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

13 files changed, 190 insertions, 0 deletions

diff --git a/doc/bugs/No_manual_page_on_prebuilt_linux_version.mdwn b/doc/bugs/No_manual_page_on_prebuilt_linux_version.mdwn
new file mode 100644
index 000000000..0d6e99b24
--- /dev/null
+++ b/doc/bugs/No_manual_page_on_prebuilt_linux_version.mdwn
@@ -0,0 +1,16 @@
+### Please describe the problem, What steps will reproduce the problem?
+
+    $ which git-annex
+    ~/.local/bin/git-annex
+    $ git help annex
+    No manual entry for git-annex
+    $ git annex --help
+    No manual entry for git-annex
+
+(either that or it display the manual of system-installed git-annex, not the locally installed one)
+
+### What version of git-annex are you using? On what operating system?
+
+Fedora 20
+
+`git-annex --version` doesn't work and the webapp tells me Version: 5.20131130-gc25be33
diff --git a/doc/bugs/when_syncing_a_direct_repository__44___git_annex_delete_non_annexed_new_git_files/comment_5_95fcc19327b57222844302bb81236ee9._comment b/doc/bugs/when_syncing_a_direct_repository__44___git_annex_delete_non_annexed_new_git_files/comment_5_95fcc19327b57222844302bb81236ee9._comment
new file mode 100644
index 000000000..af319430a
--- /dev/null
+++ b/doc/bugs/when_syncing_a_direct_repository__44___git_annex_delete_non_annexed_new_git_files/comment_5_95fcc19327b57222844302bb81236ee9._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawmLdL4zLty4fsfaIXNtPMS5RXs4y8OAk0o"
+ nickname="Marc"
+ subject="comment 5"
+ date="2013-12-13T15:43:46Z"
+ content="""
+That's great, Joey, thanks a lot!
+"""]]
diff --git a/doc/forum/S3_Host_Question.mdwn b/doc/forum/S3_Host_Question.mdwn
new file mode 100644
index 000000000..f114d7c93
--- /dev/null
+++ b/doc/forum/S3_Host_Question.mdwn
@@ -0,0 +1,11 @@
+I have two machines A & B.  Each have their our repository.
+
+On machine A I have created a remotehost (S3) and have synced successfully.
+
+I am trying to link machine B to the same remote host.  I keep getting an error on the initremote command on machine B.
+
+I tried using the same command as I did on A and it is not working.   Is there a different command to link machine B to an existing remote repository?
+
+Any help is appreciated.
+
+Rob
diff --git a/doc/forum/S3_Host_Question/comment_1_8c8ecea703405753e47e0da5e8325929._comment b/doc/forum/S3_Host_Question/comment_1_8c8ecea703405753e47e0da5e8325929._comment
new file mode 100644
index 000000000..b8d63e5fd
--- /dev/null
+++ b/doc/forum/S3_Host_Question/comment_1_8c8ecea703405753e47e0da5e8325929._comment
@@ -0,0 +1,11 @@
+[[!comment format=mdwn
+ username="https://me.yahoo.com/a/FHnTlSBo1eCGJRwueeKeB6.RCaPbGMPr5jxx8A--#ce0d8"
+ nickname="Hamza"
+ subject="comment 1"
+ date="2013-12-13T08:37:24Z"
+ content="""
+On machine B you don't initremote you enableremote,
+
+
+    git annex enableremote mys3
+"""]]
diff --git a/doc/forum/S3_Host_Question/comment_2_3d6fa3147d59a5e0d10b005388b23c7a._comment b/doc/forum/S3_Host_Question/comment_2_3d6fa3147d59a5e0d10b005388b23c7a._comment
new file mode 100644
index 000000000..cef33d354
--- /dev/null
+++ b/doc/forum/S3_Host_Question/comment_2_3d6fa3147d59a5e0d10b005388b23c7a._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnKhw0-Tu5oHjeoz_gAP4Nu5V9uo8ta3hM"
+ nickname="Robert"
+ subject="unknown special remote"
+ date="2013-12-13T15:12:37Z"
+ content="""
+How does machine B know about the remote?  Machines A & B are separate and don't share references. Am I missing a step? 
+"""]]
diff --git a/doc/forum/Windows_S3_host_issue/comment_2_06ecc76797c430b27a2e24776761d043._comment b/doc/forum/Windows_S3_host_issue/comment_2_06ecc76797c430b27a2e24776761d043._comment
new file mode 100644
index 000000000..3e918120e
--- /dev/null
+++ b/doc/forum/Windows_S3_host_issue/comment_2_06ecc76797c430b27a2e24776761d043._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawk_bIB1Vadfc_GfPLKX_ScfWFCcaGyk8Ac"
+ nickname="Rob"
+ subject="Remove quotes"
+ date="2013-12-13T04:44:22Z"
+ content="""
+I tried the command with and without quotes it results in the same error.  I think the issue is that the host is trying to resolve a concatenation of the hostname and amazon.com when in fact it should be resolving to the host name only.
