git-annex/doc/bugs/Deleted_files_during_merge.mdwn

### Please describe the problem.

I edited a file on one machine (firefly), which then synced with another (browncoats). browncoats then deleted the changed file and comitted that with the message «git-annex in browncoats». During this time the file was only ever touched on one machine (firefly), never on browncoats (which I turned on after the two commits on firefly had been made, with git annex assistant running). The result is that the file has disappeared and I have to dig through the log and get it from a backup repository. Both machines are running the assistant in direct mode. Both on ext4 in case that matters.

I've included the daemon.log from browncoats (with filenames redacted).

### What steps will reproduce the problem?

Unknown.

### What version of git-annex are you using? On what operating system?

Both are Archlinux 64bit, both running git-annex version 5.20150219-g52daae5 from the standalone 64bit build.

### Please provide any additional information below.

First commit:
[[!format text """
Date:   Thu Mar 5 13:24:30 2015 +0100

    git-annex in firefly

diff --git a/Dokument/Dokument/Skule/Sjukepleie-s4/leseliste.ods b/Dokument/Dokument/Skule/Sjukepleie-s4/leseliste.ods
index 5a18c1e..e579681 120000
--- a/Dokument/Dokument/Skule/Sjukepleie-s4/leseliste.ods
+++ b/Dokument/Dokument/Skule/Sjukepleie-s4/leseliste.ods
@@ -1 +1 @@
-../../../../.git/annex/objects/Kg/v0/SHA256E-s39322--ca7a6d4d84b59d49a699e921438ace0d6c326c9db218a7c99b0b6626cae4b976.ods/SHA256E-s39322--ca7a6d4d84b59d49a699e921438ace0d6c326c9db218a7c99b0b6626cae4b976.ods
\ No newline at end of file
+../../../../.git/annex/objects/V8/7z/SHA256E-s39378--dfbc693d94beb76e1556ff2aefd87b5b6678b93f03bcb0113e1249872c6f7c71.ods/SHA256E-s39378--dfbc693d94beb76e1556ff2aefd87b5b6678b93f03bcb0113e1249872c6f7c71.ods
\ No newline at end of file
"""]]

Second commit:
[[!format text """
Date:   Thu Mar 5 13:27:21 2015 +0100

    git-annex in firefly

diff --git a/Dokument/Dokument/Skule/Sjukepleie-s4/leseliste.ods b/Dokument/Dokument/Skule/Sjukepleie-s4/leseliste.ods
index e579681..f7fbb69 120000
--- a/Dokument/Dokument/Skule/Sjukepleie-s4/leseliste.ods
+++ b/Dokument/Dokument/Skule/Sjukepleie-s4/leseliste.ods
@@ -1 +1 @@
-../../../../.git/annex/objects/V8/7z/SHA256E-s39378--dfbc693d94beb76e1556ff2aefd87b5b6678b93f03bcb0113e1249872c6f7c71.ods/SHA256E-s39378--dfbc693d94beb76e1556ff2aefd87b5b6678b93f03bcb0113e1249872c6f7c71.ods
\ No newline at end of file
+../../../../.git/annex/objects/0v/kG/SHA256E-s39498--d962b697df05df77275572bc03f18995b47d013708e6b775c700b3092028c54f.ods/SHA256E-s39498--d962b697df05df77275572bc03f18995b47d013708e6b775c700b3092028c54f.ods
\ No newline at end of file
"""]]

The final commit, now on the remote:

[[!format text """
Date:   Thu Mar 5 13:34:47 2015 +0100

    git-annex in browncoats

diff --git a/Dokument/Dokument/Skule/Sjukepleie-s4/leseliste.ods b/Dokument/Dokument/Skule/Sjukepleie-s4/leseliste.ods
deleted file mode 120000
index f7fbb69..0000000
--- a/Dokument/Dokument/Skule/Sjukepleie-s4/leseliste.ods
+++ /dev/null
@@ -1 +0,0 @@
-../../../../.git/annex/objects/0v/kG/SHA256E-s39498--d962b697df05df77275572bc03f18995b47d013708e6b775c700b3092028c54f.ods/SHA256E-s39498--d962b697df05df77275572bc03f18995b47d013708e6b775c700b3092028c54f.ods
\ No newline at end of file
"""]]

