@mcp-graph-workflow/mcp-graph 5.2.0 → 5.4.0

package/dist/core/skills/skill-store.js

@@ -0,0 +1,109 @@
+/**
+ * Skill Store — persistence layer for skill preferences and custom skills.
+ * Uses SQLite tables created by migration v9.
+ */
+import { generateId } from "../utils/id.js";
+import { now } from "../utils/time.js";
+import { logger } from "../utils/logger.js";
+import { ValidationError } from "../utils/errors.js";
+// ── Mapping helpers ──────────────────────────────────
+function rowToCustomSkill(row) {
+    return {
+        id: row.id,
+        projectId: row.project_id,
+        name: row.name,
+        description: row.description,
+        category: row.category,
+        phases: JSON.parse(row.phases),
+        instructions: row.instructions,
+        createdAt: row.created_at,
+        updatedAt: row.updated_at,
+    };
+}
+// ── Preferences ──────────────────────────────────────
+export function setSkillEnabled(db, projectId, skillName, enabled) {
+    logger.debug("skill-store:setEnabled", { projectId, skillName, enabled });
+    db.prepare(`
+    INSERT INTO skill_preferences (project_id, skill_name, enabled, updated_at)
+    VALUES (?, ?, ?, ?)
+    ON CONFLICT(project_id, skill_name) DO UPDATE SET enabled = excluded.enabled, updated_at = excluded.updated_at
+  `).run(projectId, skillName, enabled ? 1 : 0, now());
+}
+export function getSkillPreferences(db, projectId) {
+    const rows = db.prepare("SELECT skill_name, enabled FROM skill_preferences WHERE project_id = ?").all(projectId);
+    const map = new Map();
+    for (const row of rows) {
+        map.set(row.skill_name, row.enabled === 1);
+    }
+    return map;
+}
+// ── Custom Skills CRUD ───────────────────────────────
+export function createCustomSkill(db, projectId, data) {
+    const id = generateId("skill");
+    const timestamp = now();
+    logger.info("skill-store:create", { projectId, name: data.name });
+    try {
+        db.prepare(`
+      INSERT INTO custom_skills (id, project_id, name, description, category, phases, instructions, created_at, updated_at)
+      VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)
+    `).run(id, projectId, data.name, data.description, data.category ?? "know-me", JSON.stringify(data.phases), data.instructions, timestamp, timestamp);
+    }
+    catch (err) {
+        if (err instanceof Error && err.message.includes("UNIQUE constraint")) {
+            throw new ValidationError(`Custom skill '${data.name}' already exists in this project`, []);
+        }
+        throw err;
+    }
+    return {
+        id,
+        projectId,
+        name: data.name,
+        description: data.description,
+        category: data.category ?? "know-me",
+        phases: data.phases,
+        instructions: data.instructions,
+        createdAt: timestamp,
+        updatedAt: timestamp,
+    };
+}
+export function updateCustomSkill(db, projectId, id, data) {
+    const existing = db.prepare("SELECT * FROM custom_skills WHERE id = ? AND project_id = ?").get(id, projectId);
+    if (!existing) {
+        throw new ValidationError(`Custom skill not found: ${id}`, []);
+    }
+    const timestamp = now();
+    const updated = {
+        name: data.name ?? existing.name,
+        description: data.description ?? existing.description,
+        category: data.category ?? existing.category,
+        phases: data.phases ? JSON.stringify(data.phases) : existing.phases,
+        instructions: data.instructions ?? existing.instructions,
+    };
+    logger.info("skill-store:update", { projectId, id });
+    db.prepare(`
+    UPDATE custom_skills
+    SET name = ?, description = ?, category = ?, phases = ?, instructions = ?, updated_at = ?
+    WHERE id = ? AND project_id = ?
+  `).run(updated.name, updated.description, updated.category, updated.phases, updated.instructions, timestamp, id, projectId);
+    return rowToCustomSkill({
+        ...existing,
+        ...updated,
+        updated_at: timestamp,
+    });
+}
+export function deleteCustomSkill(db, projectId, id) {
+    logger.info("skill-store:delete", { projectId, id });
+    const result = db.prepare("DELETE FROM custom_skills WHERE id = ? AND project_id = ?").run(id, projectId);
+    if (result.changes === 0) {
+        throw new ValidationError(`Custom skill not found: ${id}`, []);
+    }
+}
+export function getCustomSkills(db, projectId) {
+    const rows = db.prepare("SELECT * FROM custom_skills WHERE project_id = ? ORDER BY created_at").all(projectId);
+    return rows.map(rowToCustomSkill);
+}
+export function getCustomSkillByName(db, projectId, name) {
+    const row = db.prepare("SELECT * FROM custom_skills WHERE project_id = ? AND name = ?").get(projectId, name);
+    return row ? rowToCustomSkill(row) : undefined;
+}
+//# sourceMappingURL=skill-store.js.map

