Implement local SQLite index database with repositories

- Add SQLite database connection management with proper error handling
- Implement schema for files, chunks, blobs, and snapshots tables
- Create repository pattern for each database table
- Add transaction support with proper rollback handling
- Integrate database module with fx dependency injection
- Make index path configurable via VAULTIK_INDEX_PATH env var
- Add fatal error handling for database integrity issues
- Update DESIGN.md to clarify file_chunks vs chunk_files distinction
- Remove FinalHash from BlobInfo (blobs are content-addressable)
- Add file metadata support (mtime, ctime, mode, uid, gid, symlinks)

internal/database/repositories.go

@@ -0,0 +1,90 @@
+package database
+
+import (
+	"context"
+	"database/sql"
+	"fmt"
+)
+
+type Repositories struct {
+	db         *DB
+	Files      *FileRepository
+	Chunks     *ChunkRepository
+	Blobs      *BlobRepository
+	FileChunks *FileChunkRepository
+	BlobChunks *BlobChunkRepository
+	ChunkFiles *ChunkFileRepository
+	Snapshots  *SnapshotRepository
+}
+
+func NewRepositories(db *DB) *Repositories {
+	return &Repositories{
+		db:         db,
+		Files:      NewFileRepository(db),
+		Chunks:     NewChunkRepository(db),
+		Blobs:      NewBlobRepository(db),
+		FileChunks: NewFileChunkRepository(db),
+		BlobChunks: NewBlobChunkRepository(db),
+		ChunkFiles: NewChunkFileRepository(db),
+		Snapshots:  NewSnapshotRepository(db),
+	}
+}
+
+type TxFunc func(ctx context.Context, tx *sql.Tx) error
+
+func (r *Repositories) WithTx(ctx context.Context, fn TxFunc) error {
+	tx, err := r.db.BeginTx(ctx, nil)
+	if err != nil {
+		return fmt.Errorf("beginning transaction: %w", err)
+	}
+
+	defer func() {
+		if p := recover(); p != nil {
+			if rollbackErr := tx.Rollback(); rollbackErr != nil {
+				Fatal("failed to rollback transaction: %v", rollbackErr)
+			}
+			panic(p)
+		} else if err != nil {
+			if rollbackErr := tx.Rollback(); rollbackErr != nil {
+				Fatal("failed to rollback transaction: %v", rollbackErr)
+			}
+		}
+	}()
+
+	err = fn(ctx, tx)
+	if err != nil {
+		return err
+	}
+
+	return tx.Commit()
+}
+
+func (r *Repositories) WithReadTx(ctx context.Context, fn TxFunc) error {
+	opts := &sql.TxOptions{
+		ReadOnly: true,
+	}
+	tx, err := r.db.BeginTx(ctx, opts)
+	if err != nil {
+		return fmt.Errorf("beginning read transaction: %w", err)
+	}
+
+	defer func() {
+		if p := recover(); p != nil {
+			if rollbackErr := tx.Rollback(); rollbackErr != nil {
+				Fatal("failed to rollback transaction: %v", rollbackErr)
+			}
+			panic(p)
+		} else if err != nil {
+			if rollbackErr := tx.Rollback(); rollbackErr != nil {
+				Fatal("failed to rollback transaction: %v", rollbackErr)
+			}
+		}
+	}()
+
+	err = fn(ctx, tx)
+	if err != nil {
+		return err
+	}
+
+	return tx.Commit()
+}