We cannot know from looking at .gitmodules whether a directory is a submodule or not. We need the index or tree we are comparing against to tell us. Otherwise we have to assume the entry in .gitmodules is stale or otherwise invalid. Thus we pass the index of the repository into the workdir iterator, even if we do not want to compare against it. This follows what git does, which even for `git diff <tree>`, it will consider staged submodules as such.
When we free the global state at thread termination, we must also free the error message in order not to leak the string once per thread.
Move the definition of git_thread_yield() to the test which needs it and add the correct definition for it for FreeBSD and derivatives. Original patch adding FreeBSD and derivatives by @jacquesg.
It seems that with the various recent changes to reference updating and reflog writing, that the thread safety of refdb updates has been reduced (either that or it was never thread safe and the window for error has increased). Either way, this test is now sometimes segfaulting which is no good, so let's disable the test for now. We don't really make any public promises about thread safety for this type of operation, so I think this is acceptable, at least in the short term.
In the threading tests, I was still seeing a race condition where the same item could end up being inserted multiple times into the index. Preserving the sorted-ness of the index outside of the `index_insert` call fixes the issue.
This is a big refactoring of the attribute file cache to be a bit simpler which in turn makes it easier to enforce a lock around any updates to the cache so that it can be used in a threaded env. Tons of changes to the attributes and ignores code.