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git-annex-4.20131024: doc/bugs/Windows_and_Linux_in_direct_mode_confuses_git.mdwn

### Please describe the problem.
I try to share some files between a windows machine and a linux machine in direct mode, with a remote repository between the two. I can't seem to reproduce the problem in indirect mode...

I add a file on the windows machine then copy it to the remote repository. I then get it on the linux machine and edit it there. If I `git annex sync` and copy the file's data to the remote repository, a `git annex sync` on windows will fail like this:

[[!format sh """
$ git annex sync
commit
ok
pull origin
remote: Counting objects: 41, done.
remote: Compressing objects: 100% (24/24), done.
remote: Total 31 (delta 9), reused 0 (delta 0)
Unpacking objects: 100% (31/31), done.
From ssh://192.168.1.29:/home/raz/work/test
   b23cb44..9073cc3  git-annex  -> origin/git-annex
   7d4f0e2..87438fc  master     -> origin/master
   57a661c..b33b025  synced/git-annex -> origin/synced/git-annex
   7d4f0e2..87438fc  synced/master -> origin/synced/master
ok
(merging origin/git-annex origin/synced/git-annex into git-annex...)
(Recording state in git...)
push origin
Counting objects: 17, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (4/4), done.
Writing objects: 100% (5/5), 565 bytes | 0 bytes/s, done.
Total 5 (delta 2), reused 0 (delta 0)
To ssh://192.168.1.29:/home/raz/work/test.git
   b33b025..dcfaf23  git-annex -> synced/git-annex
 ! [rejected]        master -> synced/master (non-fast-forward)
error: failed to push some refs to 'ssh://192.168.1.29:/home/raz/work/test.git'
hint: Updates were rejected because a pushed branch tip is behind its remote
hint: counterpart. Check out this branch and merge the remote changes
hint: (e.g. 'git pull') before pushing again.
hint: See the 'Note about fast-forwards' in 'git push --help' for details.
failed
git-annex: sync: 1 failed
"""]]

A `git log` tells me the master branch is not properly merged so I assume the pull failed silently (I paste the log in the transcript).

I can then try to manually fix the windows working copy and sometimes it kind of work, but sometimes I have a hard time recovering and I am better off cloning a new version and moving data's around...

### What steps will reproduce the problem?
Create a repository on a windows.

Add a file.

`git clone --bare` the repository and put it on a remote machine.

Clone the remote repository to a linux machine.

Get the file's data.

Edit the file on linux.

Commit it and copy the data's to the remote machine.

`git clone sync` on the windows machine --> Error.

### What version of git-annex are you using? On what operating system?
On Windows:
[[!format sh """
git-annex version: 4.20130827-g4f18612
build flags: Pairing Testsuite S3 WebDAV DNS
local repository version: 4
default repository version: 3
supported repository versions: 3 4
upgrade supported from repository versions: 2
"""]]

On Linux
[[!format sh """
git-annex version: 4.20130815
build flags: Assistant Webapp Pairing Testsuite S3 WebDAV Inotify DBus XMPP
local repository version: 4
default repository version: 3
supported repository versions: 3 4
upgrade supported from repository versions: 0 1 2
"""]]

### Please provide any additional information below.
[[!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

### On Windows

$ mkdir test_windows

$ cd test_windows/

$ git init
Initialized empty Git repository in c:/Users/raz/test_windows/.git/

$ git annex init windows
init windows
  Detected a crippled filesystem.

  Enabling direct mode.

  Detected a filesystem without fifo support.

  Disabling ssh connection caching.
ok
(Recording state in git...)

$ echo "test 1" > test.txt

$ git annex add test.txt
add test.txt (checksum...) ok
(Recording state in git...)

$ git annex sync
commit
ok
git-annex: no branch is checked out

$ cd ..

$ git clone --bare test_windows/ test.git
Cloning into bare repository 'test.git'...
done.

