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### Please describe the problem.
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I had set up git-annex on a mac; I had created an initial repository at ~/annex; I had created a second repository on an external drive, at /Volumes/Biblio/annex; I had paired with three other machines on the same network, (two linux, one other mac) and set up a remote server as a backup-type repository. All seemed well. It had finally finished syncing everything to the remote server (my upload speeds are slow).
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I closed the firefox window showing the dashboard. I wanted to reopen it, so I ran the git-annex.app again, presuming on a running instance that that just opens the browser back at the webapp. Firefox window opened, but the only repository was the second one I'd made on the external drive.
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I restarted, as best as I could work out: git-annex assistant --stop, then because that left behind a process, killall git-annex. Then restarted the app.
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Firefox opened on the webapp. I had two repositories: The one on the external drive (now the "Here" repo) and the one on ~/annex but only as if it was paired from a different machine.
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ie: I see only "celestia.local (rachel@celestia.local~/annex)". This machine *is* celestia.local.
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That's it. Startup scan took a couple of minutes but didn't add anything. Then it decided to sync to celestia.local, which it took a little time over but didn't apparently do anything.
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If I drop files into ~/annex they are not synced anywhere. ~/annex still has a .git directory, populated with git files, it looks intact. It's just not being seen.
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Is it possible because the user is prompted to create their initial repo at ~/Desktop/annex it will by default only look there, then start looking in external drives for it? So the fact I didn't want it on my desktop, but put it directly in home, meant it got lost on restart?
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git-annex vicfg in ~/annex shows me this:
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[[!format sh """
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# git-annex configuration
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#
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# Changes saved to this file will be recorded in the git-annex branch.
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#
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# Lines in this file have the format:
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# setting uuid = value
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# Repository trust configuration
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# (Valid trust levels: trusted semitrusted untrusted dead)
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# (for web)
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#trust 00000000-0000-0000-0000-000000000001 = semitrusted
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# (for rachel@octavia:~/annex)
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#trust 161dec38-e8be-43b8-86c5-555d35ce3416 = semitrusted
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# (for rachel@celestia.local:~/annex)
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#trust 179fcddf-e247-4577-804b-267feed8abb1 = semitrusted
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# (for 192.168.1.103_annex (rachel@rainbow.local:~/annex))
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#trust 256d5762-150d-4d5d-9340-517de298c874 = semitrusted
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# (for twilight.local_annex (rachel@twilight:~/annex))
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#trust aeef7490-ce27-4255-b800-1947706c4a06 = semitrusted
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# (for rachel@octavia:~/annex)
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#trust c469fbce-f3b4-4e27-a54f-0b747797a7d5 = semitrusted
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# (for annex (Biblio's Copy))
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#trust c9e307e2-1189-47ed-8ad4-03b5c1b64e36 = semitrusted
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# (for luna.strangenoises.org_annex)
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#trust f36dbdf8-1bba-11e3-9dbe-f33cfb0e2bed = semitrusted
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# (for octavia.local_annex (rachel@octavia:~/annex))
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#trust f748a5ed-d870-48fb-b3ec-811488eb2faa = semitrusted
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# (for rachel@twilight:~/annex)
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#trust fcaba03e-1ba5-11e3-90f1-57fe1467e006 = semitrusted
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# Repository groups
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# (Standard groups: client transfer backup incrementalbackup smallarchive archive source manual public unwanted)
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# (Separate group names with spaces)
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# (for rachel@octavia:~/annex)
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group 161dec38-e8be-43b8-86c5-555d35ce3416 = client
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# (for rachel@celestia.local:~/annex)
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group 179fcddf-e247-4577-804b-267feed8abb1 = client
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# (for 192.168.1.103_annex (rachel@rainbow.local:~/annex))
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group 256d5762-150d-4d5d-9340-517de298c874 = client
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# (for twilight.local_annex (rachel@twilight:~/annex))
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group aeef7490-ce27-4255-b800-1947706c4a06 = client
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# (for rachel@octavia:~/annex)
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group c469fbce-f3b4-4e27-a54f-0b747797a7d5 = client
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# (for annex (Biblio's Copy))
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group c9e307e2-1189-47ed-8ad4-03b5c1b64e36 = client
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# (for octavia.local_annex (rachel@octavia:~/annex))
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group f748a5ed-d870-48fb-b3ec-811488eb2faa = client
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# (for rachel@twilight:~/annex)
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group fcaba03e-1ba5-11e3-90f1-57fe1467e006 = client
