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

19 files changed, 203 insertions, 1 deletions

diff --git a/doc/bugs/Android_app_permission_denial_on_startup/comment_11_b444cd6717658116533745c51481dd3d._comment b/doc/bugs/Android_app_permission_denial_on_startup/comment_11_b444cd6717658116533745c51481dd3d._comment
new file mode 100644
index 000000000..b776c2e7d
--- /dev/null
+++ b/doc/bugs/Android_app_permission_denial_on_startup/comment_11_b444cd6717658116533745c51481dd3d._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ nickname="joey"
+ subject="comment 11"
+ date="2013-05-29T17:01:55Z"
+ content="""
+Today's autobuild of git-annex for Android has a workaround for this problem. You can select \"Open WebApp\" from the menu in the terminal emulator app, and it should work. Would appreciate confirmation from someone who has seen this problem. If that menu item works, I may later be able to make it open automatically.
+"""]]
diff --git a/doc/bugs/Android_app_permission_denial_on_startup/comment_12_66181f34ed7496d1f6601b39e5ae3c65._comment b/doc/bugs/Android_app_permission_denial_on_startup/comment_12_66181f34ed7496d1f6601b39e5ae3c65._comment
new file mode 100644
index 000000000..5a099121c
--- /dev/null
+++ b/doc/bugs/Android_app_permission_denial_on_startup/comment_12_66181f34ed7496d1f6601b39e5ae3c65._comment
@@ -0,0 +1,13 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkGCmVc5qIJaQQgG82Hc5zzBdAVdhe2JEM"
+ nickname="Bruno"
+ subject="comment 12"
+ date="2013-05-29T17:20:40Z"
+ content="""
+It works!
+
+Note that the \"open webapp\" menu item is not available if my phone is set to French.
+
+French: http://i.imgur.com/cik0sIL.png
+English: http://i.imgur.com/8Oh6FEw.png
+"""]]
diff --git a/doc/bugs/Direct_mode_repositories_end_up_with_unstaged_changes/comment_1_300a2b246182be3079db20a7e3322261._comment b/doc/bugs/Direct_mode_repositories_end_up_with_unstaged_changes/comment_1_300a2b246182be3079db20a7e3322261._comment
new file mode 100644
index 000000000..87e90ebe7
--- /dev/null
+++ b/doc/bugs/Direct_mode_repositories_end_up_with_unstaged_changes/comment_1_300a2b246182be3079db20a7e3322261._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ nickname="joey"
+ subject="comment 1"
+ date="2013-05-29T16:18:33Z"
+ content="""
+This does not indicate a problem. Nor are there any unstaged changes. `git status` simply does not know about git-annex's direct mode. Please see [[/direct_mode]] for caveats about this and other problems with using regular git commands with git-annex repositories in direct mode.
+"""]]
diff --git a/doc/bugs/Glacier_remote_uploads_duplicates/comment_5_6980a912d3582c2f2511e4827e9e76b3._comment b/doc/bugs/Glacier_remote_uploads_duplicates/comment_5_6980a912d3582c2f2511e4827e9e76b3._comment
new file mode 100644
index 000000000..1d4bbf1fd
--- /dev/null
+++ b/doc/bugs/Glacier_remote_uploads_duplicates/comment_5_6980a912d3582c2f2511e4827e9e76b3._comment
@@ -0,0 +1,21 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ nickname="joey"
+ subject="comment 5"
+ date="2013-05-29T17:54:11Z"
+ content="""
+I started to make a branch with the change I suggested, but then I had another idea.
+
+The checkpresent hook can return either True or, False, or fail with a message if it cannot successfully check the remote. Currently for glacier, when --trust-glacier is not set, it always returns False. Crucially, in the case when a file is in glacier, this is telling git-annex it's not there, so copy re-uploads it. What if it instead, when the glacier inventory is missing a file, it returns False. And when the glacier inventory has a file, unless --trust-glacier is set, it *fails*.
+
+The result would be:
+
+* `git annex copy --to glacier` would only send things not listed in inventory. If a file is listed in the inventory, `copy`
+  would complain that --trust-glacier` is not set, and not re-upload the file.
