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.)
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