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/files.go

@@ -0,0 +1,145 @@
+package database
+
+import (
+	"context"
+	"database/sql"
+	"fmt"
+	"time"
+)
+
+type FileRepository struct {
+	db *DB
+}
+
+func NewFileRepository(db *DB) *FileRepository {
+	return &FileRepository{db: db}
+}
+
+func (r *FileRepository) Create(ctx context.Context, tx *sql.Tx, file *File) error {
+	query := `
+		INSERT INTO files (path, mtime, ctime, size, mode, uid, gid, link_target)
+		VALUES (?, ?, ?, ?, ?, ?, ?, ?)
+		ON CONFLICT(path) DO UPDATE SET
+			mtime = excluded.mtime,
+			ctime = excluded.ctime,
+			size = excluded.size,
+			mode = excluded.mode,
+			uid = excluded.uid,
+			gid = excluded.gid,
+			link_target = excluded.link_target
+	`
+
+	var err error
+	if tx != nil {
+		_, err = tx.ExecContext(ctx, query, file.Path, file.MTime.Unix(), file.CTime.Unix(), file.Size, file.Mode, file.UID, file.GID, file.LinkTarget)
+	} else {
+		_, err = r.db.conn.ExecContext(ctx, query, file.Path, file.MTime.Unix(), file.CTime.Unix(), file.Size, file.Mode, file.UID, file.GID, file.LinkTarget)
+	}
+
+	if err != nil {
+		return fmt.Errorf("inserting file: %w", err)
+	}
+
+	return nil
+}
+
+func (r *FileRepository) GetByPath(ctx context.Context, path string) (*File, error) {
+	query := `
+		SELECT path, mtime, ctime, size, mode, uid, gid, link_target
+		FROM files
+		WHERE path = ?
+	`
+
+	var file File
+	var mtimeUnix, ctimeUnix int64
+	var linkTarget sql.NullString
+
+	err := r.db.conn.QueryRowContext(ctx, query, path).Scan(
+		&file.Path,
+		&mtimeUnix,
+		&ctimeUnix,
+		&file.Size,
+		&file.Mode,
+		&file.UID,
+		&file.GID,
+		&linkTarget,
+	)
+
+	if err == sql.ErrNoRows {
+		return nil, nil
+	}
+	if err != nil {
+		return nil, fmt.Errorf("querying file: %w", err)
+	}
+
+	file.MTime = time.Unix(mtimeUnix, 0)
+	file.CTime = time.Unix(ctimeUnix, 0)
+	if linkTarget.Valid {
+		file.LinkTarget = linkTarget.String
+	}
+
+	return &file, nil
+}
+
+func (r *FileRepository) ListModifiedSince(ctx context.Context, since time.Time) ([]*File, error) {
+	query := `
+		SELECT path, mtime, ctime, size, mode, uid, gid, link_target
+		FROM files
+		WHERE mtime >= ?
+		ORDER BY path
+	`
+
+	rows, err := r.db.conn.QueryContext(ctx, query, since.Unix())
+	if err != nil {
+		return nil, fmt.Errorf("querying files: %w", err)
+	}
+	defer CloseRows(rows)
+
+	var files []*File
+	for rows.Next() {
+		var file File
+		var mtimeUnix, ctimeUnix int64
+		var linkTarget sql.NullString
+
+		err := rows.Scan(
+			&file.Path,
+			&mtimeUnix,
+			&ctimeUnix,
+			&file.Size,
+			&file.Mode,
+			&file.UID,
+			&file.GID,
+			&linkTarget,
+		)
+		if err != nil {
+			return nil, fmt.Errorf("scanning file: %w", err)
+		}
+
+		file.MTime = time.Unix(mtimeUnix, 0)
+		file.CTime = time.Unix(ctimeUnix, 0)
+		if linkTarget.Valid {
+			file.LinkTarget = linkTarget.String
+		}
+
+		files = append(files, &file)
+	}
+
+	return files, rows.Err()
+}
+
+func (r *FileRepository) Delete(ctx context.Context, tx *sql.Tx, path string) error {
+	query := `DELETE FROM files WHERE path = ?`
+
+	var err error
+	if tx != nil {
+		_, err = tx.ExecContext(ctx, query, path)
+	} else {
+		_, err = r.db.conn.ExecContext(ctx, query, path)
+	}
+
+	if err != nil {
+		return fmt.Errorf("deleting file: %w", err)
+	}
+
+	return nil
+}