package/dist/core/skills/skill-store.js.map

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

@@ -1,6 +1,6 @@
 /**
  * Knowledge Store — CRUD, FTS search, and dedup for knowledge_documents.
- * Follows DocsCacheStore pattern. All sources (upload, serena, code_context,
+ * Follows DocsCacheStore pattern. All sources (upload, memory, code_context,
  * docs, web_capture) stored in a single table with source_type discriminator.
  */
 import type Database from "better-sqlite3";

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

@@ -1,6 +1,6 @@
 /**
  * Knowledge Store — CRUD, FTS search, and dedup for knowledge_documents.
- * Follows DocsCacheStore pattern. All sources (upload, serena, code_context,
+ * Follows DocsCacheStore pattern. All sources (upload, memory, code_context,
  * docs, web_capture) stored in a single table with source_type discriminator.
  */
 import { createHash } from "node:crypto";

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

@@ -1 +1 @@
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+{"version":3,"file":"migrations.d.ts","sourceRoot":"","sources":["../../../src/core/store/migrations.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,QAAQ,MAAM,gBAAgB,CAAC;AAwV3C,wBAAgB,aAAa,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,GAAG,IAAI,CA6BzD;AAED,wBAAgB,WAAW,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,GAAG,IAAI,CAGvD"}

package/dist/core/store/migrations.js

@@ -204,6 +204,134 @@ const migrations = [
       );
     `,
     },
+    {
+        version: 6,
+        description: "Code Intelligence — symbols, relations, FTS5 index, index metadata",
+        sql: `
+      CREATE TABLE IF NOT EXISTS code_symbols (
+        id          TEXT PRIMARY KEY,
+        project_id  TEXT NOT NULL,
+        name        TEXT NOT NULL,
+        kind        TEXT NOT NULL,
+        file        TEXT NOT NULL,
+        start_line  INTEGER NOT NULL,
+        end_line    INTEGER NOT NULL,
+        exported    INTEGER NOT NULL DEFAULT 0,
+        module_path TEXT,
+        signature   TEXT,
+        metadata    TEXT,
+        indexed_at  TEXT NOT NULL
+      );
+
+      CREATE TABLE IF NOT EXISTS code_relations (
+        id          TEXT PRIMARY KEY,
+        project_id  TEXT NOT NULL,
+        from_symbol TEXT NOT NULL REFERENCES code_symbols(id),
+        to_symbol   TEXT NOT NULL REFERENCES code_symbols(id),
+        type        TEXT NOT NULL,
+        file        TEXT,
+        line        INTEGER,
+        metadata    TEXT,
+        indexed_at  TEXT NOT NULL
+      );
+
+      CREATE VIRTUAL TABLE IF NOT EXISTS code_symbols_fts USING fts5(
+        name, file, signature,
+        content='code_symbols', content_rowid='rowid'
+      );
+
+      -- FTS5 sync triggers
+      CREATE TRIGGER IF NOT EXISTS code_fts_insert AFTER INSERT ON code_symbols BEGIN
+        INSERT INTO code_symbols_fts(rowid, name, file, signature)
+          VALUES (NEW.rowid, NEW.name, NEW.file, COALESCE(NEW.signature, ''));
+      END;
+
+      CREATE TRIGGER IF NOT EXISTS code_fts_delete AFTER DELETE ON code_symbols BEGIN
+        INSERT INTO code_symbols_fts(code_symbols_fts, rowid, name, file, signature)
+          VALUES ('delete', OLD.rowid, OLD.name, OLD.file, COALESCE(OLD.signature, ''));
+      END;
+
+      CREATE TRIGGER IF NOT EXISTS code_fts_update AFTER UPDATE ON code_symbols BEGIN
+        INSERT INTO code_symbols_fts(code_symbols_fts, rowid, name, file, signature)
