (applied.has(migration.version))
+            continue;
+        logger.info("migration:run", { version: migration.version, description: migration.description });
+        db.transaction(() => {
+            db.exec(migration.sql);
+            db.prepare("INSERT INTO _migrations (version, description, applied_at) VALUES (?, ?, ?)").run(migration.version, migration.description, new Date().toISOString());
+        })();
+        logger.info("migration:ok", { version: migration.version });
+    }
+}
+export function configureDb(db) {
+    db.pragma("journal_mode = WAL");
+    db.pragma("foreign_keys = ON");
+}
+//# sourceMappingURL=migrations.js.map

package/dist/core/store/migrations.js.map

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