diff --git a/cmd/main.go b/cmd/main.go
index 4615708..ca578ee 100644
--- a/cmd/main.go
+++ b/cmd/main.go
@@ -1,11 +1,6 @@
 package main
 
 import (
-	"database/sql"
-	"log"
-	"path/filepath"
-
-	"github.com/KristianJBorgwarth/dendrite.daemon/persistence"
   "github.com/KristianJBorgwarth/dendrite.daemon/core"
 	_ "modernc.org/sqlite"
 )
@@ -15,20 +10,3 @@ func main() {
 	server.Run()
 }
 
-func runMigration() {
-	dbPath := filepath.Join("persistence", "index.db")
-
-	db, err := sql.Open("sqlite", dbPath)
-	if err != nil {
-		log.Fatal(err)
-	}
-	defer db.Close()
-
-	migrationsDir := filepath.Join("persistence", "migrations")
-
-	if err := persistence.ApplyMigrations(db, migrationsDir); err != nil {
-		log.Fatal(err)
-	}
-
-	log.Println("migrations applied successfully")
-}
diff --git a/core/handlers/init.go b/core/handlers/init.go
index dfa2fde..f6ff12b 100644
--- a/core/handlers/init.go
+++ b/core/handlers/init.go
@@ -2,8 +2,8 @@ package handlers
 
 import (
 	"encoding/json"
-
 	"github.com/KristianJBorgwarth/dendrite.daemon/config"
+	"github.com/KristianJBorgwarth/dendrite.daemon/persistence"
 )
 
 type initializeParams struct {
@@ -24,6 +24,7 @@ type initializeParams struct {
 
 func Initialize(raw json.RawMessage) (*config.Config, error) {
 	var params initializeParams
+
 	if err := json.Unmarshal(raw, &params); err != nil {
 		return nil, err
 	}
@@ -41,7 +42,14 @@ func Initialize(raw json.RawMessage) (*config.Config, error) {
 			FilenameFormat: params.DailyNote.FilenameFormat,
 		},
 	}
+
 	cfg.SetDefaults()
 
+	err := persistence.InitializeIndex(cfg.VaultPath)
+	if err != nil {
+		return nil, err
+	}
+
 	return cfg, nil
 }
+
diff --git a/core/server.go b/core/server.go
index 03a65ea..f0dc480 100644
--- a/core/server.go
+++ b/core/server.go
@@ -115,13 +115,13 @@ func (s *Server) handleRequest(req types.Request) {
 		err    error
 	)
 
+	// move to handler package?
 	switch req.Method {
 	case "initialize":
 		s.config, err = handlers.Initialize(req.Params)
 		result = map[string]any{"status": "ok"}
 	default:
 		err = fmt.Errorf("unknown method: %s", req.Method)
-
 	}
 
 	s.writeResponse(req.ID, result, err)
diff --git a/dendrite b/dendrite
index c732010..9264e4e 100755
Binary files a/dendrite and b/dendrite differ
diff --git a/persistence/db_migrator.go b/persistence/db_migrator.go
index 438dc43..e2cb22a 100644
--- a/persistence/db_migrator.go
+++ b/persistence/db_migrator.go
@@ -1,5 +1,5 @@
 // Package persistence handles database schema migrations
-package persistence 
+package persistence
 
 import (
 	"database/sql"
@@ -8,7 +8,24 @@ import (
 	"sort"
 )
 
-func ApplyMigrations(db *sql.DB, dir string) error {
+func InitializeIndex(vaulPath string) error {
+	dbPath := filepath.Join(vaulPath, "index.db")
+
+	db, err := sql.Open("sqlite", dbPath)
+	if err != nil {
+		return err
+	}
+	defer db.Close()
+
+	migrationsDir := filepath.Join("persistence", "migrations")
+
+	if err := applyMigrations(db, migrationsDir); err != nil {
+		return err
+	}
+	return nil
+}
+
+func applyMigrations(db *sql.DB, dir string) error {
 	_, err := db.Exec(`CREATE TABLE IF NOT EXISTS schema_migrations (version TEXT PRIMARY KEY);`)
 	if err != nil {
 		return err