[[!format sh """
# If you can, paste a complete transcript of the problem occurring here.
# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log
[2015-03-05 13:32:49 CET] main: starting assistant version 5.20150219-g52daae5
[2015-03-05 13:32:51 CET] Cronner: Consistency check in progress
[2015-03-05 13:34:40 CET] TransferScanner: Syncing with firefly, serenity, zoe, river 
p11-kit: couldn't load module: /usr/lib/x86_64-linux-gnu/pkcs11/p11-kit-trust.so: /usr/lib/x86_64-linux-gnu/pkcs11/p11-kit-trust.so: cannot open shared object file: Ingen slik fil eller filkatalog
p11-kit: couldn't load module: /usr/lib/x86_64-linux-gnu/pkcs11/gnome-keyring-pkcs11.so: /usr/lib/x86_64-linux-gnu/pkcs11/gnome-keyring-pkcs11.so: cannot open shared object file: Ingen slik fil eller filkatalog
Warning: the ECDSA host key for 'firefly' differs from the key for the IP address '10.0.0.17'
Offending key for IP in /home/zerodogg/.ssh/known_hosts:103
Matching host key in /home/zerodogg/.ssh/known_hosts:148
X11 forwarding request failed
Warning: the ECDSA host key for 'firefly' differs from the key for the IP address '10.0.0.17'
Offending key for IP in /home/zerodogg/.ssh/known_hosts:103
Matching host key in /home/zerodogg/.ssh/known_hosts:148
X11 forwarding request failed on channel 0
(scanning...) [2015-03-05 13:34:41 CET] Watcher: Performing startup scan
ERROR: ld.so: object '/usr/lib/arm-linux-gnueabihf/libcofi_rpi.so' from /etc/ld.so.preload cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object '/usr/lib/arm-linux-gnueabihf/libcofi_rpi.so' from /etc/ld.so.preload cannot be preloaded (cannot open shared object file): ignored.
git-annex-shell: expected repository UUID b158aa97-4b68-4c37-a109-f3df91480185 but found UUID 2a6ccda4-f94c-484f-aep11-kit: couldn't load module: /usr/lib/x86_64-linux-gnu/pkcs11/p11-kit-trust.so: /usr/lib/x86_64-linux-gnu/pkcs11/p11-kit-trust.so: cannot open shared object file: Ingen slik fil eller filkatalog
p11-kit: couldn't load module: /usr/lib/x86_64-linux-gnu/pkcs11/gnome-keyring-pkcs11.so: /usr/lib/x86_64-linux-gnu/pkcs11/gnome-keyring-pkcs11.so: cannot open shared object file: Ingen slik fil eller filkatalog
gpg: Signature made to. 19. feb. 2015 kl. 23.44 +0100 CET using DSA key ID 89C809CB
gpg: /tmp/git-annex-gpg.tmp.0/trustdb.gpg: trustdb created
gpg: Good signature from "git-annex distribution signing key (for Joey Hess) <id@joeyh.name>"
gpg: WARNING: This key is not certified with a trusted signature!
gpg:          There is no indication that the signature belongs to the owner.
Primary key fingerprint: 4005 5C6A FD2D 526B 2961  E78F 5EE1 DBA7 89C8 09CB
ERROR: ld.so: object '/usr/lib/arm-linux-gnueabihf/libcofi_rpi.so' from /etc/ld.so.preload cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object '/usr/lib/arm-linux-gnueabihf/libcofi_rpi.so' from /etc/ld.so.preload cannot be preloaded (cannot open shared object file): ignored.
git-annex-shell: expected repository UUID b158aa97-4b68-4c37-a109-f3df91480185 but found UUID 2a6ccda4-f94c-484f-aefe-ce49c1767eab
ssh: connect to host river port 22: No route to host
fsck FILENAME ERROR: ld.so: object '/usr/lib/arm-linux-gnueabihf/libcofi_rpi.so' from /etc/ld.so.preload cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object '/usr/lib/arm-linux-gnueabihf/libcofi_rpi.so' from /etc/ld.so.preload cannot be preloaded (cannot open shared object file): ignored.
git-annex-shell: expected repository UUID b158aa97-4b68-4c37-a109-f3df91480185 but found UUID 2a6ccda4-f94c-484f-aefe-ce49c1767eab
From firefly:Documents/annexed
   66ab32c..decb072  annex/direct/master -> firefly/annex/direct/master
   7a45b9c..66cf859  git-annex  -> firefly/git-annex
   94362e9..decb072  master     -> firefly/master
   66ab32c..decb072  synced/master -> firefly/synced/master
(checksum...)
ok
fsck FILENAME (merging firefly/git-annex into git-annex...)
(started...) (checksum...)
