Any chance you can build git-annex from source, so we can try a few modifications to try to narrow this down?
sudo apt-get build-dep git-annex apt-get source git-annex cd git-annex-6.20180509 make PATH=`pwd`:$PATH export PATH Then see if you can reproduce the problem, and then try applying the attached patch, and re-making and see if it avoids the problem. The patch tries to avoid doing anything before forking when starting the assistant, so it should do only the same pre-fork operations as git-annex watch. (Other than some differences due to argument parsing I suppose.) -- see shy jo
diff --git a/Command/Assistant.hs b/Command/Assistant.hs
index 70088674d..b148b2566 100644
--- a/Command/Assistant.hs
+++ b/Command/Assistant.hs
@@ -60,8 +60,8 @@ start o
liftIO autoStop
stop
| otherwise = do
- liftIO ensureInstalled
- ensureInitialized
+ --liftIO ensureInstalled
+ --ensureInitialized
Command.Watch.start True (daemonOptions o) (startDelayOption o)
startNoRepo :: AssistantOptions -> IO ()
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