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# (for luna.strangenoises.org_annex)
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group f36dbdf8-1bba-11e3-9dbe-f33cfb0e2bed = transfer
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# (for web)
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#group 00000000-0000-0000-0000-000000000001 =
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# Repository preferred contents
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# (for rachel@octavia:~/annex)
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content 161dec38-e8be-43b8-86c5-555d35ce3416 = standard
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# (for rachel@celestia.local:~/annex)
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content 179fcddf-e247-4577-804b-267feed8abb1 = standard
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# (for 192.168.1.103_annex (rachel@rainbow.local:~/annex))
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content 256d5762-150d-4d5d-9340-517de298c874 = standard
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# (for twilight.local_annex (rachel@twilight:~/annex))
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content aeef7490-ce27-4255-b800-1947706c4a06 = standard
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# (for rachel@octavia:~/annex)
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content c469fbce-f3b4-4e27-a54f-0b747797a7d5 = standard
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# (for annex (Biblio's Copy))
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content c9e307e2-1189-47ed-8ad4-03b5c1b64e36 = standard
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# (for luna.strangenoises.org_annex)
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content f36dbdf8-1bba-11e3-9dbe-f33cfb0e2bed = standard
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# (for octavia.local_annex (rachel@octavia:~/annex))
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content f748a5ed-d870-48fb-b3ec-811488eb2faa = standard
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# (for rachel@twilight:~/annex)
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content fcaba03e-1ba5-11e3-90f1-57fe1467e006 = standard
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# (for web)
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#content 00000000-0000-0000-0000-000000000001 =
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"""]]
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while the same command in /Volumes/Biblio/annex gives:
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[[!format sh """
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# git-annex configuration
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#
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# Changes saved to this file will be recorded in the git-annex branch.
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#
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# Lines in this file have the format:
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# setting uuid = value
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# Repository trust configuration
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# (Valid trust levels: trusted semitrusted untrusted dead)
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# (for web)
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#trust 00000000-0000-0000-0000-000000000001 = semitrusted
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# (for rachel@octavia:~/annex)
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#trust 161dec38-e8be-43b8-86c5-555d35ce3416 = semitrusted
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# (for celestia.local (rachel@celestia.local:~/annex))
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#trust 179fcddf-e247-4577-804b-267feed8abb1 = semitrusted
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# (for rachel@rainbow.local:~/annex)
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#trust 256d5762-150d-4d5d-9340-517de298c874 = semitrusted
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# (for rachel@twilight:~/annex)
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#trust aeef7490-ce27-4255-b800-1947706c4a06 = semitrusted
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# (for rachel@octavia:~/annex)
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#trust c469fbce-f3b4-4e27-a54f-0b747797a7d5 = semitrusted
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# (for Biblio's Copy)
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#trust c9e307e2-1189-47ed-8ad4-03b5c1b64e36 = semitrusted
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# (for )
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#trust f36dbdf8-1bba-11e3-9dbe-f33cfb0e2bed = semitrusted
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# (for rachel@octavia:~/annex)
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#trust f748a5ed-d870-48fb-b3ec-811488eb2faa = semitrusted
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# (for rachel@twilight:~/annex)
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#trust fcaba03e-1ba5-11e3-90f1-57fe1467e006 = semitrusted
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# Repository groups
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# (Standard groups: client transfer backup incrementalbackup smallarchive archive source manual public unwanted)
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# (Separate group names with spaces)
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# (for rachel@octavia:~/annex)
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group 161dec38-e8be-43b8-86c5-555d35ce3416 = client
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# (for celestia.local (rachel@celestia.local:~/annex))
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group 179fcddf-e247-4577-804b-267feed8abb1 = client
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# (for rachel@rainbow.local:~/annex)
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group 256d5762-150d-4d5d-9340-517de298c874 = client
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# (for rachel@twilight:~/annex)
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group aeef7490-ce27-4255-b800-1947706c4a06 = client
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# (for rachel@octavia:~/annex)
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group c469fbce-f3b4-4e27-a54f-0b747797a7d5 = client
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# (for Biblio's Copy)
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group c9e307e2-1189-47ed-8ad4-03b5c1b64e36 = client
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# (for rachel@octavia:~/annex)
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group f748a5ed-d870-48fb-b3ec-811488eb2faa = client
