[[!comment format=mdwn
 username="joey"
 subject="""comment 1"""
 date="2015-02-09T17:54:00Z"
 content="""
I've confirmed this behavior. Normally git-annex propigates --git-dir
to git commands it runs, but this is not done in a few cases in the
assistant, including when it starts `git-annex remotedaemon` but also
`git-annex fsck`, `git annex unused`, and `git annex transferkeys`.

(Just search for readProgramFile; Remote.Git.fsckOnRemote is the only
place outside the assistant that uses it, and it does take care to
propigate --git-dir and --work-tree.)

Also, restarting the assistant, either in the web ui or automatically due to
an upgrade also doesn't propigate --git-dir.

And, the assistant's autostart file doesn't support --git-dir.

All of which could be fixed, but I have to wonder, why? What's the use case
for a separate --git-dir with the assistant? I guess not vcsh because the
assistant would watch for all changes to the home directory, and add them,
and that's not how vcsh is used.

I'm tempted to just make the assistant refuse to start when given a
nonstandard --git-dir..
"""]]