+          VALUES ('delete', OLD.rowid, OLD.name, OLD.file, COALESCE(OLD.signature, ''));
+        INSERT INTO code_symbols_fts(rowid, name, file, signature)
+          VALUES (NEW.rowid, NEW.name, NEW.file, COALESCE(NEW.signature, ''));
+      END;
+
+      CREATE TABLE IF NOT EXISTS code_index_meta (
+        project_id    TEXT PRIMARY KEY,
+        last_indexed  TEXT NOT NULL,
+        file_count    INTEGER DEFAULT 0,
+        symbol_count  INTEGER DEFAULT 0,
+        relation_count INTEGER DEFAULT 0,
+        git_hash      TEXT
+      );
+
+      CREATE INDEX IF NOT EXISTS idx_code_sym_project ON code_symbols(project_id);
+      CREATE INDEX IF NOT EXISTS idx_code_sym_name ON code_symbols(name);
+      CREATE INDEX IF NOT EXISTS idx_code_sym_file ON code_symbols(file);
+      CREATE INDEX IF NOT EXISTS idx_code_rel_from ON code_relations(from_symbol);
+      CREATE INDEX IF NOT EXISTS idx_code_rel_to ON code_relations(to_symbol);
+      CREATE INDEX IF NOT EXISTS idx_code_rel_type ON code_relations(type);
+    `,
+    },
+    {
+        version: 7,
+        description: "Tool token usage tracking for benchmark analytics",
+        sql: `
+      CREATE TABLE IF NOT EXISTS tool_token_usage (
+        id            INTEGER PRIMARY KEY AUTOINCREMENT,
+        project_id    TEXT NOT NULL REFERENCES projects(id),
+        tool_name     TEXT NOT NULL,
+        input_tokens  INTEGER NOT NULL DEFAULT 0,
+        output_tokens INTEGER NOT NULL DEFAULT 0,
+        called_at     TEXT NOT NULL
+      );
+
+      CREATE INDEX IF NOT EXISTS idx_ttu_project ON tool_token_usage(project_id);
+      CREATE INDEX IF NOT EXISTS idx_ttu_tool    ON tool_token_usage(tool_name);
+      CREATE INDEX IF NOT EXISTS idx_ttu_called  ON tool_token_usage(called_at);
+    `,
+    },
+    {
+        version: 8,
+        description: "Global mode — fs_path on projects, project_id on knowledge_documents",
+        sql: `
+      ALTER TABLE projects ADD COLUMN fs_path TEXT;
+      CREATE INDEX IF NOT EXISTS idx_projects_fs_path ON projects(fs_path);
+
+      ALTER TABLE knowledge_documents ADD COLUMN project_id TEXT;
+      CREATE INDEX IF NOT EXISTS idx_knowledge_project ON knowledge_documents(project_id);
+    `,
+    },
+    {
+        version: 9,
+        description: "Skill preferences and custom skills tables",
+        sql: `
+      CREATE TABLE IF NOT EXISTS skill_preferences (
+        project_id  TEXT NOT NULL,
+        skill_name  TEXT NOT NULL,
+        enabled     INTEGER NOT NULL DEFAULT 1,
+        updated_at  TEXT NOT NULL,
+        PRIMARY KEY (project_id, skill_name)
+      );
+
+      CREATE TABLE IF NOT EXISTS custom_skills (
+        id          TEXT PRIMARY KEY,
+        project_id  TEXT NOT NULL,
+        name        TEXT NOT NULL,
+        description TEXT NOT NULL,
+        category    TEXT NOT NULL DEFAULT 'know-me',
+        phases      TEXT NOT NULL,
+        instructions TEXT NOT NULL,
+        created_at  TEXT NOT NULL,
+        updated_at  TEXT NOT NULL,
+        UNIQUE(project_id, name)
+      );
+
+      CREATE INDEX IF NOT EXISTS idx_custom_skills_project ON custom_skills(project_id);
+    `,
+    },
 ];
 export function runMigrations(db) {
     // Create migrations tracking table

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

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package/dist/core/store/path-resolver.d.ts