ok
fsck FILENAME From serenity:/home/zerodogg/Documents/annexed
   7a45b9c..66cf859  synced/git-annex -> serenity/synced/git-annex
   66ab32c..decb072  synced/master -> serenity/synced/master
Automatic merge went well; stopped before committing as requested
(checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME ssh: connect to host river port 22: No route to host
(checksum...)
ok
fsck FILENAME [2015-03-05 13:34:47 CET] Committer: Committing changes to git
(checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME [2015-03-05 13:34:47 CET] Pusher: Syncing with firefly, serenity, zoe, river 
Warning: the ECDSA host key for 'firefly' differs from the key for the IP address '10.0.0.17'
Offending key for IP in /home/zerodogg/.ssh/known_hosts:103
Matching host key in /home/zerodogg/.ssh/known_hosts:148
(checksum...)
ok
fsck FILENAME X11 forwarding request failed on channel 0
(checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME To zerodogg@firefly:Documents/annexed
   7a45b9c..510e591  git-annex -> synced/git-annex
   decb072..0f076c0  annex/direct/master -> synced/master
(checksum...)
ok
fsck FILENAME To serenity:/home/zerodogg/Documents/annexed
   66cf859..510e591  git-annex -> synced/git-annex
   decb072..0f076c0  annex/direct/master -> synced/master
(checksum...)
ok
fsck FILENAME [2015-03-05 13:34:49 CET] RemoteControl: Syncing with firefly 
X11 forwarding request failed
(checksum...)
ok
fsck FILENAME ERROR: ld.so: object '/usr/lib/arm-linux-gnueabihf/libcofi_rpi.so' from /etc/ld.so.preload cannot be preloaded (cannot open shared object file): ignored.
ssh: connect to host river port 22: No route to host
ssh: connect to host rivefatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
r port 22: No route to host
ERROR: ld.so: object '/usr/lib/arm-linux-gnueabihf/libcofi_rpi.so' from /etc/ld.so.preload cannot be preloaded (cannot open shared object file): ignored.
git-annex-shell: expected repository UUID b158aa97-4b68-4c37-a109-f3df91480185 but found UUID 2a6ccda4-f94c-484f-aefe-ce49c1767eab
(checksum...)
ok
fsck FILENAME From firefly:Documents/annexed
   decb072..0f076c0  annex/direct/master -> firefly/annex/direct/master
   66cf859..1de4042  git-annex  -> firefly/git-annex
(checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME ssh: connect to host river port 22: No route to host
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
(checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME Warning: the ECDSA host key for 'firefly' differs from the key for the IP address '10.0.0.17'
Offending key for IP in /home/zerodogg/.ssh/known_hosts:103
Matching host key in /home/zerodogg/.ssh/known_hosts:148
(checksum...)
ok
fsck FILENAME X11 forwarding request failed on channel 0
To zerodogg@firefly:Documents/annexed
   510e591..1de4042  git-annex -> synced/git-annex
(checksum...)
ok
fsck FILENAME Everything up-to-date
(checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME ssh: connect to host river port 22: No route to host
ssh: connect to host river port 22: Nfatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
(checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME ERROR: ld.so: object '/usr/lib/arm-linux-gnueabihf/libcofi_rpi.so' from /etc/ld.so.preload cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object '/usr/lib/arm-linux-gnueabihf/libcofi_rpi.so' from /etc/ld.so.preload cannot be preloaded (cannot open shared object file): ignored.
(checksum...)
ok
fsck FILENAME git-annex-shell: expected repository UUID b158aa97-4b68-4c37-a109-f3df91480185 but found UUID 2a6ccda4-f94c-484f-aefe-ce49c1767eab
(checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME ssh: connect to host river port 22: No route to host
(checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME fatal: Unable to create '/home/zerodogg/Documents/annexed/.git/refs/heads/synced/git-annex.lock': File exists.

