[[!comment format=mdwn
 username="joey"
 subject="""comment 4"""
 date="2020-01-23T15:51:46Z"
 content="""
I notice that debug output has no BatchMode=true in any ssh call. But
the version of git-annex you show always runs ssh with that when
-J is used, unless sshcaching is disabled.

More evidence that sshcaching is disabled in your transcript is that when
it does run ssh, it does not pass -S.

I think the repository must be on a crippled filesystem, on which
git-annex can't do ssh connection caching, because the filesystem
does not support unix sockets. (Or it potentially could be crippled in some
other way.) So it ignores the annex.sshcaching setting.
You could work around this by setting the (undocumented)
GIT_ANNEX_TMP_DIR to some temporary directory on a non-crippled filesystem.

I'm going to add a warning message in this situation.
"""]]
