feat: deterministic manifests by default, remove atime, rate-limit checker progress

- Remove atime field from proto schema (field 304 reserved)
- Omit createdAt timestamp by default for deterministic output
- Add --include-timestamps flag to gen and freshen commands to opt in
- Add Builder.SetIncludeTimestamps() and ScannerOptions.IncludeTimestamps
- Rate-limit Checker progress updates to once per second (matching Scanner)
- Add tests for all changes

Closes design decisions: deterministic-by-default, atime removal.

internal/cli/freshen.go

@@ -226,6 +226,9 @@ func (mfa *CLIApp) freshenManifestOperation(ctx *cli.Context) error {
 	var hashedBytes int64
 
 	builder := mfer.NewBuilder()
+	if ctx.Bool("include-timestamps") {
+		builder.SetIncludeTimestamps(true)
+	}
 
 	// Set up signing options if sign-key is provided
 	if signKey := ctx.String("sign-key"); signKey != "" {

internal/cli/gen.go

@@ -20,9 +20,10 @@ func (mfa *CLIApp) generateManifestOperation(ctx *cli.Context) error {
 	log.Debug("generateManifestOperation()")
 
 	opts := &mfer.ScannerOptions{
-		IncludeDotfiles: ctx.Bool("include-dotfiles"),
-		FollowSymLinks:  ctx.Bool("follow-symlinks"),
-		Fs:              mfa.Fs,
+		IncludeDotfiles:   ctx.Bool("include-dotfiles"),
+		FollowSymLinks:    ctx.Bool("follow-symlinks"),
+		IncludeTimestamps: ctx.Bool("include-timestamps"),
+		Fs:                mfa.Fs,
 	}
 
 	// Set seed for deterministic UUID if provided

internal/cli/mfer.go

@@ -159,6 +159,10 @@ func (mfa *CLIApp) run(args []string) {
 						Usage:   "Seed value for deterministic manifest UUID",
 						EnvVars: []string{"MFER_SEED"},
 					},
+					&cli.BoolFlag{
+						Name:  "include-timestamps",
+						Usage: "Include createdAt timestamp in manifest (omitted by default for determinism)",
+					},
 				),
 			},
 			{
@@ -231,6 +235,10 @@ func (mfa *CLIApp) run(args []string) {
 						Usage:   "GPG key ID to sign the manifest with",
 						EnvVars: []string{"MFER_SIGN_KEY"},
 					},
+					&cli.BoolFlag{
+						Name:  "include-timestamps",
+						Usage: "Include createdAt timestamp in manifest (omitted by default for determinism)",
+					},
 				),
 			},
 			{