+* `git annex drop` would only trust that glacier has a file when --trust-glacier is set. Behavior unchanged.
+* `git annex move --to glacier`, when the file is not listed in inventory, would send the file, and delete it locally. Behavior unchanged.
+* `git annex move --to glacier`, when the file is listed in inventory, would only trust that glacier has the file when --trust-glacier is set
+* `git annex copy --from glacier` / `git annex get`, when the file is located in glacier, would trust the location log, and attempt to get the file from glacier.
+
+This seems like it should do the right thing in all cases, but I have not tested it. I've pushed a `glacier` branch with this change.
+"""]]
diff --git a/doc/bugs/Hard_links_not_synced_in_direct_mode/comment_2_213aa10909d1fd0f20ed078a7ed93e79._comment b/doc/bugs/Hard_links_not_synced_in_direct_mode/comment_2_213aa10909d1fd0f20ed078a7ed93e79._comment
new file mode 100644
index 000000000..39d601dba
--- /dev/null
+++ b/doc/bugs/Hard_links_not_synced_in_direct_mode/comment_2_213aa10909d1fd0f20ed078a7ed93e79._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ nickname="joey"
+ subject="comment 2"
+ date="2013-05-29T15:39:48Z"
+ content="""
+git does not support hard linked files, so neither can git-annex.
+"""]]
diff --git a/doc/bugs/Hard_links_not_synced_in_direct_mode/comment_3_e6b783d9aaae20c0d35e9888d878716a._comment b/doc/bugs/Hard_links_not_synced_in_direct_mode/comment_3_e6b783d9aaae20c0d35e9888d878716a._comment
new file mode 100644
index 000000000..179d80b21
--- /dev/null
+++ b/doc/bugs/Hard_links_not_synced_in_direct_mode/comment_3_e6b783d9aaae20c0d35e9888d878716a._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ nickname="joey"
+ subject="comment 3"
+ date="2013-05-29T16:11:46Z"
+ content="""
+It would be possible to make the assistant use the inotify CREATE event (which it currently ignores) to add a file to the repository when a hard link is created. However, when a hard linked file is modified, inotify only sends an event for the file that was changed, not for other hard links to it. So, without keeping track of all hard links that exist on my own, there's no way for the assistant to automatically handle that case. And even if it tried to, hard links to files in the repository from outside the repository would still allow modifying them without the assistant being able to detect it.
+
+Since hard links cannot be propigated over git anyway, I don't want to get into this mess. It's best to wontfix this I think.
+"""]]
diff --git a/doc/bugs/Hard_links_not_synced_in_direct_mode/comment_4_b008ae7b1cf8685d92c9a87a7609de1e._comment b/doc/bugs/Hard_links_not_synced_in_direct_mode/comment_4_b008ae7b1cf8685d92c9a87a7609de1e._comment
new file mode 100644
index 000000000..8e8acd9cb
--- /dev/null
+++ b/doc/bugs/Hard_links_not_synced_in_direct_mode/comment_4_b008ae7b1cf8685d92c9a87a7609de1e._comment
@@ -0,0 +1,18 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkx5V3MTbzCXS3J7Mn9FEq8M9bPPYMkAHY"
+ nickname="Pedro"
+ subject="comment 4"
+ date="2013-05-29T18:48:10Z"
+ content="""
+I agree with your assessment for the traditional git-annex, as it's an extension of git. For the assistant (in direct mode at least) it seems like broken behavior, there will be files that exist on one side but not the other and files that have the same content on one side but not the other.