$ scp -r test.git 192.168.1.29:/home/raz/work/
config                                        100%  183     0.2KB/s   00:00
description                                   100%   73     0.1KB/s   00:00
HEAD                                          100%   23     0.0KB/s   00:00
applypatch-msg.sample                         100%  452     0.4KB/s   00:00
commit-msg.sample                             100%  896     0.9KB/s   00:00
post-commit.sample                            100%  160     0.2KB/s   00:00
post-receive.sample                           100%  552     0.5KB/s   00:00
post-update.sample                            100%  189     0.2KB/s   00:00
pre-applypatch.sample                         100%  398     0.4KB/s   00:00
pre-commit.sample                             100% 1704     1.7KB/s   00:00
pre-push.sample                               100% 1348     1.3KB/s   00:00
pre-rebase.sample                             100% 4951     4.8KB/s   00:00
prepare-commit-msg.sample                     100% 1239     1.2KB/s   00:00
update.sample                                 100% 3611     3.5KB/s   00:00
exclude                                       100%  240     0.2KB/s   00:00
825dc642cb6eb9a060e54bf8d69288fbee4904        100%   15     0.0KB/s   00:00
a31b7a55380d79248658d3fffff6d2dc41a726        100%  116     0.1KB/s   00:00
dcabbf728abe62b6e2bcc06b8306eb3aa9a497        100%  176     0.2KB/s   00:00
332ecbfe923879df51a7a3f9bb86ebdfb64273        100%   45     0.0KB/s   00:00
4f0e20d38d6dc757340a8c569270b5a857fc67        100%  160     0.2KB/s   00:00
62956bcf45c63b24a637b22a742db0d9458248        100%   86     0.1KB/s   00:00
7ec519eb1b257a85ae8f9373d0835dea9ddc04        100%   82     0.1KB/s   00:00
1d1559a050b4a2df2e653b1e7ac15bdf7d56b1        100%   51     0.1KB/s   00:00
b74dbedfac4d6a0a90580cff2088a5d61f6675        100%  130     0.1KB/s   00:00
0ca042f439ef997f04a25a449aa1f539b93cf4        100%   53     0.1KB/s   00:00
bbce5e51e5a90ffd26900de3546fc4f9704181        100%  151     0.2KB/s   00:00
18bd66316298fcc5c06af9865c30a2fe4d2476        100%  176     0.2KB/s   00:00
edf8b5cc207e16ca0173785a2ba569c5d4208c        100%   71     0.1KB/s   00:00
packed-refs                                   100%  160     0.2KB/s   00:00

$ cd test_windows/

$ git remote add origin ssh://192.168.1.29:/home/raz/work/test.git

$ git annex copy --to origin
copy test.txt (checking origin...) (to origin...)
test.txt
           7 100%    0.00kB/s    0:00:00 (xfer#1, to-check=0/1)

sent 79 bytes  received 31 bytes  220.00 bytes/sec
total size is 7  speedup is 0.06
ok
(Recording state in git...)

$ git annex sync
commit
ok
pull origin
remote: Counting objects: 11, done.
remote: Compressing objects: 100% (5/5), done.
remote: Total 6 (delta 1), reused 0 (delta 0)
Unpacking objects: 100% (6/6), done.
From ssh://192.168.1.29:/home/raz/work/test
 * [new branch]      git-annex  -> origin/git-annex
 * [new branch]      master     -> origin/master
ok
(merging origin/git-annex into git-annex...)
(Recording state in git...)
push origin
Counting objects: 18, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (8/8), done.
Writing objects: 100% (10/10), 874 bytes | 0 bytes/s, done.
Total 10 (delta 4), reused 0 (delta 0)
To ssh://192.168.1.29:/home/raz/work/test.git
 * [new branch]      git-annex -> synced/git-annex
 * [new branch]      master -> synced/master
ok

### On Linux

$ git clone test.git test_linux
Cloning into 'test_linux'...
done.

$ cd test_linux 

$ git annex init linux
init linux ok
(Recording state in git...)

$ git annex sync
(merging origin/git-annex origin/synced/git-annex into git-annex...)
(Recording state in git...)
commit  
ok
pull origin 
ok
push origin 
Counting objects: 11, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (6/6), done.
Writing objects: 100% (8/8), 775 bytes | 0 bytes/s, done.
Total 8 (delta 3), reused 0 (delta 0)
To /home/raz/work/test.git
   0b4f175..41fba1d  git-annex -> synced/git-annex
ok

$ git annex get
get test.txt (from origin...) ok
(Recording state in git...)