@@ -0,0 +1,38 @@
+/**
+ * Centralized store path resolution for global/local/explicit modes.
+ *
+ * Resolution precedence:
+ * 1. --db flag / MCP_GRAPH_DB env (explicit)
+ * 2. {cwd}/workflow-graph/graph.db (local — backward compat)
+ * 3. ~/.mcp-graph/graph.db (global — default)
+ */
+export type StoreMode = "local" | "global" | "explicit";
+export interface ResolvedStore {
+    /** How the DB was resolved */
+    mode: StoreMode;
+    /** Absolute path to the graph.db file */
+    dbPath: string;
+    /** Project root directory (for code index, PRD, etc.) */
+    basePath: string;
+    /** Absolute path to memories directory */
+    memoriesPath: string;
+}
+export interface ResolveOptions {
+    /** Explicit DB path override (--db flag or MCP_GRAPH_DB env) */
+    explicitDb?: string;
+    /** Current working directory (defaults to process.cwd()) */
+    cwd?: string;
+    /** Global store directory (defaults to ~/.mcp-graph/) — injectable for tests */
+    globalDir?: string;
+    /** Project ID for global memories scoping */
+    projectId?: string;
+    /** If true, creates global DB when no DB exists anywhere. Default: false */
+    createGlobal?: boolean;
+}
+/**
+ * Resolve which store DB to use based on precedence rules.
+ *
+ * @throws {Error} If no DB can be found and createGlobal is false.
+ */
+export declare function resolveStorePath(options?: ResolveOptions): ResolvedStore;
+//# sourceMappingURL=path-resolver.d.ts.map

package/dist/core/store/path-resolver.d.ts.map

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

@@ -0,0 +1,92 @@
+/**
+ * Centralized store path resolution for global/local/explicit modes.
+ *
+ * Resolution precedence:
+ * 1. --db flag / MCP_GRAPH_DB env (explicit)
+ * 2. {cwd}/workflow-graph/graph.db (local — backward compat)
+ * 3. ~/.mcp-graph/graph.db (global — default)
+ */
+import path from "node:path";
+import { existsSync, mkdirSync } from "node:fs";
+import Database from "better-sqlite3";
+import { STORE_DIR, DB_FILE, GLOBAL_DB_DIR } from "../utils/constants.js";
+import { configureDb, runMigrations } from "./migrations.js";
+import { logger } from "../utils/logger.js";
+/**
+ * Resolve which store DB to use based on precedence rules.
+ *
+ * @throws {Error} If no DB can be found and createGlobal is false.
+ */
+export function resolveStorePath(options) {
+    const cwd = options?.cwd ?? process.cwd();
+    const globalDir = options?.globalDir ?? GLOBAL_DB_DIR;
+    const createGlobal = options?.createGlobal ?? false;
+    // 1. Explicit mode: --db flag or MCP_GRAPH_DB env
+    if (options?.explicitDb) {
+        logger.debug("path-resolver:explicit", { dbPath: options.explicitDb });
+        return {
+            mode: "explicit",
+            dbPath: options.explicitDb,
+            basePath: cwd,
+            memoriesPath: resolveMemoriesDir("explicit", cwd, globalDir, options.projectId),
+        };
+    }
+    // 2. Local mode: {cwd}/workflow-graph/graph.db
+    const localDbPath = path.join(cwd, STORE_DIR, DB_FILE);
+    if (existsSync(localDbPath)) {
+        logger.debug("path-resolver:local", { dbPath: localDbPath });
+        return {
+            mode: "local",
+            dbPath: localDbPath,
+            basePath: cwd,
+            memoriesPath: resolveMemoriesDir("local", cwd, globalDir, options?.projectId),
+        };
+    }
+    // 3. Global mode: ~/.mcp-graph/graph.db
+    const globalDbPath = path.join(globalDir, DB_FILE);
+    if (existsSync(globalDbPath)) {
+        logger.debug("path-resolver:global", { dbPath: globalDbPath });
+        return {
+            mode: "global",
+            dbPath: globalDbPath,
+            basePath: cwd,
+            memoriesPath: resolveMemoriesDir("global", cwd, globalDir, options?.projectId),
+        };
+    }
+    // 4. No DB found — create global if requested
+    if (createGlobal) {
+        logger.info("path-resolver:create-global", { globalDir });
+        mkdirSync(globalDir, { recursive: true });
+        const db = new Database(globalDbPath);
+        configureDb(db);
+        runMigrations(db);
+        db.close();
+        return {
+            mode: "global",
+            dbPath: globalDbPath,
+            basePath: cwd,
+            memoriesPath: resolveMemoriesDir("global", cwd, globalDir, options?.projectId),
+        };
+    }
+    throw new Error(`No graph database found. Checked:\n` +
+        `  local:  ${localDbPath}\n` +
+        `  global: ${globalDbPath}\n` +
+        `Run 'mcp-graph init' to create a local store, or 'mcp-graph init --global' for a global one.`);
+}
+/**
+ * Resolve the memories directory based on mode.
+ * - local: {cwd}/workflow-graph/memories/
+ * - global: {globalDir}/memories/{projectId}/
+ * - explicit: same as local (basePath)
+ */
+function resolveMemoriesDir(mode, basePath, globalDir, projectId) {
+    if (mode === "global" && projectId) {
+        return path.join(globalDir, "memories", projectId);
+    }
+    if (mode === "global") {
+        return path.join(globalDir, "memories");
+    }
+    // local or explicit
+    return path.join(basePath, STORE_DIR, "memories");
+}
+//# sourceMappingURL=path-resolver.js.map

