Hi! I've noticed that if I turn a subdirectory into a submodule, I'm having severe trouble merging branches from before that change, even if they don't modify that subdirectory at all. I've posted this problem on Stack Overflow and started a bounty for it. See http://stackoverflow.com/q/31821219/1468366. So far I haven't received an answer, so I decided to ask here as well. Here is an example. # Create one project, to be used as a subproject later on git init a cd a echo aaa > aa git add -A git commit -m a1 cd .. # Create a second project, containing a as a normal directory initially git init b cd b mkdir a b echo aaa > a/aa echo bbb > b/bb git add -A git commit -m b1 # Replace directory with submodule git rm -r a git submodule add ../a a git commit -m b2 # Create feature brach starting at version without submodule git submodule deinit . # will error if I don't do this git checkout -b branch HEAD^ echo abc > b/bb git commit -a -m b3 # Try to merge the feature branch git checkout master git merge branch This prints an error message: > CONFLICT (file/directory): There is a directory with name a in branch. > Adding a as a~HEAD > Automatic merge failed; fix conflicts and then commit the result. I get the same error if I do a git submodule update --init before the git merge branch. I don't see any a~HEAD anywhere, neither in my directory tree nor in the output from git status, which reads like this: > On branch master > You have unmerged paths. > (fix conflicts and run "git commit") > > Changes to be committed: > > modified: b/bb > > Unmerged paths: > (use "git add <file>..." to mark resolution) > > added by us: a If I do git add a as suggested, I get another error: > error: unable to index file a > fatal: updating files failed If I do git submodules update --init just before the merge, then I can do git add a successfully. But if I forget to do so, and then try doing that after the merge, I receive this error message: > Submodule 'a' (…/a) registered for path 'a' > Skipping unmerged submodule a How do I recover from this situation? Something other than git merge --abort, since I'd like to use it for things like git rebase as well, and since in some scenarios (don't know how to reproduce) I couldn't even abort the merge cleanly, and had to do a hard reset instead. How can I avoid it in the first place? Is there some magic setting which makes git do the right thing with submodules vs. directories during merges, so that I don't have to manually post-process a merge which only modifies files unrelated to the submodules? If there is no easy way to avoid this, do you think I should file a bug report for this? After all, replacing a subdirectory by a submodule shouldn't be that rare, and neither should be merges across such a change. So in my opinion, git should be able to cope with this. Greetings, Martin von Gagern -- To unsubscribe from this list: send the line "unsubscribe git" in the body of a message to majordomo@xxxxxxxxxxxxxxx More majordomo info at http://vger.kernel.org/majordomo-info.html