fix: resolve store path correctly when not in project root

- Use import.meta.dirname for proper path resolution
- Handle store path resolution priority: env var > legacy path > standard path
- Ensure database directory exists before initialization

Author: arabold

src/store/DocumentManagementService.test.ts

@@ -59,7 +59,8 @@ describe("DocumentManagementService", () => {
   let docService: DocumentManagementService; // For general tests
 
   // Define expected paths consistently
-  const expectedOldDbPath = path.join(process.cwd(), ".store", "documents.db");
+  const projectRoot = path.resolve(import.meta.dirname, "..");
+  const expectedOldDbPath = path.join(projectRoot, ".store", "documents.db");
   const expectedStandardDbPath = path.join(mockEnvPaths.data, "documents.db");
 
   beforeEach(() => {

src/store/DocumentManagementService.ts

@@ -41,7 +41,9 @@ export class DocumentManagementService {
       logger.debug(`💾 Using database directory from DOCS_MCP_STORE_PATH: ${dbDir}`);
     } else {
       // 2. Check Old Local Path
-      const oldDbDir = path.join(process.cwd(), ".store");
+      const projectRoot = path.resolve(import.meta.dirname, "..");
+      const oldDbDir = path.join(projectRoot, ".store");
+      console.log("Old DB Directory:", oldDbDir);
       const oldDbPath = path.join(oldDbDir, "documents.db");
       const oldDbExists = existsSync(oldDbPath); // Check file existence specifically