One of my repositories worked just fine for months, until I have decided to put an encfs folder within it. Encfs is encrypting folders and files, resulting in weird file and folder names. However, rsync just seems to fail.

This has already been a topic here a few times, for example [1] and [2].

Unfortunately, I have not been lucky enough to recover the situation by the hints given.

What I did to investigate is that I have re-run one of the shell commands stuck client-side and appended --debug to gain a deeper look. This is the output:

$ /opt/git-annex/2016-01-14/exe/ssh --library-path /opt/git-annex/2016-01-14//etc/ /opt/git-annex/2016-01-14/shimmed/ssh/ssh -S .git/annex/ssh/user@ -o ControlMaster=auto -o ControlPersist=yes -T user@ git-annex-shell 'recvkey' '/mnt/path/to/share/' 'SHA256E-s262670--e004c6e3f87ad2b5d74d206de85de5449c9f263d83e6ef1c87ffb03be8b7e725' --debug --uuid e34522e4-1dab-459c-b295-1fe41e7692e4 '--' 'remoteuuid=07820aec-e2a3-4c60-bd57-b39b7213e056' 'unlocked=1' 'direct=1' 'associatedfile=.encfs_folder/CMG23xCwkemocE-Gq9WHpO-n/1vqfTkJChNm5CgjBsZ--,9r,ZOcSBTxE-Ogz5ytA8R23st52LWf4d9MjRref56VhbEB/4ezakoEn8dqOT8s,K4X,ueSs' '--' dummy rsync --server -pe.Lsfx --log-format=X --inplace . .
[2016-03-16 22:52:18.922914] transfer start
[2016-03-16 22:52:18.949417] call: rsync ["--server","-t","--inplace","-e.Lsf",".","../../mnt/path/to/share/.git/annex/tmp/SHA256E-s262670--e004c6e3f87ad2b5d74d206de85de5449c9f263d83e6ef1c87ffb03be8b7e725"]
protocol version mismatch -- is your shell clean?
(see the rsync man page for an explanation)
rsync error: protocol incompatibility (code 2) at compat.c(176) [Receiver=3.1.1]
[2016-03-16 22:59:05.890987] process done ExitFailure 2
[2016-03-16 22:59:05.899506] transfer done

What can I do other than to just move the encfs outside my repository, which is of course the least favorable option for me to do?