+"""]]
diff --git a/doc/forum/is_there_a_way_to_only_commit_some_files_in_direct-mode___63__/comment_2_299ad6cd0225daa166d36af3726a9ef2._comment b/doc/forum/is_there_a_way_to_only_commit_some_files_in_direct-mode___63__/comment_2_299ad6cd0225daa166d36af3726a9ef2._comment
new file mode 100644
index 000000000..0fb4a0097
--- /dev/null
+++ b/doc/forum/is_there_a_way_to_only_commit_some_files_in_direct-mode___63__/comment_2_299ad6cd0225daa166d36af3726a9ef2._comment
@@ -0,0 +1,14 @@
+[[!comment format=mdwn
+ username="Renaud"
+ ip="182.171.224.143"
+ subject="comment 2"
+ date="2013-12-13T06:16:12Z"
+ content="""
+Thanks for the reply!
+
+I tried to commit manually but I got confused by the (recently introduced?) annex/direct/master branch and I am not sure which branch I need to commit/merge/pull/push my changes to.
+I also got blocked when pulling from origin fail due to file changes needed to be overwritten.
+I see git-annex cleverly merges those in .git/annex/merge folder so I could try doing the same but I am not too confortable doing a large part of git-annex's job...
+
+Is there a simpler way to sync with a remote repository?
+"""]]
diff --git a/doc/forum/local_pairing_with_2_mac/comment_5_bcac18e137c00d4279774dec51963289._comment b/doc/forum/local_pairing_with_2_mac/comment_5_bcac18e137c00d4279774dec51963289._comment
new file mode 100644
index 000000000..063906866
--- /dev/null
+++ b/doc/forum/local_pairing_with_2_mac/comment_5_bcac18e137c00d4279774dec51963289._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.87"
+ subject="comment 5"
+ date="2013-12-12T21:40:16Z"
+ content="""
+Well, I was wrong, we don't know only one of the 2 has the problem. The other one will probably not have run ssh-keygen yet.
+
+Can you run `/Applications/git-annex.app/Contents/MacOS/bundle/ssh-keygen --help` on both of them and see if it manages to print its help, or fails with an error?
+"""]]
diff --git a/doc/forum/local_pairing_with_2_mac/comment_6_76b62eafda1ecbf88abe288cbe778e17._comment b/doc/forum/local_pairing_with_2_mac/comment_6_76b62eafda1ecbf88abe288cbe778e17._comment
new file mode 100644
index 000000000..e9cd8cc32
--- /dev/null
+++ b/doc/forum/local_pairing_with_2_mac/comment_6_76b62eafda1ecbf88abe288cbe778e17._comment
@@ -0,0 +1,17 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnfC02DTOZygFDDvvg0maRciYYMhEIFgkw"
+ nickname="Utku"
+ subject="comment 6"
+ date="2013-12-12T21:50:15Z"
+ content="""
+ok so it is ok on my computer, but here is what I got on the other one : 
+dyld: lazy symbol binding failed: Symbol not found: ___strlcpy_chk
+ Referenced from: /Applications/git-annex.app/Contents/MacOS/bundle/ssh-keygen
+ Expected in: /usr/lib/libSystem.B.dylib
+
+dyld: Symbol not found: ___strlcpy_chk
+ Referenced from: /Applications/git-annex.app/Contents/MacOS/bundle/ssh-keygen
+ Expected in: /usr/lib/libSystem.B.dylib
+
+Trace/BPT trap: 5
+"""]]
diff --git a/doc/forum/local_pairing_with_2_mac/comment_7_13fe788f2e9a823ad2e4844f114675a7._comment b/doc/forum/local_pairing_with_2_mac/comment_7_13fe788f2e9a823ad2e4844f114675a7._comment
new file mode 100644
index 000000000..883cb4e14
--- /dev/null
+++ b/doc/forum/local_pairing_with_2_mac/comment_7_13fe788f2e9a823ad2e4844f114675a7._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="209.250.56.87"
+ subject="comment 7"
+ date="2013-12-12T21:53:56Z"
+ content="""
+So it does only fail on one machine and not the other. I wonder what is different?
+
+Can you also try running `/Volumes/git-annex/git-annex.app/Contents/MacOS/bundle/cp` on both? (I think it uses the same symbol.)
+"""]]
diff --git a/doc/forum/local_pairing_with_2_mac/comment_8_f81b454e9cfc14dcb33148798be55de3._comment b/doc/forum/local_pairing_with_2_mac/comment_8_f81b454e9cfc14dcb33148798be55de3._comment
new file mode 100644
index 000000000..b4af1ce69
--- /dev/null
+++ b/doc/forum/local_pairing_with_2_mac/comment_8_f81b454e9cfc14dcb33148798be55de3._comment
@@ -0,0 +1,16 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawnfC02DTOZygFDDvvg0maRciYYMhEIFgkw"
+ nickname="Utku"
+ subject="comment 8"
+ date="2013-12-12T22:03:54Z"
+ content="""
+you mean /Applications/git-annex.app/Contents/MacOS/bundle/cp ?