If no other git process is currently running, this probably means a
git process crashed in this repository earlier. Make sure no other git
process is running and remove the file manually to continue.
fatal: The remote end hung up unexpectedly
fatal: The remote end hung up unexpectedly
(checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME From zoe:Documents/annexed
   61b7ec9..1de4042  synced/git-annex -> zoe/synced/git-annex
   e3b0e2e..0f076c0  synced/master -> zoe/synced/master
(checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME ERROR: ld.so: object '/usr/lib/arm-linux-gnueabihf/libcofi_rpi.so' from /etc/ld.so.preload cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object '/usr/lib/arm-linux-gnueabihf/libcofi_rpi.so' from /etc/ld.so.preload cannot be preloaded (cannot open shared object file): ignored.
git-annex-shell: expected repository UUID b158aa97-4b68-4c37-a109-f3df91480185 but found UUID 2a6ccda4-f94c-484f-aefe-ce49c1767eab
(checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME ssh: connect to host river port 22: No route to host
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
(checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME fra 2013-02-15 00:05:43.png Everything up-to-date
(checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME ssh: connect to host river port 22: No route to host
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
(checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME ssh: connect to host river port 22: No route to host
ssh: connect to hofatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
st river port 22: No route to host
(checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME To zerodogg@zoe:Documents/annexed
   61b7ec9..1de4042  git-annex -> synced/git-annex
   e3b0e2e..0f076c0  annex/direct/master -> synced/master
(checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME ssh: connect to host river port 22: No route to host
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
(checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME ssh: connect to host river port 22: No route to host
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
(checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME ssh: connect to host river port 22: No route to host
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.
(checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
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fsck FILENAME ERROR: ld.so: object '/usr/lib/arm-linux-gnueabihf/libcofi_rpi.so' from /etc/ld.so.preload cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object '/usr/lib/arm-linux-gnueabihf/libcofi_rpi.so' from /etc/ld.so.preload cannot be preloaded (cannot open shared object file): ignored.
git-annex-shell: expected repository UUID b158aa97-4b68-4c37-a109-f3df91480185 but found UUID 2a6ccda4-f94c-484f-aefe-ce49c1767eab
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fsck FILENAME ERROR: ld.so: object '/usr/lib/arm-linux-gnueabihf/libcofi_rpi.so' from /etc/ld.so.preload cannot be preloaded (cannot open shared object file): ignored.
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fsck FILENAME ERROR: ld.so: object '/usr/lib/arm-linux-gnueabihf/libcofi_rpi.so' from /etc/ld.so.preload cannot be preloaded (cannot open shared object file): ignored.
git-annex-shell: expected repository UUID b158aa97-4b68-4c37-a109-f3df91480185 but found UUID 2a6ccda4-f94c-484f-aefe-ce49c1767eab
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fsck FILENAME ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
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fsck FILENAME ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
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fsck FILENAME ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
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fsck FILENAME ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
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fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
(checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME (checksum...)
ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok
fsck FILENAME ok

  Time limit (5m) reached!
ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]
ssh: connect to host river port 22: No route to host
rsync: connection unexpectedly closed (0 bytes received so far) [sender]
rsync error: unexplained error (code 255) at io.c(226) [sender=3.1.1]

# End of transcript or log.
"""]]

> This seems very like the problem described in
> [[git_annex_still_deleting_content_when_merging]]. Without a way to
> reproduce it, I can't tell for sure, but the circumstances of both seem
> the same. I'm going to close this as a duplicate, and have updated the
> other bug report to point to it as more evidence of the bug. [[done]]

[[!meta title="Assistant deleted modified file during merge"]]