Adhere to the XDG Base Directory Specification instead of clogging up the home directory with another directory.

http://standards.freedesktop.org/basedir-spec/basedir-spec-latest.html

Should be a simple fix. You could continue to use the current ~/.minecraft, but create new installs in $XDG_DATA_HOME/minecraft | .local/share/minecraft and prefer it when it exists.

This is standards compliance.