Remove ignored files by default when they are in the way

Remove ignored files by default when they are in the way

Change several commands to remove ignored files by default when they are
in the way.  Since some commands (checkout, merge) take a
--no-overwrite-ignore option to allow the user to configure this, and it
may make sense to add that option to more commands (and in the case of
merge, actually plumb that configuration option through to more of the
backends than just the fast-forwarding special case), add little
comments about where such flags would be used.

Incidentally, this fixes a test failure in t7112.

Signed-off-by: Elijah Newren <newren@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>