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+[[!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..
+"""]]