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/freshen.go

@@ -40,7 +40,7 @@ func (mfa *CLIApp) freshenManifestOperation(ctx *cli.Context) error {
 
 	basePath := ctx.String("base")
 	showProgress := ctx.Bool("progress")
-	ignoreDotfiles := ctx.Bool("IgnoreDotfiles")
+	includeDotfiles := ctx.Bool("IncludeDotfiles")
 	followSymlinks := ctx.Bool("FollowSymLinks")
 
 	// Find manifest file
@@ -112,7 +112,7 @@ func (mfa *CLIApp) freshenManifestOperation(ctx *cli.Context) error {
 		}
 
 		// Handle dotfiles
-		if ignoreDotfiles && pathIsHidden(relPath) {
+		if !includeDotfiles && pathIsHidden(relPath) {
 			if info.IsDir() {
 				return filepath.SkipDir
 			}