package/dist/core/store/path-resolver.js.map

@@ -0,0 +1 @@
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package/dist/core/store/sqlite-store.d.ts

@@ -18,6 +18,12 @@ export declare class SqliteStore {
      * - If neither → create `workflow-graph/`
      */
     static open(basePath?: string): SqliteStore;
+    /**
+     * Open a store at an absolute DB file path.
+     * Creates the file and parent dirs if they don't exist.
+     * Useful for global mode where the DB is at ~/.mcp-graph/graph.db.
+     */
+    static openDb(dbPath: string): SqliteStore;
     /** Expose the raw database instance for extension modules (e.g. DocsCacheStore). */
     getDb(): Database.Database;
     close(): void;
@@ -29,6 +35,21 @@ export declare class SqliteStore {
     listProjects(): GraphProject[];
     /** Switch the active project. Throws if project ID does not exist. */
     activateProject(projectId: string): void;
+    /**
+     * Find a project by its filesystem path.
+     * Returns null if no project is registered at that path.
+     */
+    findProjectByPath(fsPath: string): GraphProject | null;
+    /**
+     * Register a project with a filesystem path.
+     * If a project already exists at that path, returns the existing one.
+     * Creates and activates a new project otherwise.
+     */
+    registerProject(name: string, fsPath: string): GraphProject;
+    /**
+     * Set or update the filesystem path for a project.
+     */
+    setProjectFsPath(projectId: string, fsPath: string): void;
     private ensureProject;
     insertNode(node: GraphNode): void;
     getNodeById(id: string): GraphNode | null;

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

@@ -1 +1 @@
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package/dist/core/store/sqlite-store.js

