Exclude dotfiles by default, add --include-dotfiles flag

Changed the default behavior to exclude dotfiles (files/dirs starting with .)
which is the more common use case. Added --include-dotfiles flag for when
hidden files need to be included in the manifest.

internal/cli/gen.go

@@ -16,9 +16,9 @@ func (mfa *CLIApp) generateManifestOperation(ctx *cli.Context) error {
 	log.Debug("generateManifestOperation()")
 
 	opts := &scanner.Options{
-		IgnoreDotfiles: ctx.Bool("IgnoreDotfiles"),
-		FollowSymLinks: ctx.Bool("FollowSymLinks"),
-		Fs:             mfa.Fs,
+		IncludeDotfiles: ctx.Bool("IncludeDotfiles"),
+		FollowSymLinks:  ctx.Bool("FollowSymLinks"),
+		Fs:              mfa.Fs,
 	}
 
 	s := scanner.NewWithOptions(opts)