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/chunk_files_test.go

@@ -0,0 +1,142 @@
+package database
+
+import (
+	"context"
+	"testing"
+)
+
+func TestChunkFileRepository(t *testing.T) {
+	db, cleanup := setupTestDB(t)
+	defer cleanup()
+
+	ctx := context.Background()
+	repo := NewChunkFileRepository(db)
+
+	// Test Create
+	cf1 := &ChunkFile{
+		ChunkHash:  "chunk1",
+		FilePath:   "/file1.txt",
+		FileOffset: 0,
+		Length:     1024,
+	}
+
+	err := repo.Create(ctx, nil, cf1)
+	if err != nil {
+		t.Fatalf("failed to create chunk file: %v", err)
+	}
+
+	// Add same chunk in different file (deduplication scenario)
+	cf2 := &ChunkFile{
+		ChunkHash:  "chunk1",
+		FilePath:   "/file2.txt",
+		FileOffset: 2048,
+		Length:     1024,
+	}
+	err = repo.Create(ctx, nil, cf2)
+	if err != nil {
+		t.Fatalf("failed to create second chunk file: %v", err)
+	}
+
+	// Test GetByChunkHash
+	chunkFiles, err := repo.GetByChunkHash(ctx, "chunk1")
+	if err != nil {
+		t.Fatalf("failed to get chunk files: %v", err)
+	}
+	if len(chunkFiles) != 2 {
+		t.Errorf("expected 2 files for chunk, got %d", len(chunkFiles))
+	}
+
+	// Verify both files are returned
+	foundFile1 := false
+	foundFile2 := false
+	for _, cf := range chunkFiles {
+		if cf.FilePath == "/file1.txt" && cf.FileOffset == 0 {
+			foundFile1 = true
+		}
+		if cf.FilePath == "/file2.txt" && cf.FileOffset == 2048 {
+			foundFile2 = true
+		}
+	}
+	if !foundFile1 || !foundFile2 {
+		t.Error("not all expected files found")
+	}
+
+	// Test GetByFilePath
+	chunkFiles, err = repo.GetByFilePath(ctx, "/file1.txt")
+	if err != nil {
+		t.Fatalf("failed to get chunks by file path: %v", err)
+	}
+	if len(chunkFiles) != 1 {
+		t.Errorf("expected 1 chunk for file, got %d", len(chunkFiles))
+	}
+	if chunkFiles[0].ChunkHash != "chunk1" {
+		t.Errorf("wrong chunk hash: expected chunk1, got %s", chunkFiles[0].ChunkHash)
+	}
+
+	// Test duplicate insert (should be idempotent)
+	err = repo.Create(ctx, nil, cf1)
+	if err != nil {
+		t.Fatalf("failed to create duplicate chunk file: %v", err)
+	}
+}
+
+func TestChunkFileRepositoryComplexDeduplication(t *testing.T) {
+	db, cleanup := setupTestDB(t)
+	defer cleanup()
+
+	ctx := context.Background()
+	repo := NewChunkFileRepository(db)
+
+	// Simulate a scenario where multiple files share chunks
+	// File1: chunk1, chunk2, chunk3
+	// File2: chunk2, chunk3, chunk4
+	// File3: chunk1, chunk4
+
+	chunkFiles := []ChunkFile{
+		// File1
+		{ChunkHash: "chunk1", FilePath: "/file1.txt", FileOffset: 0, Length: 1024},
+		{ChunkHash: "chunk2", FilePath: "/file1.txt", FileOffset: 1024, Length: 1024},
+		{ChunkHash: "chunk3", FilePath: "/file1.txt", FileOffset: 2048, Length: 1024},
+		// File2
+		{ChunkHash: "chunk2", FilePath: "/file2.txt", FileOffset: 0, Length: 1024},
+		{ChunkHash: "chunk3", FilePath: "/file2.txt", FileOffset: 1024, Length: 1024},
+		{ChunkHash: "chunk4", FilePath: "/file2.txt", FileOffset: 2048, Length: 1024},
+		// File3
+		{ChunkHash: "chunk1", FilePath: "/file3.txt", FileOffset: 0, Length: 1024},
+		{ChunkHash: "chunk4", FilePath: "/file3.txt", FileOffset: 1024, Length: 1024},
+	}
+
+	for _, cf := range chunkFiles {
+		err := repo.Create(ctx, nil, &cf)
+		if err != nil {
+			t.Fatalf("failed to create chunk file: %v", err)
+		}
+	}
+
+	// Test chunk1 (used by file1 and file3)
+	files, err := repo.GetByChunkHash(ctx, "chunk1")
+	if err != nil {
+		t.Fatalf("failed to get files for chunk1: %v", err)
+	}
+	if len(files) != 2 {
+		t.Errorf("expected 2 files for chunk1, got %d", len(files))
+	}
+
+	// Test chunk2 (used by file1 and file2)
+	files, err = repo.GetByChunkHash(ctx, "chunk2")
+	if err != nil {
+		t.Fatalf("failed to get files for chunk2: %v", err)
+	}
+	if len(files) != 2 {
+		t.Errorf("expected 2 files for chunk2, got %d", len(files))
+	}
+
+	// Test file2 chunks
+	chunks, err := repo.GetByFilePath(ctx, "/file2.txt")
+	if err != nil {
+		t.Fatalf("failed to get chunks for file2: %v", err)
+	}
+	if len(chunks) != 3 {
+		t.Errorf("expected 3 chunks for file2, got %d", len(chunks))
+	}
+}