+
+I just had a look and unfortunately there doesn't seem to be a general way to do inode to path lookup in UNIX, so an inode cache would really be needed. It would look something like:
+
+* On inotify CREATE detect that the file has other hardlinked instances, find out if they are in the repository by keeping a inode->path cache of all files
+* When the file is a hardlink to another file already in the repository commit some kind of special file to git that states \"hardlink to /path/to/otherfile\" and add metadata to the original file saying what files are hardlinks to it
+* When a remote gets a special file after a sync it will itself run a \"ln /path/to/otherfile /path/to/newfile\" or alteratively a copy when the two paths span filesystems or the filesystem is crippled
+* When a crippled remote gets a write to a file with hardlinks, it will replicate those writes to the other files (this is where the metadata is needed)
+* When a crippled remote does a write to a file with hardlinks that file becomes independent in the remotes with hardlinks since the content is now different between the two (or more) files.
+
+This does get pretty hairy with the corner cases. Right now the simple case of \"sync between two non-crippled filesystems\" shows pretty surprising results though so I'd argue something needs to change. I think that for direct mode to really be a \"transparent folder sync\" kind of solution this should be fixed.
+"""]]
diff --git a/doc/bugs/Killing_the_assistant_daemon_leaves_ssh_mux_sessions_behind/comment_1_17879b98a5e79ace03b543064751e46e._comment b/doc/bugs/Killing_the_assistant_daemon_leaves_ssh_mux_sessions_behind/comment_1_17879b98a5e79ace03b543064751e46e._comment
new file mode 100644
index 000000000..17c91ca99
--- /dev/null
+++ b/doc/bugs/Killing_the_assistant_daemon_leaves_ssh_mux_sessions_behind/comment_1_17879b98a5e79ace03b543064751e46e._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ nickname="joey"
+ subject="comment 1"
+ date="2013-05-29T15:36:48Z"
+ content="""
+There is a --stop option that can be used to stop the assistant. It will clean up ssh sessions. git-annex also automatically cleans up stale ssh sessions whenever it starts a new one.
+"""]]
diff --git a/doc/bugs/Killing_the_assistant_daemon_leaves_ssh_mux_sessions_behind/comment_2_2dc877e281750004b16619ea7b931160._comment b/doc/bugs/Killing_the_assistant_daemon_leaves_ssh_mux_sessions_behind/comment_2_2dc877e281750004b16619ea7b931160._comment
new file mode 100644
index 000000000..7c39be61b
--- /dev/null
+++ b/doc/bugs/Killing_the_assistant_daemon_leaves_ssh_mux_sessions_behind/comment_2_2dc877e281750004b16619ea7b931160._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkx5V3MTbzCXS3J7Mn9FEq8M9bPPYMkAHY"
+ nickname="Pedro"
+ subject="comment 2"
+ date="2013-05-29T18:08:51Z"
+ content="""
+I see the --stop option in the manpage now, it's under watch and not assistant, so that's why I missed it. I had a problem with the mux sessions not being cleaned up when I changed the remote's hostname. Only after killing old mux's and restarting the assistant did I get it to sync properly.
+"""]]
diff --git a/doc/bugs/Manual_mode_weirdness/comment_1_f8ab3bac9e9a6768e5fd5a052f0d920f._comment b/doc/bugs/Manual_mode_weirdness/comment_1_f8ab3bac9e9a6768e5fd5a052f0d920f._comment
new file mode 100644
index 000000000..fcacc3b33
--- /dev/null
+++ b/doc/bugs/Manual_mode_weirdness/comment_1_f8ab3bac9e9a6768e5fd5a052f0d920f._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ nickname="joey"
+ subject="comment 1"
+ date="2013-05-29T16:13:10Z"
+ content="""
+Yes,  4.20130501 is broken WRT manual mode. This has been fixed for a while in the current git master branch and autobuilds and there will be a new release soon with the fix.
+"""]]
diff --git a/doc/bugs/Manual_mode_weirdness/comment_2_e810daa488fad32ca8bdaae620051da8._comment b/doc/bugs/Manual_mode_weirdness/comment_2_e810daa488fad32ca8bdaae620051da8._comment
new file mode 100644
index 000000000..3a4cd9881
--- /dev/null
+++ b/doc/bugs/Manual_mode_weirdness/comment_2_e810daa488fad32ca8bdaae620051da8._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="robconnolly"
+ ip="203.167.218.84"
+ subject="comment 2"
+ date="2013-05-29T23:18:23Z"
+ content="""
+Excellent, Thank you!
