BTW: submodule diff should always get stored, can you provide some error logs on fail cases?

It's hard to pinpoint, I have a repository with several submodules, some changes are found, others not. I've added untracked files, but sometimes it simply doesn't pick them. Running git diff --submodule=diff (which is the same command in the GitDetector class) always return the correct results

Before manually modifying the diff:
If you have local commits (i.e. un-pushed) this might fail the diff apply, in that case you can set the following in your clearml.conf

I have both:
store_uncommitted_code_diff: true
and
store_code_diff_from_remote: true
set