doc/bugs/data_loss:_incorrect_merge_upon_conflicting_directory-file_of_direct_repos.mdwn

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+### Please describe the problem.
+Data loss due to incorrect merge of repos in direct mode.
+
+Given 2 repos A and B, in direct mode, where a has no remotes and b has a as remote (not sure if the latter is relevant):
+1. in A: mkdir f, with a file f in it
+2. in B: touch f
+3. in B: sync 
+
+Result: Only an f.variant-f###remains, which is file f of B, and the merge conflict has already been automatically resolved. I.e. Directory f containing file f, is lost.
+
+### What steps will reproduce the problem?
+Execute the script given below in additional information.
+
+### What version of git-annex are you using?
+git-annex version: 4.20130911-g6625d0e
+build flags: Assistant Webapp Pairing Testsuite S3 WebDAV Inotify DBus XMPP Feeds Quvi
+
+### On what operating system?
+Linux basementcat 3.10.10-1-ARCH #1 SMP PREEMPT Fri Aug 30 11:30:06 CEST 2013 x86_64 GNU/Linux
+
+### Please provide any additional information below.
+
+[[!format sh """
+[~]$ mkdir test
+[~/test]$ mkdir a
+[~/test/a]$ git init
+Initialized empty Git repository in /home/limyreth/test/a/.git/
+[~/test/a]$ git annex init test
+init test ok
+(Recording state in git...)
+[~/test/a]$ touch firstfile
+[~/test/a]$ git annex add firstfile 
+add firstfile (checksum...) ok
+(Recording state in git...)
+[~/test/a]$ git annex sync
+commit  
+ok
+git-annex: no branch is checked out
+[~]$ git clone test/a
+Cloning into 'a'...
+done.
+[~]$ mv a test/b
+[~/test/a]$ git annex direct
+commit  
+# On branch master
+nothing to commit, working directory clean
+ok
+direct firstfile ok
+direct  ok
+[~/test/a]$ ls -l
+total 0
+-rw-r--r-- 1 limyreth users 0 Oct 12 15:09 firstfile
+[~/test/a]$ mkdir f
+[~/test/a]$ touch f/f
+[~/test/a]$ git annex add f/f
+add f/f (checksum...) ok
+(Recording state in git...)
+[~/test/a]$ git annex sync
+commit  
+ok
+[~/test/b]$ git remote -v
+origin	/home/limyreth/test/a (fetch)
+origin	/home/limyreth/test/a (push)
+[~/test/b]$ ls
+firstfile
+[~/test/b]$ git annex direct
+commit  
+(Recording state in git...)
+# On branch master
+nothing to commit, working directory clean
+ok
+direct  ok
+[~/test/b]$ touch f
+[~/test/b]$ git annex add f
+add f (checksum...) ok
+(Recording state in git...)
+[~/test/b]$ git annex sync
+(merging origin/git-annex into git-annex...)
+(Recording state in git...)
+commit  
+ok
+pull origin 
+remote: Counting objects: 14, done.
+remote: Compressing objects: 100% (7/7), done.
+remote: Total 9 (delta 1), reused 0 (delta 0)
+Unpacking objects: 100% (9/9), done.
+From /home/limyreth/test/a
+   2a8fa45..ad6802d  master     -> origin/master
+   1f39016..19e3e12  git-annex  -> origin/git-annex
+ * [new branch]      synced/master -> origin/synced/master
+
+Adding f/f
+CONFLICT (file/directory): There is a directory with name f in refs/remotes/origin/master. Adding f as f~HEAD
+Automatic merge failed; fix conflicts and then commit the result.
+f: needs merge
+(Recording state in git...)
+ok
+[master 37a8019] git-annex automatic merge conflict fix
+
+Already up-to-date.
+ok
+(merging origin/git-annex into git-annex...)
+(Recording state in git...)
+push origin 
+Counting objects: 36, done.
+Delta compression using up to 4 threads.
+Compressing objects: 100% (20/20), done.
+Writing objects: 100% (25/25), 2.16 KiB | 0 bytes/s, done.
+Total 25 (delta 5), reused 0 (delta 0)
+To /home/limyreth/test/a
+   ad6802d..37a8019  master -> synced/master
+ * [new branch]      git-annex -> synced/git-annex
+ok
+[~/test/b]$ ls -l
+total 0
+-rw-r--r-- 1 limyreth users 0 Oct 12 15:11 firstfile
+-rw-r--r-- 1 limyreth users 0 Oct 12 15:11 f.variant-f874
+[~/test/b]$ git log --summary
+commit 37a80199abe3cf82100bbdb5dd2217ed6bcb4b62
+Merge: 5a8942a ad6802d
+Author: timdiels <timdiels.m@gmail.com>
+Date:   Sat Oct 12 15:11:47 2013 +0200
+
+    git-annex automatic merge conflict fix
+
+commit 5a8942a9a1735cb313c1f6624cbd3f48b252d9d9
+Author: timdiels <timdiels.m@gmail.com>
+Date:   Sat Oct 12 15:11:47 2013 +0200
+
+    git-annex automatic sync
+
+ create mode 120000 f
+
+commit ad6802dc231d389b86154e2df900a70b18e17b29
+Author: timdiels <timdiels.m@gmail.com>
+Date:   Sat Oct 12 15:11:40 2013 +0200
+
+    git-annex automatic sync
+
+ create mode 120000 f/f
+
+commit 2a8fa45bea996ab5ae219a017d4b642153e6d9c9
+Author: timdiels <timdiels.m@gmail.com>
+Date:   Sat Oct 12 15:09:40 2013 +0200
+
+    git-annex automatic sync
+
+ create mode 120000 firstfile
+[~/test/a]$ git annex sync
+(merging synced/git-annex into git-annex...)
+commit  
+ok
+merge synced/master 
+Updating ad6802d..37a8019
+Fast-forward
+ f.variant-f874 | 1 +
+ f/f            | 1 -
+ 2 files changed, 1 insertion(+), 1 deletion(-)
+ create mode 120000 f.variant-f874
+ delete mode 120000 f/f
+ok
+[~/test/a]$ git log --summary
+commit 37a80199abe3cf82100bbdb5dd2217ed6bcb4b62
+Merge: 5a8942a ad6802d
+Author: timdiels <timdiels.m@gmail.com>
+Date:   Sat Oct 12 15:11:47 2013 +0200
+
+    git-annex automatic merge conflict fix
+
+commit 5a8942a9a1735cb313c1f6624cbd3f48b252d9d9
+Author: timdiels <timdiels.m@gmail.com>
+Date:   Sat Oct 12 15:11:47 2013 +0200
+
+    git-annex automatic sync
+
+ create mode 120000 f
+
+commit ad6802dc231d389b86154e2df900a70b18e17b29
+Author: timdiels <timdiels.m@gmail.com>
+Date:   Sat Oct 12 15:11:40 2013 +0200
+
+    git-annex automatic sync
+
+ create mode 120000 f/f
+
+commit 2a8fa45bea996ab5ae219a017d4b642153e6d9c9
+Author: timdiels <timdiels.m@gmail.com>
+Date:   Sat Oct 12 15:09:40 2013 +0200
+
+    git-annex automatic sync
+
+ create mode 120000 firstfile
+
+"""]]