Merge branch 'master' of ssh://git-annex.branchable.com

doc/bugs/Remotes_only_start_showing_changes_after_both_sides_have_written_to_the_repository.mdwn

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+### Please describe the problem.
+
+I've setup two (actually more) direct mode repositories pointing at each other with ssh keys allowing them to talk to each other. I run the assistant in both repositories. Once I add a file to one repository I can see in the assistant log that it's been sent to the other side but it doesn't show up. Once I add a file to the other repository both repositories get both files.
+
+### What steps will reproduce the problem?
+
+In the first host:
+[[!format sh """
+$ ls -l
+total 0
+$ date | tee fromhostA
+Fri May 31 19:25:12 WEST 2013
+"""]]
+
+And then in the second host
+
+[[!format sh """
+$ ls
+$ date | tee fromhostB
+Fri May 31 19:25:27 WEST 2013
+$ ls
+fromhostB
+$ ls # After a little while
+fromhostA  fromhostB
+"""]]
+
+Back at hostA
+
+[[!format sh """
+$ ls -l
+total 8
+-rw-r--r-- 1 pedrocr pedrocr 30 May 31 19:25 fromhostA
+-rw-r--r-- 1 pedrocr pedrocr 30 May 31 19:25 fromhostB
+"""]]
+
+I looked at the logs for hostA and it seemed like it was pushing the changes right away. In hostB this is the moment where fromhostB gets added:
+
+[[!format sh """
+[2013-05-31 19:22:04 WEST] Pusher: Syncing with zeus, wintermute, ulisses 
+[2013-05-31 19:25:27 WEST] Committer: Adding fromhostB
+
+(merging zeus/git-annex into git-annex...)
+(Recording state in git...)
+(merging wintermute/git-annex into git-annex...)
+(Recording state in git...)
+(merging ulisses/git-annex into git-annex...)
+(Recording state in git...)
+"""]]
+
+It seems to be that merging in the remotes only gets done when there's an added file and that's why fromhostA didn't show up until fromhostB was there. I don't think this is the correct behavior. I want to be able to setup a new repository with other repositories as remotes and have it automatically pull in all the contents without having to create content itself.
+
+### What version of git-annex are you using? On what operating system?
+
+[[!format sh """
+$ git annex version
+git-annex version: 4.20130516.1
+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
+$ lsb_release -a
+No LSB modules are available.
+Distributor ID:	Ubuntu
+Description:	Ubuntu 12.04.2 LTS
+Release:	12.04
+Codename:	precise
+"""]]

doc/bugs/assistant_doesn__39__t_sync_empty_directories.mdwn

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+### Please describe the problem.
+
+The assistant seems to only sync files and not directories, so empty directories will not be synced.
+
+### What steps will reproduce the problem?
+
+- Create an empty directory on HostA
+- See that nothing gets synced (daemon.log is silent) and the directory doesn't exist on the other HostB
+- Create an empty file inside the empty directory on HostA
+- See that now HostB has the empty file inside the directory
+
+I'm sure this comes directly from the git behavior but is at least surprising for a direct mode repository using the assistant.
+
+### What version of git-annex are you using? On what operating system?
+
+[[!format sh """
+$ git annex version
+git-annex version: 4.20130516.1
+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
+$ lsb_release -a
+No LSB modules are available.
+Distributor ID:	Ubuntu
+Description:	Ubuntu 12.04.2 LTS
+Release:	12.04
+Codename:	precise
+"""]]

doc/bugs/assistant_doesn__39__t_sync_file_permissions.mdwn

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+### Please describe the problem.
+
+The assistant does not sync file permissions so if you set something as executable it won't be set the same on the other repositories.
+
+### What steps will reproduce the problem?
+
+On the first host:
+
+[[!format sh """
+$ echo -e '#!/bin/sh\necho "Hello World!"' > testscript
+$ chmod ugo+x testscript 
+$ ./testscript 
+Hello World!
+$ ls -l
+total 4
+-rwxr-xr-x 1 pedrocr pedrocr 30 May 31 20:00 testscript
+"""]]
+
+And on the second host:
+
+[[!format sh """
+$ ls -l
+total 4
+-rw-r--r-- 1 pedrocr pedrocr 30 May 31 20:00 testscript
+$ ./testscript
+bash: ./testscript: Permission denied
+"""]]
+
+### What version of git-annex are you using? On what operating system?
+
+[[!format sh """
+$ git annex version
+git-annex version: 4.20130516.1
+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
+$ lsb_release -a
+No LSB modules are available.
+Distributor ID:	Ubuntu
+Description:	Ubuntu 12.04.2 LTS
+Release:	12.04
+Codename:	precise
+"""]]

doc/bugs/git-annex:___60__socket:_16__62__:_hPutBuf:_resource_vanished___40__Broken_pipe__41__/comment_5_4af107f3184bc2abd2c9693167018628._comment

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+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ nickname="joey"
+ subject="comment 5"
+ date="2013-05-31T18:17:59Z"
+ content="""
+It will now detect if any of the long-running git processes crash, and automatically restart them. I don't know if this addresses the crash that was originally reported.
+"""]]

doc/bugs/git_annex_sync_in_direct_mode_does_not_honor_skip-worktree/comment_3_6bfd4e9a7853af93e72b717249de9439._comment

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+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ nickname="joey"
+ subject="comment 3"
+ date="2013-05-31T18:22:12Z"
+ content="""
+I accept patches by email, or pull requests.
+"""]]

doc/bugs/restart_daemon_required/comment_1_f79ac16cc9f1e3b08cd121bf5efb29c3._comment

@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ nickname="joey"
+ subject="comment 1"
+ date="2013-05-31T18:15:03Z"
+ content="""
+Enabling debugging, and send a log. XMPP may not be working.
+"""]]

doc/bugs/restart_daemon_required/comment_2_50c1b268a3cc4514681059eabca674e3._comment

@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ nickname="joey"
+ subject="comment 2"
+ date="2013-05-31T18:20:26Z"
+ content="""
+You could also try upgrading to a current nightly build. There have been a lot of XMPP improvements recently.
+"""]]

doc/forum/XBMC__44___NFS___38___git-annex_/comment_4_01767f3f864954cf8080274e206da9d4._comment

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+[[!comment format=mdwn
+ username="ka7"
+ ip="2001:7b8:155d:0:222:64ff:fe16:dc52"
+ subject="comment 4"
+ date="2013-05-31T18:46:29Z"
+ content="""
+after a quick check I realized that sha256E is available -- migrate and yepey!
+"""]]