Major refactoring: UUID-based storage, streaming architecture, and CLI improvements

This commit represents a significant architectural overhaul of vaultik:

Database Schema Changes:
- Switch files table to use UUID primary keys instead of path-based keys
- Add UUID primary keys to blobs table for immediate chunk association
- Update all foreign key relationships to use UUIDs
- Add comprehensive schema documentation in DATAMODEL.md
- Add SQLite busy timeout handling for concurrent operations

Streaming and Performance Improvements:
- Implement true streaming blob packing without intermediate storage
- Add streaming chunk processing to reduce memory usage
- Improve progress reporting with real-time metrics
- Add upload metrics tracking in new uploads table

CLI Refactoring:
- Restructure CLI to use subcommands: snapshot create/list/purge/verify
- Add store info command for S3 configuration display
- Add custom duration parser supporting days/weeks/months/years
- Remove old backup.go in favor of enhanced snapshot.go
- Add --cron flag for silent operation

Configuration Changes:
- Remove unused index_prefix configuration option
- Add support for snapshot pruning retention policies
- Improve configuration validation and error messages

Testing Improvements:
- Add comprehensive repository tests with edge cases
- Add cascade delete debugging tests
- Fix concurrent operation tests to use SQLite busy timeout
- Remove tolerance for SQLITE_BUSY errors in tests

Documentation:
- Add MIT LICENSE file
- Update README with new command structure
- Add comprehensive DATAMODEL.md explaining database schema
- Update DESIGN.md with UUID-based architecture

Other Changes:
- Add test-config.yml for testing
- Update Makefile with better test output formatting
- Fix various race conditions in concurrent operations
- Improve error handling throughout

internal/database/chunks.go

@@ -4,6 +4,8 @@ import (
 	"context"
 	"database/sql"
 	"fmt"
+
+	"git.eeqj.de/sneak/vaultik/internal/log"
 )
 
 type ChunkRepository struct {
@@ -25,7 +27,7 @@ func (r *ChunkRepository) Create(ctx context.Context, tx *sql.Tx, chunk *Chunk)
 	if tx != nil {
 		_, err = tx.ExecContext(ctx, query, chunk.ChunkHash, chunk.SHA256, chunk.Size)
 	} else {
-		_, err = r.db.ExecWithLock(ctx, query, chunk.ChunkHash, chunk.SHA256, chunk.Size)
+		_, err = r.db.ExecWithLog(ctx, query, chunk.ChunkHash, chunk.SHA256, chunk.Size)
 	}
 
 	if err != nil {
@@ -139,3 +141,26 @@ func (r *ChunkRepository) ListUnpacked(ctx context.Context, limit int) ([]*Chunk
 
 	return chunks, rows.Err()
 }
+
+// DeleteOrphaned deletes chunks that are not referenced by any file
+func (r *ChunkRepository) DeleteOrphaned(ctx context.Context) error {
+	query := `
+		DELETE FROM chunks 
+		WHERE NOT EXISTS (
+			SELECT 1 FROM file_chunks 
+			WHERE file_chunks.chunk_hash = chunks.chunk_hash
+		)
+	`
+
+	result, err := r.db.ExecWithLog(ctx, query)
+	if err != nil {
+		return fmt.Errorf("deleting orphaned chunks: %w", err)
+	}
+
+	rowsAffected, _ := result.RowsAffected()
+	if rowsAffected > 0 {
+		log.Debug("Deleted orphaned chunks", "count", rowsAffected)
+	}
+
+	return nil
+}