om init may not preserve file permissions when instantiating templates

[cameronraysmith]

Briefly, direnv fails after instantiating a template with om init because the template relies on an executable script and the template instantiation doesn't seem to preserve the permissions of the files from the template.

Git-tracked file permissions are not preserved on template instantiation

Steps to reproduce:

Clone the git repo and check script file permissions

❯ git clone https://github.com/sciexp/python-nix-template test-pnt
❯ cd test-pnt
❯ git checkout 7d17d0dbffe756f1804aa86fe95bf61a1867d4d3
❯ ls -alh ./scripts
.rwxr-xr-x user group 838 B Fri Feb 28 22:51:50 2025  set-git-env.sh
❯ stat -c "%a %n" scripts/set-git-env.sh
755 scripts/set-git-env.sh

Use om init to instantiate the template and check file permissions

❯ om init github:sciexp/python-nix-template/7d17d0dbffe756f1804aa86fe95bf61a1867d4d3 -o test-om-pnt
❯ cd test-om-pnt
❯ ls -alh scripts
.rw-r--r-- user group 838 B Wed Dec 31 19:00:01 1969  set-git-env.sh
❯ stat -c "%a %n" scripts/set-git-env.sh
644 scripts/set-git-env.sh

The modification date for scripts/set-git-env.sh has been set to the Unix epoch and the permissions have been changed from 755 to 644.

See ASCII cast from #425 and discussion in #424, #424 (comment) for additional context.