$ git annex direct
commit  
# On branch master
nothing to commit, working directory clean
ok
direct test.txt ok
direct  ok

$ git annex sync
commit  
ok
pull origin 
ok
push origin 
Counting objects: 9, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (4/4), done.
Writing objects: 100% (5/5), 492 bytes | 0 bytes/s, done.
Total 5 (delta 1), reused 0 (delta 0)
To /home/raz/work/test.git
   41fba1d..57a661c  git-annex -> synced/git-annex
ok

$ cat test.txt  
test 1

$ echo "test 2" > test.txt

$ git annex sync
add test.txt (checksum...) ok
(Recording state in git...)
commit  
(Recording state in git...)
ok
pull origin 
ok
push origin 
Counting objects: 22, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (12/12), done.
Writing objects: 100% (16/16), 1.40 KiB | 0 bytes/s, done.
Total 16 (delta 4), reused 0 (delta 0)
To /home/raz/work/test.git
   57a661c..4883cad  git-annex -> synced/git-annex
   7d4f0e2..87438fc  master -> synced/master
ok

$ git annex copy --to origin
copy test.txt (to origin...) ok
(Recording state in git...)

$ git annex sync            
commit  
ok
pull origin 
remote: Counting objects: 6, done.
remote: Compressing objects: 100% (4/4), done.
remote: Total 5 (delta 0), reused 0 (delta 0)
Unpacking objects: 100% (5/5), done.
From /home/raz/work/test
   b23cb44..9073cc3  git-annex  -> origin/git-annex
ok
(merging origin/git-annex into git-annex...)
(Recording state in git...)
push origin 
Counting objects: 18, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (8/8), done.
Writing objects: 100% (10/10), 924 bytes | 0 bytes/s, done.
Total 10 (delta 3), reused 0 (delta 0)
To /home/raz/work/test.git
   4883cad..b33b025  git-annex -> synced/git-annex
ok

$ 


### On Windows

$ git annex sync
commit
ok
pull origin
remote: Counting objects: 41, done.
remote: Compressing objects: 100% (24/24), done.
remote: Total 31 (delta 9), reused 0 (delta 0)
Unpacking objects: 100% (31/31), done.
From ssh://192.168.1.29:/home/raz/work/test
   b23cb44..9073cc3  git-annex  -> origin/git-annex
   7d4f0e2..87438fc  master     -> origin/master
   57a661c..b33b025  synced/git-annex -> origin/synced/git-annex
   7d4f0e2..87438fc  synced/master -> origin/synced/master
ok
(merging origin/git-annex origin/synced/git-annex into git-annex...)
(Recording state in git...)
push origin
Counting objects: 17, done.
Delta compression using up to 8 threads.
Compressing objects: 100% (4/4), done.
Writing objects: 100% (5/5), 565 bytes | 0 bytes/s, done.
Total 5 (delta 2), reused 0 (delta 0)
To ssh://192.168.1.29:/home/raz/work/test.git
   b33b025..dcfaf23  git-annex -> synced/git-annex
 ! [rejected]        master -> synced/master (non-fast-forward)
error: failed to push some refs to 'ssh://192.168.1.29:/home/raz/work/test.git'
hint: Updates were rejected because a pushed branch tip is behind its remote
hint: counterpart. Check out this branch and merge the remote changes
hint: (e.g. 'git pull') before pushing again.
hint: See the 'Note about fast-forwards' in 'git push --help' for details.
failed
git-annex: sync: 1 failed

$ git log --graph --oneline --decorate --all
* 87438fc (origin/synced/master, origin/master) git-annex automatic sync
* 7d4f0e2 (HEAD, synced/master, master) git-annex automatic sync
*-.   dcfaf23 (origin/synced/git-annex, git-annex) merging origin/git-annex orig
|\ \
| | *   b33b025 merging origin/git-annex into git-annex
| | |\
| | |/
| |/|
| * | 9073cc3 (origin/git-annex) update
| | * 73518bc update
| | * 4883cad update
| | * 1b447f5 update
| |/
|/|
* | 57a661c update
| |
|  \
*-. \   41fba1d merging origin/git-annex origin/synced/git-annex into git-annex
|\ \ \
| | |/
| |/|
| | *   0b4f175 merging origin/git-annex into git-annex
| | |\
| | |/
| |/|
| * | b23cb44 update
| | * b5755a2 update
| |/
| * 6adcabb update
| * df18bd6 update
| * dcbbce5 branch created
* 0d138eb update
* fe6bccc branch created

$

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