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# (for rachel@twilight:~/annex)
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group fcaba03e-1ba5-11e3-90f1-57fe1467e006 = client
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# (for )
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group f36dbdf8-1bba-11e3-9dbe-f33cfb0e2bed = transfer
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# (for web)
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#group 00000000-0000-0000-0000-000000000001 =
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# Repository preferred contents
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# (for rachel@octavia:~/annex)
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content 161dec38-e8be-43b8-86c5-555d35ce3416 = standard
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# (for celestia.local (rachel@celestia.local:~/annex))
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content 179fcddf-e247-4577-804b-267feed8abb1 = standard
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# (for rachel@rainbow.local:~/annex)
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content 256d5762-150d-4d5d-9340-517de298c874 = standard
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# (for rachel@twilight:~/annex)
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content aeef7490-ce27-4255-b800-1947706c4a06 = standard
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# (for rachel@octavia:~/annex)
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content c469fbce-f3b4-4e27-a54f-0b747797a7d5 = standard
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# (for Biblio's Copy)
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content c9e307e2-1189-47ed-8ad4-03b5c1b64e36 = standard
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# (for )
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content f36dbdf8-1bba-11e3-9dbe-f33cfb0e2bed = standard
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# (for rachel@octavia:~/annex)
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content f748a5ed-d870-48fb-b3ec-811488eb2faa = standard
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# (for rachel@twilight:~/annex)
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content fcaba03e-1ba5-11e3-90f1-57fe1467e006 = standard
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# (for web)
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#content 00000000-0000-0000-0000-000000000001 =
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"""]]
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### What steps will reproduce the problem?
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As above. I have no idea what just happened, but apart from git-annex assistant --stop and having to mop up leftover processes, I didn't use the git-annex commandline for anything.
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### What version of git-annex are you using? On what operating system?
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Mac OS X 10.8.4
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Version: 4.20130909-ga29f960
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Build flags: Assistant Webapp Pairing Testsuite S3 WebDAV FsEvents XMPP DNS Feeds Quvi
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### Please provide any additional information below.
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The log on ~/annex/.git/annex/daemon.log is huge and full of transfers of files with my personal filenames. I'd rather not. It appears to end normally.
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Now there is a short log in /Volumes/Biblio/annex/.git/annex/daemon.log from, I guess, the time I tried to restart. For some reason therefore, after the successful session finished, on restart it only looks here. This log is appended.
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[[!format sh """
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[2013-09-12 21:35:39 BST] main: starting assistant version 4.20130909-ga29f960
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[2013-09-12 21:35:39 BST] TransferScanner: Syncing with celestia.local
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Already up-to-date.
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(scanning...) [2013-09-12 21:35:39 BST] Watcher: Performing startup scan
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From /Users/rachel/annex
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* [new branch] git-annex -> celestia.local/git-annex
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* [new branch] master -> celestia.local/master
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* [new branch] synced/git-annex -> celestia.local/synced/git-annex
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* [new branch] synced/master -> celestia.local/synced/master
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Updating 4f974a8..74770d9
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Fast-forward
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Already up-to-date.
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Already up-to-date.
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Already up-to-date.
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[2013-09-12 21:36:39 BST] Pusher: Syncing with celestia.local
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(merging celestia.local/git-annex celestia.local/synced/git-annex into git-annex...)
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(Recording state in git...)
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(started...) error: Ref refs/heads/synced/git-annex is at 5b4ed9b3098e936d60b61a1d3915fa29e8c823d0 but expected 792d2a5c14b0b6327d2089e174063c474ba5a764
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remote: error: failed to lock refs/heads/synced/git-annex
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To /Users/rachel/annex
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792d2a5..5b4ed9b git-annex -> synced/git-annex
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To /Users/rachel/annex
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! [remote rejected] git-annex -> synced/git-annex (failed to lock)
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error: failed to push some refs to '/Users/rachel/annex'
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Everything up-to-date
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"""]]
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Well, I see that thing about "failed to lock". I can imagine that my 'killall git-annex' to kill a leftover process that was hanging around after I'd done git-annex assistant --stop might have left stale lock files, somewhere... but of course I only got as far as doing that because I was already encountering problems, just trying to return to the webapp.
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