+
+on both computers it prints : 
+usage: cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file target_file
+       cp [-R [-H | -L | -P]] [-fi | -n] [-apvX] source_file ... target_directory
+
+
+/Volumes/git-annex/git-annex.app/Contents/MacOS/bundle/cp doesn't work
+
+"""]]
diff --git a/doc/todo/Improve_direct_mode_using_copy_on_write.mdwn b/doc/todo/Improve_direct_mode_using_copy_on_write.mdwn
new file mode 100644
index 000000000..d9d9795cb
--- /dev/null
+++ b/doc/todo/Improve_direct_mode_using_copy_on_write.mdwn
@@ -0,0 +1,42 @@
+Direct mode is great because it removes symlinks. A must-have for directories like `~/Documents`. Unfortunately, it removes the possibility to use `git` commands other than `git-annex`. Also, it doen't preserve history of files.
+
+I would be great to have a mode where:
+
+- files are available in plain, not as sylinks
+- the repository could still be trusted to hold version of some files from other repositories
+- from a user point of view, the history of a file before the checkout would be preserved.
+
+In feature rich file systems that have copy on write feature, it could be implemented by having the files in both places at the same time:
+
+- the current version of a file would be in the working copy
+- the file in the working copy would be a copy-on-write of the file in the annex repository
+- when the file in the working copy changes, `git-annex` notices it and copy the file in the annex repository using copy-on-write semantic
+
+If the file system do not support copy-on-write, it could be an option (do you want secure direct mode that takes twice the disk space or light direct mode that don't preserve the history of your files?)
+
+This would make direct more much more robust.
+
+copy on write is available using `cp --reflink=always`. It correspond to the following code ([coreutils src/copy.c line 224](http://git.savannah.gnu.org/cgit/coreutils.git/tree/src/copy.c#n224)):
+
+    /* Perform the O(1) btrfs clone operation, if possible.
+       Upon success, return 0.  Otherwise, return -1 and set errno.  */
+    static inline int
+    clone_file (int dest_fd, int src_fd)
+    {
+    #ifdef __linux__
+    # undef BTRFS_IOCTL_MAGIC
+    # define BTRFS_IOCTL_MAGIC 0x94
+    # undef BTRFS_IOC_CLONE
+    # define BTRFS_IOC_CLONE _IOW (BTRFS_IOCTL_MAGIC, 9, int)
+      return ioctl (dest_fd, BTRFS_IOC_CLONE, src_fd);
+    #else
+      (void) dest_fd;
+      (void) src_fd;
+      errno = ENOTSUP;
+      return -1;
+    #endif
+    }
+
+Looking at the code it would be preferable to exec directly to `cp`, see [copy_range() on LWN](http://lwn.net/Articles/550621/) and this [more recent article about splice() on LWN](http://lwn.net/Articles/567086/)
+
+Also, `cp --reflink` fall back to copy when copy-on-write is not available while `cp --reflink=always` do not.
diff --git a/doc/todo/symlink_git-annex_binaries_to___126____47__.local__47__bin_for_prebuilt_package.mdwn b/doc/todo/symlink_git-annex_binaries_to___126____47__.local__47__bin_for_prebuilt_package.mdwn
new file mode 100644
index 000000000..516e20f79
--- /dev/null
+++ b/doc/todo/symlink_git-annex_binaries_to___126____47__.local__47__bin_for_prebuilt_package.mdwn
@@ -0,0 +1,19 @@
+Instead of changing the `PATH`, it should be possible to symlink the binaries to the `~/.local/bin` directory.
+
+Here is a script I put on the prebuilt package (its basename is unimportant but it must be placed along with the git-annex script):
+
+    #!/bin/sh
+    link="$(readlink "$0")"
+    base="$(cd "$(dirname "$0")"; cd "$(dirname "$link")"; echo "$PWD")"
+    name="$(basename "$0")"
+    exec "$base/$name" "$@"
+
+Symlink this script to `~/.local/bin/git-annex`, `~/.local/bin/git-annex-shell` and `~/.local/bin/git-annex-webapp`. on my system I have:
+
+    lrwxrwxrwx. 1 mildred mildred 36 Dec 13 12:12 git-annex -> ../opt/git-annex.linux/run-git-annex
+    lrwxrwxrwx. 1 mildred mildred 36 Dec 13 12:12 git-annex-shell -> ../opt/git-annex.linux/run-git-annex
+    lrwxrwxrwx. 1 mildred mildred 36 Dec 13 12:12 git-annex-webapp -> ../opt/git-annex.linux/run-git-annex
+
+The script will detect the installation directory using `readlink`. Both absolute and relative links works. Then it starts the correct script depending on the basename of the link.
+
+It should be possible to link the `git-annex`, `git-annex-webapp` and `git-annex-shell` scripts instead if they used `readlink` to find out the location of the prebuilt package.