Project.pm: compensate for Git 2.1.0 - 2.2.1 bugs
Git versions 2.1.0 - 2.2.1 make the config file executable when
using git init or git clone to first initialize a .git directory.
Compensate for this behavior that increases the attach surface
by explicitly setting the mode of the config file after git init
to remove the bogus execute permission bit(s).
While this is not necessary on other Git versions, it does not
cause any problems (and ends up setting the file mode to the
value it already has which is harmless).