Make mode handling during init more like git

When creating files, instead of actually using GIT_FILEMODE_BLOB
and the other various constants that happen to correspond to
mode values, apparently I should be just using 0666 and 0777, and
relying on the umask to clear bits and make the value sane.

This fixes the rules for copying a template directory and fixes
the checks to match that new behavior.  (Further changes to the
checkout logic to follow separately.)