diff --git a/core/models/note_tag.go b/core/models/note_tag.go
index c7e6090..d9b132f 100644
--- a/core/models/note_tag.go
+++ b/core/models/note_tag.go
@@ -12,7 +12,7 @@ func NewNoteTag(noteID, tagID string) *NoteTag {
 	}
 }
 
-func NewNoteTags(noteID string, tagIDs []string) []*NoteTag {
+func CreateNoteTags(noteID string, tagIDs []string) []*NoteTag {
 	noteTags := make([]*NoteTag, len(tagIDs))
 	for i, tagID := range tagIDs {
 		noteTags[i] = NewNoteTag(noteID, tagID)
diff --git a/dendrite b/dendrite
index a42ce71..a53eca9 100755
Binary files a/dendrite and b/dendrite differ
diff --git a/persistence/db_dir.go b/persistence/db_dir.go
new file mode 100644
index 0000000..c9ecfd7
--- /dev/null
+++ b/persistence/db_dir.go
@@ -0,0 +1,19 @@
+package persistence
+
+import (
+	"os"
+	"path/filepath"
+)
+
+func getIndexDBPath(vaultPath string) (string, error) {
+	dir := os.Getenv("XDG_DATA_HOME")
+	if dir == "" {
+		home, err := os.UserHomeDir()
+		if err != nil {
+			return "", err
+		}
+		dir = filepath.Join(home, ".local", "share")
+	}
+
+	return filepath.Join(dir, "dendrite", vaultPath), nil
+}
diff --git a/persistence/db_migrator.go b/persistence/db_migrator.go
index 1ddc700..37da0c3 100644
--- a/persistence/db_migrator.go
+++ b/persistence/db_migrator.go
@@ -13,9 +13,13 @@ import (
 var migrationsFS embed.FS
 
 func InitializeIndex(vaultPath string) (*sql.DB, error) {
-	indexDir := filepath.Join(vaultPath, ".index")
+	indexDir, err := getIndexDBPath(vaultPath)
+	if err != nil {
+		slog.Error("failed to get index directory path", "error", err)
+		return nil, err
+	}
 
-	if err := os.MkdirAll(indexDir, 0755); err != nil {
+	if err = os.MkdirAll(indexDir, 0755); err != nil {
 		slog.Error("failed to create index directory", "error", err)
 		return nil, err
 	}
diff --git a/persistence/services/doc.go b/persistence/services/doc.go
new file mode 100644
index 0000000..829c45f
--- /dev/null
+++ b/persistence/services/doc.go
@@ -0,0 +1,2 @@
+// Package peristenceServices provides services for data persistence, including database interactions and storage management.
+package services
diff --git a/persistence/services/index_rebuilder.go b/persistence/services/index_rebuilder.go
new file mode 100644
index 0000000..9bd90de
--- /dev/null
+++ b/persistence/services/index_rebuilder.go
@@ -0,0 +1,116 @@
+package services
+
+import (
+	"database/sql"
+	"io/fs"
+	"path/filepath"
+
+	filehandling "github.com/KristianJBorgwarth/dendrite.daemon/core/file_handling"
+	"github.com/KristianJBorgwarth/dendrite.daemon/core/models"
+)
+
+type IIndexRebuilder interface {
+	RebuildIndex(vaultRoot string) error
+}
+
+type IndexRebuilder struct {
+	db *sql.DB
+}
+
+func (r *IndexRebuilder) RebuildIndex(vaultRoot string) error {
+	files, err := r.ReadFiles(vaultRoot)
+	if err != nil {
+		return err
+	}
+
+	notes, links, tags, noteTags := r.buildDBModels(files)
+
+	tx, err := r.db.Begin()
+	if err != nil {
+		return err
+	}
+
+	if err = r.wipeIndex(tx); err != nil {
+		tx.Rollback()
+		return err
+	}
+
+	if err = r.InsertData(tx, notes, links, tags, noteTags); err != nil {
+		tx.Rollback()
+		return err
+	}
+
+	tx.Commit()
+
+	return nil
+}
+
+func (r *IndexRebuilder) InsertData(
+	tx *sql.Tx, 
+	notes []*models.Note, 
+	links []*models.Link, 
+	tags []*models.Tag, 
+	noteTags []*models.NoteTag) error {
+	panic("not implemented")
+}
+
+func (r *IndexRebuilder) ReadFiles(vault string) ([]*filehandling.File, error) {
+	var files []*filehandling.File
+
+	err := filepath.WalkDir(vault, func(path string, d fs.DirEntry, err error) error {
+		if err != nil {
+			return err
+		}
+
+		if d.IsDir() || filepath.Ext(path) != ".md" {
+			return nil
+		}
+		pendingFile, err := filehandling.ReadFile(path)
+		if err != nil {
+			return err
+		}
+
+		files = append(files, pendingFile)
+
+		return nil
+	})
+	if err != nil {
+		return nil, err
+	}
+
+	return files, nil
+}
+
+func (r *IndexRebuilder) buildDBModels(files []*filehandling.File) ([]*models.Note, []*models.Link, []*models.Tag, []*models.NoteTag) {
+	var notes []*models.Note
+	var links []*models.Link
+	tagMap := make(map[string]*models.Tag)
+	var noteTags []*models.NoteTag
+
+	for _, file := range files {
+		note := models.CreateNote(file.Path, file.Title, file.Slug)
+		notes = append(notes, note)
+		for _, t := range models.CreateTags(file.FrontMatter.Tags) {
+			tagMap[t.Name()] = t
+		}
+		noteTags = append(noteTags, models.CreateNoteTags(note.ID(), file.FrontMatter.Tags)...)
+		links = append(links, models.MapToLinkModel(note.ID(), file.ExtractedLinks)...)
+	}
+
+	tags := make([]*models.Tag, 0, len(tagMap))
+	for _, tag := range tagMap {
+		tags = append(tags, tag)
+	}
+
+	return notes, links, tags, noteTags
+}
+
+func (r *IndexRebuilder) wipeIndex(tx *sql.Tx) error {
+	cmd := `DELETE FROM notes; 
+	DELETE FROM tags;
+	DELETE FROM note_tags;
+	DELETE FROM link;`
+
+	_, err := tx.Exec(cmd)
+	return err
+}