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/cli/app.go

@@ -15,7 +15,9 @@ import (
 	"go.uber.org/fx"
 )
 
-// AppOptions contains common options for creating the fx application
+// AppOptions contains common options for creating the fx application.
+// It includes the configuration file path, logging options, and additional
+// fx modules and invocations that should be included in the application.
 type AppOptions struct {
 	ConfigPath string
 	LogOptions log.LogOptions
@@ -27,13 +29,16 @@ type AppOptions struct {
 func setupGlobals(lc fx.Lifecycle, g *globals.Globals) {
 	lc.Append(fx.Hook{
 		OnStart: func(ctx context.Context) error {
-			g.StartTime = time.Now()
+			g.StartTime = time.Now().UTC()
 			return nil
 		},
 	})
 }
 
-// NewApp creates a new fx application with common modules
+// NewApp creates a new fx application with common modules.
+// It sets up the base modules (config, database, logging, globals) and
+// combines them with any additional modules specified in the options.
+// The returned fx.App is ready to be started with RunApp.
 func NewApp(opts AppOptions) *fx.App {
 	baseModules := []fx.Option{
 		fx.Supply(config.ConfigPath(opts.ConfigPath)),
@@ -53,7 +58,10 @@ func NewApp(opts AppOptions) *fx.App {
 	return fx.New(allOptions...)
 }
 
-// RunApp starts and stops the fx application within the given context
+// RunApp starts and stops the fx application within the given context.
+// It handles graceful shutdown on interrupt signals (SIGINT, SIGTERM) and
+// ensures the application stops cleanly. The function blocks until the
+// application completes or is interrupted. Returns an error if startup fails.
 func RunApp(ctx context.Context, app *fx.App) error {
 	// Set up signal handling for graceful shutdown
 	sigChan := make(chan os.Signal, 1)
@@ -101,7 +109,9 @@ func RunApp(ctx context.Context, app *fx.App) error {
 	}
 }
 
-// RunWithApp is a helper that creates and runs an fx app with the given options
+// RunWithApp is a helper that creates and runs an fx app with the given options.
+// It combines NewApp and RunApp into a single convenient function. This is the
+// preferred way to run CLI commands that need the full application context.
 func RunWithApp(ctx context.Context, opts AppOptions) error {
 	app := NewApp(opts)
 	return RunApp(ctx, app)