Why does Git show that all my files changed when I didn't change them?

Due to some quirks on our storage system your git repo may show that all of your files have modifications. If you perform a ‘git diff’ you will see a list that looks like:

diff --git a/SharePermissions.psm1 b/SharePermissions.psm1
old mode 100644
new mode 100755
diff --git a/audit-homedirs.ps1 b/audit-homedirs.ps1
old mode 100644
new mode 100755
diff --git a/clearSPconfigcache.ps1 b/clearSPconfigcache.ps1
old mode 100644
new mode 100755

These changes mean that metadata about your file changed, however the content of your file did not. If you’re working in a group, this may start to interfere with pushes or just add noise to your commits. In order to ignore these changes, please run one of the the following sets of commands.

Bash Shell
From the bash shell run the commands in your git code directory:

git config --unset core.filemode
git config --global core.filemode false

R or R Studio
Or, if you’re using R studio or just R, you can run the following from your console window:

system("git config --unset core.filemode")
system("git config --global core.filemode false")