I came across this rather inscrutable Atlassian Stash error after I had made changes to my submodules in git. If you run across this error it may be because you’ve manually edited your .gitmodules file:

An error occurred while executing an external process: Missing configuration path for module section: <module name>

The submodule repository itself will come up fine, but the parent repository will be completely inaccessible. In my particular case I had somehow managed to fat-finger my.gitmodules to look like this:

Simply removing the last two lines fixed the issue; “submodules” isn’t even a valid entry in .gitmodules. Good luck!