@@ -107,6 +107,18 @@ function rowToEdge(row) {
         edge.metadata = JSON.parse(row.metadata);
     return edge;
 }
+// ── Row → Domain mapping ─────────────────────────────────
+function rowToProject(row) {
+    const project = {
+        id: row.id,
+        name: row.name,
+        createdAt: row.created_at,
+        updatedAt: row.updated_at,
+    };
+    if (row.fs_path)
+        project.fsPath = row.fs_path;
+    return project;
+}
 // ── SqliteStore ──────────────────────────────────────────
 export class SqliteStore {
     db;
@@ -166,6 +178,27 @@ export class SqliteStore {
         logger.info(`Store opened${basePath === ":memory:" ? " (in-memory)" : ` at ${basePath}`}`);
         return store;
     }
+    /**
+     * Open a store at an absolute DB file path.
+     * Creates the file and parent dirs if they don't exist.
+     * Useful for global mode where the DB is at ~/.mcp-graph/graph.db.
+     */
+    static openDb(dbPath) {
+        const dir = path.dirname(dbPath);
+        mkdirSync(dir, { recursive: true });
+        const db = new Database(dbPath);
+        configureDb(db);
+        runMigrations(db);
+        const store = new SqliteStore(db);
+        // Auto-load project if one exists
+        const row = db
+            .prepare("SELECT id FROM projects LIMIT 1")
+            .get();
+        if (row)
+            store.projectId = row.id;
+        logger.info(`Store opened at ${dbPath}`);
+        return store;
+    }
     /** Expose the raw database instance for extension modules (e.g. DocsCacheStore). */
     getDb() {
         return this.db;
@@ -192,12 +225,7 @@ export class SqliteStore {
             if (existing) {
                 this.projectId = existing.id;
                 logger.info("Project activated by name", { name, projectId: existing.id });
-                return {
-                    id: existing.id,
-                    name: existing.name,
-                    createdAt: existing.created_at,
-                    updatedAt: existing.updated_at,
-                };
+                return rowToProject(existing);
             }
         }
         // No active project, or different name — check if project already exists by name
@@ -208,12 +236,7 @@ export class SqliteStore {
         if (existing) {
             this.projectId = existing.id;
             logger.info("Project activated by name", { name: projectName, projectId: existing.id });
-            return {
-                id: existing.id,
-                name: existing.name,
-                createdAt: existing.created_at,
-                updatedAt: existing.updated_at,
-            };
+            return rowToProject(existing);
         }
         // If no name provided but a project exists in DB, reuse it
         if (!name) {
@@ -223,12 +246,7 @@ export class SqliteStore {
             if (anyProject) {
                 this.projectId = anyProject.id;
                 logger.info("Project activated (existing)", { name: anyProject.name, projectId: anyProject.id });
-                return {
-                    id: anyProject.id,
-                    name: anyProject.name,
-                    createdAt: anyProject.created_at,
-                    updatedAt: anyProject.updated_at,
-                };
+                return rowToProject(anyProject);
             }
         }
         // Truly no project exists — create new
@@ -249,12 +267,7 @@ export class SqliteStore {
             .get(this.projectId);
         if (!row)
             return null;
-        return {
-            id: row.id,
-            name: row.name,
-            createdAt: row.created_at,
-            updatedAt: row.updated_at,
-        };
+        return rowToProject(row);
     }
     /** Alias for getProject — returns the currently active project. */
     getActiveProject() {
@@ -265,12 +278,7 @@ export class SqliteStore {
         const rows = this.db
             .prepare("SELECT * FROM projects ORDER BY created_at")
             .all();
-        return rows.map((row) => ({
-            id: row.id,
-            name: row.name,
-            createdAt: row.created_at,
-            updatedAt: row.updated_at,
-        }));
+        return rows.map(rowToProject);
     }
     /** Switch the active project. Throws if project ID does not exist. */
     activateProject(projectId) {
@@ -283,6 +291,49 @@ export class SqliteStore {
         this.projectId = projectId;
         logger.info("Project activated", { projectId });
     }
+    /**
+     * Find a project by its filesystem path.
+     * Returns null if no project is registered at that path.
+     */
+    findProjectByPath(fsPath) {
+        const row = this.db
+            .prepare("SELECT * FROM projects WHERE fs_path = ?")
+            .get(fsPath);
+        return row ? rowToProject(row) : null;
+    }
+    /**
+     * Register a project with a filesystem path.
+     * If a project already exists at that path, returns the existing one.
+     * Creates and activates a new project otherwise.
+     */
+    registerProject(name, fsPath) {
+        // Check if project already exists at this path
+        const existing = this.findProjectByPath(fsPath);
+        if (existing) {
+            this.projectId = existing.id;
+            logger.info("Project found by path", { name: existing.name, fsPath, projectId: existing.id });
+            return existing;
+        }
+        // Create new project with fs_path
+        const id = generateId("proj");
+        const timestamp = now();
+        this.db
+            .prepare("INSERT INTO projects (id, name, fs_path, created_at, updated_at) VALUES (?, ?, ?, ?, ?)")
+            .run(id, name, fsPath, timestamp, timestamp);
+        this.projectId = id;
+        logger.info(`Project registered: ${name} at ${fsPath} (${id})`);
+        return { id, name, fsPath, createdAt: timestamp, updatedAt: timestamp };
+    }
+    /**
+     * Set or update the filesystem path for a project.
+     */
+    setProjectFsPath(projectId, fsPath) {
+        const timestamp = now();
+        this.db
+            .prepare("UPDATE projects SET fs_path = ?, updated_at = ? WHERE id = ?")
+            .run(fsPath, timestamp, projectId);
+        logger.info("Project fs_path updated", { projectId, fsPath });
+    }
     ensureProject() {
         if (!this.projectId) {
             throw new GraphNotInitializedError();