Implement SQLite index database layer

- Add pure Go SQLite driver (modernc.org/sqlite) to avoid CGO dependency
- Implement database connection management with WAL mode
- Add write mutex for serializing concurrent writes
- Create schema for all tables matching DESIGN.md specifications
- Implement repository pattern for all database entities:
  - Files, FileChunks, Chunks, Blobs, BlobChunks, ChunkFiles, Snapshots
- Add transaction support with proper rollback handling
- Add fatal error handling for database integrity issues
- Add snapshot fields for tracking file sizes and compression ratios
- Make index path configurable via VAULTIK_INDEX_PATH environment variable
- Add comprehensive test coverage for all repositories
- Add format check to Makefile to ensure code formatting

internal/database/database.go

@@ -4,16 +4,18 @@ import (
 	"context"
 	"database/sql"
 	"fmt"
+	"sync"
 
-	_ "github.com/mattn/go-sqlite3"
+	_ "modernc.org/sqlite"
 )
 
 type DB struct {
-	conn *sql.DB
+	conn      *sql.DB
+	writeLock sync.Mutex
 }
 
 func New(ctx context.Context, path string) (*DB, error) {
-	conn, err := sql.Open("sqlite3", path+"?_journal_mode=WAL&_synchronous=NORMAL&_busy_timeout=5000")
+	conn, err := sql.Open("sqlite", path+"?_journal_mode=WAL&_synchronous=NORMAL&_busy_timeout=5000")
 	if err != nil {
 		return nil, fmt.Errorf("opening database: %w", err)
 	}
@@ -51,6 +53,30 @@ func (db *DB) BeginTx(ctx context.Context, opts *sql.TxOptions) (*sql.Tx, error)
 	return db.conn.BeginTx(ctx, opts)
 }
 
+// LockForWrite acquires the write lock
+func (db *DB) LockForWrite() {
+	db.writeLock.Lock()
+}
+
+// UnlockWrite releases the write lock
+func (db *DB) UnlockWrite() {
+	db.writeLock.Unlock()
+}
+
+// ExecWithLock executes a write query with the write lock held
+func (db *DB) ExecWithLock(ctx context.Context, query string, args ...interface{}) (sql.Result, error) {
+	db.writeLock.Lock()
+	defer db.writeLock.Unlock()
+	return db.conn.ExecContext(ctx, query, args...)
+}
+
+// QueryRowWithLock executes a write query that returns a row with the write lock held
+func (db *DB) QueryRowWithLock(ctx context.Context, query string, args ...interface{}) *sql.Row {
+	db.writeLock.Lock()
+	defer db.writeLock.Unlock()
+	return db.conn.QueryRowContext(ctx, query, args...)
+}
+
 func (db *DB) createSchema(ctx context.Context) error {
 	schema := `
 	CREATE TABLE IF NOT EXISTS files (
@@ -105,7 +131,10 @@ func (db *DB) createSchema(ctx context.Context) error {
 		created_ts INTEGER NOT NULL,
 		file_count INTEGER NOT NULL,
 		chunk_count INTEGER NOT NULL,
-		blob_count INTEGER NOT NULL
+		blob_count INTEGER NOT NULL,
+		total_size INTEGER NOT NULL,
+		blob_size INTEGER NOT NULL,
+		compression_ratio REAL NOT NULL
 	);
 	`