Shourya Shukla <periperidip@xxxxxxxxx> writes: > + if (git_config_rename_section_in_file(index_only ? GITMODULES_INDEX : > + GITMODULES_FILE, sect.buf, NULL) < 0) { Also, is it really sufficient to pass GITMODULES_INDEX as the first argument to this function to tweak what is in the index? git_config_copy_or_rename_section_in_file() which is the implementation of that helper seems to always want to work with a file that is on disk, by making unconditional calls to hold_lock_file_for_update(), fopen(), fstat(), chmod(), etc. So I suspect that there are much more work needed. It seems to me that the config editing API is one of the older and hackier parts of the system and requires quite a lot of work to teach it to work with anything but a on-disk file. In the longer term, it may be a good thing to clean it up, but I suspect that it is way too much work for too little benefit to do so as a part of this topic, so an easier way out for now would be to: - write out the .gitmodules in the index to a temporary file (learn how to correctly call entry.c::checkout_entry() by studying how builtin/checkout-index.c::checkout_file() calls it, especially to a temporary file with the --temp option). - use git_config_rename_section_in_file() on that temporary file to remove the section about the submodule. - read that temporary file back into memory and write it out as a blob object by calling sha1-file.c::write_object_file(). - add that back to the index as .gitmodules (studying how builtin/update-index.c::add_cacheinfo() calls add_cache_entry() would be a good way to learn how to do this). The working tree side can stay as is, but as I said in the earlier message, I think you need to update the .gitmodules in the working tree and .gitmodules in the index separately (and without doing any equivalent of "git add .gitmodules").