+"""]]
diff --git a/doc/bugs/git_annex_sync_in_direct_mode_does_not_honor_skip-worktree/comment_1_69baeb997086c885f34fd1dc385cf5d6._comment b/doc/bugs/git_annex_sync_in_direct_mode_does_not_honor_skip-worktree/comment_1_69baeb997086c885f34fd1dc385cf5d6._comment
new file mode 100644
index 000000000..e7baee584
--- /dev/null
+++ b/doc/bugs/git_annex_sync_in_direct_mode_does_not_honor_skip-worktree/comment_1_69baeb997086c885f34fd1dc385cf5d6._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ nickname="joey"
+ subject="comment 1"
+ date="2013-05-29T16:45:03Z"
+ content="""
+I'm a little worried about -t being \"semi-deprecated\". I don't know if it would be possible to use either of the other commands the man page suggests to get the info needed by `stageDirect`. (Particularly the Sha of their staged contents.)
+
+All of git-annex's access to the repository tree goes via Git.LsFiles and AFAICS, all the other git commands used there do respect skip-worktree.
+
+I encourage you to work on this, since you're motivated.
+"""]]
diff --git a/doc/bugs/warning_-_WebApp_crashed:___60__file_descriptor_15__62__:_hPutStr:_illegal_operation___40__handle_is_closed__41___on_Android.mdwn b/doc/bugs/warning_-_WebApp_crashed:___60__file_descriptor_15__62__:_hPutStr:_illegal_operation___40__handle_is_closed__41___on_Android.mdwn
new file mode 100644
index 000000000..02b05f4a1
--- /dev/null
+++ b/doc/bugs/warning_-_WebApp_crashed:___60__file_descriptor_15__62__:_hPutStr:_illegal_operation___40__handle_is_closed__41___on_Android.mdwn
@@ -0,0 +1,21 @@
+### Please describe the problem.
+The first time I open the webapp on Android I see the following warning :
+
+`WebApp crashed:<file descriptor 15>: hPutStr: illegal operation(handle_is_closed)`
+
+See screen capture : [http://i.imgur.com/K0wkk2n.png](http://i.imgur.com/K0wkk2n.png)
+
+### What steps will reproduce the problem?
+1. Close git-annex if running
+2. Open the WebApp
+
+### What version of git-annex are you using? On what operating system?
+It says 1.0.52 in the Android settings but I'm using the daily build that I downloaded around 2013-05-29 13:10:00 (Eastern Time)
+
+### Please provide any additional information below.
+
+Git annex still syncs with `box.com` even if the warning is showing.
+
+I'm using a Nexus 4 (4.2.2)
+
+I didn't find `daemon.log`.
diff --git a/doc/design/assistant/blog/day_276__fuzzing_continues/comment_2_a56c4c26a9e7bb8cfe3f598dbeed0813._comment b/doc/design/assistant/blog/day_276__fuzzing_continues/comment_2_a56c4c26a9e7bb8cfe3f598dbeed0813._comment
new file mode 100644
index 000000000..3a98c8a09
--- /dev/null
+++ b/doc/design/assistant/blog/day_276__fuzzing_continues/comment_2_a56c4c26a9e7bb8cfe3f598dbeed0813._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ nickname="joey"
+ subject="comment 2"
+ date="2013-05-29T16:30:20Z"
+ content="""
+The terminal has options to take the wake lock, and also the wifi lock, in its menu.
+
+Currently this has to be managed manually. The assistant does not try to deal with this.
+"""]]
diff --git a/doc/forum/Help_with_syncing_file_contents/comment_3_b26cfa20dc81517d93e760f4809bdc24._comment b/doc/forum/Help_with_syncing_file_contents/comment_3_b26cfa20dc81517d93e760f4809bdc24._comment
new file mode 100644
index 000000000..ff9902e8d
--- /dev/null
+++ b/doc/forum/Help_with_syncing_file_contents/comment_3_b26cfa20dc81517d93e760f4809bdc24._comment
@@ -0,0 +1,12 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ nickname="joey"
+ subject="comment 3"
+ date="2013-05-29T16:50:35Z"
+ content="""
+Treating each version of a file as a separate object that is stored and transmitted separately is one of the core simplifying assumptions of git-annex. Amoung other things it makes it easy to have dumb special remotes that are mere key/value stores. And it keeps it easy to understand.
