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.

contrib/usage.sh

@@ -15,5 +15,5 @@ trap cleanup EXIT
 echo "Building mfer..."
 go build -o "$TMPDIR/mfer" ./cmd/mfer
 
-"$TMPDIR/mfer" generate --ignore-dotfiles -o "$MANIFEST" .
+"$TMPDIR/mfer" generate -o "$MANIFEST" .
 "$TMPDIR/mfer" check --base . "$MANIFEST"