builtin-apply: prevent non-explicit permission changes

builtin-apply: prevent non-explicit permission changes

A git patch that does not change the executable bit records the mode bits
on its "index" line.  "git apply" used to interpret this mode exactly the
same way as it interprets the mode recorded on "new mode" line, as the
wish by the patch submitter to set the mode to the one recorded on the
line.

The reason the mode does not agree between the submitter and the receiver
in the first place is because there is _another_ commit that only appears
on one side but not the other since their histories diverged, and that
commit changes the mode.  The patch has "index" line but not "new mode"
line because its change is about updating the contents without affecting
the mode.  The application of such a patch is an explicit wish by the
submitter to only cherry-pick the commit that updates the contents without
cherry-picking the commit that modifies the mode.  Viewed this way, the
current behaviour is problematic, even though the command does warn when
the mode of the path being patched does not match this mode, and a careful
user could detect this inconsistencies between the patch submitter and the
patch receiver.

This changes the semantics of the mode recorded on the "index" line;
instead of interpreting it as the submitter's wish to set the mode to the
recorded value, it merely informs what the mode submitter happened to
have, and the presense of the "index" line is taken as submitter's wish to
keep whatever the mode is on the receiving end.

This is based on the patch originally done by Alexander Potashev with a
minor fix; the tests are mine.

Signed-off-by: Junio C Hamano <gitster@pobox.com>