t4111 (apply): refresh index before applying patches to it

t4111 (apply): refresh index before applying patches to it

"git apply", like most plumbing, does not automatically refresh the
index file even if it is only stat-dirty.  So unless the two "cp"
commands in reset_preimage() for a given file happen to have the same
time stamp, there will be a spurious

	error: sub/dir/file: does not match index

Refresh the index to eliminate this timing dependency.  Noticed by
running the test with --valgrind (which slows things down a lot).

Reported-by: Thomas Rast <trast@student.ethz.ch>
Signed-off-by: Jonathan Nieder <jrnieder@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>