I've read through a few questions regarding file permissions in Git and I'm still a bit confused. I've got a repo on GitHub forked from another. Post merge, they should be identical. However:
$ git diff --summary origin/epsilon master/epsilon
mode change 100644 => 100755 ants/dist/sample_bots/csharp/compile.sh
mode change 100644 => 100755 ants/dist/starter_bots/coffeescript/MyBot.coffee
mode change 100644 => 100755 ants/dist/starter_bots/coffeescript/ants.coffee
mode change 100644 => 100755 ants/util/block_test.sh
mode change 100644 => 100755 manager/mass_skill_update.py
mode change 100644 => 100755 worker/jailguard.py
mode change 100644 => 100755 worker/release_stale_jails.py
mode change 100644 => 100755 worker/start_worker.sh
I've tried changing file permissions, but it does not alter the diff results.
I found the solution of how to change permissions (also) on Windows here: http://blog.lesc.se/2011/11/how-to-change-file-premissions-in-git.html
For example following command adds user execute permission to an arbitrary file:
git update-index --chmod=+x <file>