What steps will reproduce the problem? Move any file into a git annex repository using "mv". The symlink is created, content is stored in .git/annex, content may even be moved to other repos, but the symlink is not checked into git. A day later, the daily sanity check will add and check-in the link. What is the expected output? What do you see instead? After adding content to git-annex, "git status" should show a clean repo with everything checked in. Instead it looks like this: ~$ touch foobar ~$ rm foobar ~$ echo "foo" > bar ~$ mv bar annex/Incoming/ ~$ cd annex annex$ git status # On branch master # Untracked files: # (use "git add ..." to include in what will be committed) # # Incoming/bar nothing added to commit but untracked files present (use "git add" to track) annex$ I ran the assistant with the --debug option and this is what was in the daemon.log when this happened: [2013-03-13 09:23:36 EDT] read: git ["--git-dir=/Users/ed/annex/.git","--work-tree=/Users/ed/annex","ls-files","--others","--exclude-standard","-z","--","/Users/ed/annex/Incoming/bar"] [2013-03-13 09:23:37 EDT] read: lsof ["-F0can","+d","/Users/ed/annex/.git/annex/tmp/"] [2013-03-13 09:23:39 EDT] Committer: Adding bar (Recording state in git...) (Recording state in git...) (Recording state in git...) (Recording state in git...) add Incoming/bar (checksum...) recv: resource vanished (Connection reset by peer) [2013-03-13 09:23:39 EDT] 127.0.0.1 GET /sidebar/NotificationId%201 Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:19.0) Gecko/20100101 Firefox/19.0 [2013-03-13 09:23:40 EDT] 127.0.0.1 GET /sidebar/NotificationId%201 Mozilla/5.0 (Macintosh; Intel Mac OS X 10.7; rv:19.0) Gecko/20100101 Firefox/19.0 What version of git-annex are you using? On what operating system? A fresh compile from last night (git hash fe2df85f0db08227556897db3b076ef321e4303a). OS X Lion. Please provide any additional information below. I get the same effect when doing this with a newly created "testannex" repo with nothing in it but a newly created file -- I just haven't left the assistant running in a test repo all day to confirm that the file doesn't get checked in till the next daily sanity check. Here it is on a newly-created, empty repo: testannex$ git init Initialized empty Git repository in /Users/ed/testannex/.git/ testannex$ git annex init init ok (Recording state in git...) testannex$ git annex assistant --debug [2013-03-13 09:31:10 EDT] read: git ["--git-dir=/Users/ed/testannex/.git","--work-tree=/Users/ed/testannex","show-ref","git-annex"] [2013-03-13 09:31:10 EDT] read: git ["--git-dir=/Users/ed/testannex/.git","--work-tree=/Users/ed/testannex","show-ref","--hash","refs/heads/git-annex"] [2013-03-13 09:31:10 EDT] read: git ["--git-dir=/Users/ed/testannex/.git","--work-tree=/Users/ed/testannex","log","refs/heads/git-annex..4aeceaff629c83c35c1244da9eeeac4b7c228fef","--oneline","-n1"] [2013-03-13 09:31:10 EDT] chat: git ["--git-dir=/Users/ed/testannex/.git","--work-tree=/Users/ed/testannex","cat-file","--batch"] testannex$ cd ~$ echo "foo" > bar ~$ mv bar testannex/ ~$ cd testannex/ testannex$ git status # On branch master # # Initial commit # # Untracked files: # (use "git add ..." to include in what will be committed) # # bar nothing added to commit but untracked files present (use "git add" to track) (meanwhile.....) ~$ cd testannex/.git/annex/ annex$ tail -f daemon.log [2013-03-13 09:31:10 EDT] TransferWatcher: watching for transfers [2013-03-13 09:31:10 EDT] read: git ["--git-dir=/Users/ed/testannex/.git","--work-tree=/Users/ed/testannex","show-ref","git-annex"] [2013-03-13 09:31:10 EDT] read: git ["--git-dir=/Users/ed/testannex/.git","--work-tree=/Users/ed/testannex","show-ref","--hash","refs/heads/git-annex"] [2013-03-13 09:31:10 EDT] read: git ["--git-dir=/Users/ed/testannex/.git","--work-tree=/Users/ed/testannex","log","refs/heads/git-annex..4aeceaff629c83c35c1244da9eeeac4b7c228fef","--oneline","-n1"] [2013-03-13 09:31:10 EDT] Merger: watching /Users/ed/testannex/.git/refs [2013-03-13 09:31:10 EDT] read: git ["--git-dir=/Users/ed/testannex/.git","--work-tree=/Users/ed/testannex","ls-tree","-z","--","refs/heads/git-annex","uuid.log","remote.log","trust.log","group.log","preferred-content.log"] [2013-03-13 09:31:10 EDT] read: git ["--git-dir=/Users/ed/testannex/.git","--work-tree=/Users/ed/testannex","ls-tree","-z","--","refs/heads/git-annex","uuid.log","remote.log","trust.log","group.log","preferred-content.log"] (scanning...) [2013-03-13 09:31:10 EDT] Watcher: Performing startup scan [2013-03-13 09:31:10 EDT] read: git ["--git-dir=/Users/ed/testannex/.git","--work-tree=/Users/ed/testannex","ls-files","--deleted","-z","--","/Users/ed/testannex"] (started...) [2013-03-13 09:31:10 EDT] Watcher: watching . [2013-03-13 09:31:48 EDT] read: git ["--git-dir=/Users/ed/testannex/.git","--work-tree=/Users/ed/testannex","ls-files","--others","--exclude-standard","-z","--","/Users/ed/testannex/bar"] [2013-03-13 09:31:49 EDT] read: lsof ["-F0can","+d","/Users/ed/testannex/.git/annex/tmp/"] [2013-03-13 09:31:51 EDT] Committer: Adding bar add bar [2013-03-13 09:31:51 EDT] chat: git ["--git-dir=/Users/ed/testannex/.git","--work-tree=/Users/ed/testannex","check-attr","-z","--stdin","annex.backend","annex.numcopies","--"] (checksum...) [2013-03-13 09:31:51 EDT] chat: git ["--git-dir=/Users/ed/testannex/.git","--work-tree=/Users/ed/testannex","cat-file","--batch"] > This bug affected OSX when indirect mode repositories were used. > Direct mode repositories were ok. > I expected to get an event from fsevents when I made the symlink, > and this event is not arriving (or at least not always). Switched > the code to use the same method for fsevents as for kqueue and that fixed > it. [[done]] --[[Joey]]