+
+I don't consider this a problem as far as storage goes. Disk space is cheap; git-annex allows dropping unused versions of files from repositories that are not on large cheap storage.
+
+For file transfer, it would be nice to find optimisations that don't require changing this simplifying assumption. This can be done at least for rsync I think. The [[design/assistant/deltas]] page is where the design of this is or will be worked on.
+"""]]
diff --git a/doc/forum/Securing_a_shared_ssh_server/comment_5_bf193e02b388b4358632a169d2425b5c._comment b/doc/forum/Securing_a_shared_ssh_server/comment_5_bf193e02b388b4358632a169d2425b5c._comment
new file mode 100644
index 000000000..d0f78da92
--- /dev/null
+++ b/doc/forum/Securing_a_shared_ssh_server/comment_5_bf193e02b388b4358632a169d2425b5c._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ nickname="joey"
+ subject="comment 5"
+ date="2013-05-29T16:56:37Z"
+ content="""
+I can't say what options rsync will choose to pass to the server, when the rsync special remote uses rsync. It's up to that command.
+
+`GIT_ANNEX_SHELL_DIRECTORY` currently only supports specifying one directory. 
+"""]]
diff --git a/doc/forum/Securing_a_shared_ssh_server/comment_6_50d391992cd444080ebc70db30b215c5._comment b/doc/forum/Securing_a_shared_ssh_server/comment_6_50d391992cd444080ebc70db30b215c5._comment
new file mode 100644
index 000000000..fce7ab3df
--- /dev/null
+++ b/doc/forum/Securing_a_shared_ssh_server/comment_6_50d391992cd444080ebc70db30b215c5._comment
@@ -0,0 +1,9 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkwjBDXkP9HAQKhjTgThGOxUa1B99y_WRA"
+ nickname="Franck"
+ subject="comment 6"
+ date="2013-05-29T17:41:25Z"
+ content="""
+OK, I understand now why it is complicated to secure rsync, the best I can hope is to chroot it on a restricted account. Thanks! And the \"currently\" regarding ˋGIT_ANNEX_SHELL_DIRECTORYˋ gives me hope about a future change.  :-)
+Cheers, Franck
+"""]]
diff --git a/doc/install/Debian/comment_8_5b5a3b0e8abe8831a6a15a4e258d14fd._comment b/doc/install/Debian/comment_8_5b5a3b0e8abe8831a6a15a4e258d14fd._comment
new file mode 100644
index 000000000..253df3d07
--- /dev/null
+++ b/doc/install/Debian/comment_8_5b5a3b0e8abe8831a6a15a4e258d14fd._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ nickname="joey"
+ subject="comment 8"
+ date="2013-05-29T16:23:10Z"
+ content="""
+@mey.vn, Debian packages of git-annex, as uploaded to the Debian repositories, are built with whatever libc version the Debian autobuilder is running. You cannot, in general, install packages from Debian unstable into stable without upgrading your libc6.
+
+The release notes were not talking about the Debian packages, but about the [[Linux_standalone]] tarballs. Those are built with libc 2.13.
+"""]]
diff --git a/doc/tips/skydriveannex.mdwn b/doc/tips/skydriveannex.mdwn
index 1bac92c95..56acdd96c 100644
--- a/doc/tips/skydriveannex.mdwn
+++ b/doc/tips/skydriveannex.mdwn
@@ -1,7 +1,7 @@
 skydriveannex
 =========
 
-Hook program for gitannex to use skydrive as backend
+Hook program for gitannex to use [skydrive](http://en.wikipedia.org/wiki/SkyDrive) (previously *Windows Live SkyDrive* and *Windows Live Folders*) as backend
 
 # Requirements: