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+### Please describe the problem.
+When using git-annex in indirect mode (or even in direct mode I think, although this is not to be very reliable in this context), git repos inside a git-annex are ignored. This is due to the fact that git is ignoring nested .git folders, and then, we can safely work with git-annex and nested git repos without conflicts.
+
+Using a tool such as my-repos, one can then sync its entire home directory, containing folders and git repos, syncing the normal folders thanks to git-annex, and storing the git repos metadata for easy cloning using my-repos.
+
+However, when using the git-annex assistant (or the daemon to have automatic background sync), this is no longer the case.
+
+After discussion on IRC, we thought this could be due to the fact that files are copied sequentially and that the .git folder is not yet present when it starts copying. However, disabling the daemon, copying the files and reenabling it then leads to the same behaviour.
+
+Thanks!
+
+
+### What version of git-annex are you using? On what operating system?
+
+git-annex-bin on AUR.