Add a note regarding syncing the git submodule conf to CI doc.

What does this MR do?

Using the new CI repo permissions system, which grants a CI process permissions based on the permissions the user triggering the build has, we encountered the problem that our changes regarding relative URLs in the git submodule conf were not taken into account. As it turned out, this is because the .git Folder is shared between runs. This MR adds information on this to the docs, along with a possible way to circumvent this issue.