From ee9973019c933a58568040f8fd12fb8736dbc965 Mon Sep 17 00:00:00 2001
From: "http://ertai.myopenid.com/" <npouillard@web>
Date: Mon, 28 Mar 2011 12:32:30 +0000
Subject: [PATCH 01/15]

---
 ...d_check__47__fix_the_permissions_of_.git__47__annex.mdwn | 6 ++++++
 1 file changed, 6 insertions(+)
 create mode 100644 doc/bugs/fsck__47__fix_should_check__47__fix_the_permissions_of_.git__47__annex.mdwn

diff --git a/doc/bugs/fsck__47__fix_should_check__47__fix_the_permissions_of_.git__47__annex.mdwn b/doc/bugs/fsck__47__fix_should_check__47__fix_the_permissions_of_.git__47__annex.mdwn
new file mode 100644
index 0000000000..ec8b6d2330
--- /dev/null
+++ b/doc/bugs/fsck__47__fix_should_check__47__fix_the_permissions_of_.git__47__annex.mdwn
@@ -0,0 +1,6 @@
+git annex carefully setup restrictive permissions of .git/annex directories and files.
+
+The fsck command should check that they are still correct.
+The fix command should fix them.
+
+PS: Thanks for this nice tool!

From 02601c6b9f2129e80323abea5ad76bf64c27b574 Mon Sep 17 00:00:00 2001
From: Joey Hess <joey@kitenet.net>
Date: Mon, 28 Mar 2011 08:41:23 -0400
Subject: [PATCH 02/15] analysis; workaround

---
 ..._version_upgrade_leaves_repo_unusable.mdwn | 26 ++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

diff --git a/doc/bugs/backend_version_upgrade_leaves_repo_unusable.mdwn b/doc/bugs/backend_version_upgrade_leaves_repo_unusable.mdwn
index 1218b0e517..964a176bd1 100644
--- a/doc/bugs/backend_version_upgrade_leaves_repo_unusable.mdwn
+++ b/doc/bugs/backend_version_upgrade_leaves_repo_unusable.mdwn
@@ -1,6 +1,10 @@
 foo is a local repo, bar is a bare remote.
 
-I upgraded foo's git-annex to 0.20110325 and upgraded a local repo backend to version 2. I then ran `git annex copy . --to bar` and checked the remote. This created WORM:SHA512--123123 files in annex/objects. Understandable but unwanted. So I upgraded git-annex on bar's machine, as well.
+I upgraded foo's git-annex to 0.20110325 and upgraded a local repo backend
+to version 2. I then ran `git annex copy . --to bar` and checked the
+remote. This created WORM:SHA512--123123 files in annex/objects.
+Understandable but unwanted. So I upgraded git-annex on bar's machine, as
+well.
 
     % git annex copy . --to bar
     copy quux (checking bar) git-annex-shell: Repository version 1 is not supported. Upgrade this repository: git-annex upgrade (to bar)
@@ -33,3 +37,23 @@ Running the copy job again, I am still getting the same error as above (as expec
 > joey@kitenet.net if you don't want to post them here. --[[Joey]]
 
 >> Sent. -- RichiH
+
+>>> Ok, I'm going to go work on my reading comprehension. I see now
+>>> that you
+>>> explained the problem pretty well. The problem is caused by these
+>>> few weird v1 mixed with v2 keys in the annex.
+>>> Ones like "annex/objects/WORM:SHA512--$sha512".
+>>>
+>>> That's a v1 key, but a corrupt form of the key; it's missing the 
+>>> size and mtime fields that all WORM keys have in v1. And 
+>>> the filename is itself a key, a v2 SHA512 key. My guess at what
+>>> happened is that these were created when you did the `git annex copy`
+>>> to the v1 bare repo.
+>>>
+>>> So, assuming none of these are the only copy of your data
+>>> (which you should check), the best thing to do is delete those
+>>> keys, and re-run the copy now that it's upgraded. Not sure 
+>>> it even makes sense to fix the crash. I should probably focus
+>>> on fixing what let these mixed keys be created by the mixed-version
+>>> copy.
+>>> --[[Joey]]

From d2ed1b3a99da45ae25e84cbc832693442bab7de6 Mon Sep 17 00:00:00 2001
From: Joey Hess <joey@kitenet.net>
Date: Mon, 28 Mar 2011 08:52:42 -0400
Subject: [PATCH 03/15] second thought

---
 doc/bugs/backend_version_upgrade_leaves_repo_unusable.mdwn | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/doc/bugs/backend_version_upgrade_leaves_repo_unusable.mdwn b/doc/bugs/backend_version_upgrade_leaves_repo_unusable.mdwn
index 964a176bd1..7bbd02364f 100644
--- a/doc/bugs/backend_version_upgrade_leaves_repo_unusable.mdwn
+++ b/doc/bugs/backend_version_upgrade_leaves_repo_unusable.mdwn
@@ -56,4 +56,7 @@ Running the copy job again, I am still getting the same error as above (as expec
 >>> it even makes sense to fix the crash. I should probably focus
 >>> on fixing what let these mixed keys be created by the mixed-version
 >>> copy.
+>>>
+>>> On second thought, you shouldn't delete anything. I'll simply
+>>> make the v2 upgrade detect and work around this bug.
 >>> --[[Joey]]

From 9d86d02b3db23f0b8848f4a9a044befa58e1ecbb Mon Sep 17 00:00:00 2001
From: Joey Hess <joey@kitenet.net>
Date: Mon, 28 Mar 2011 08:55:00 -0400
Subject: [PATCH 04/15] update

---
 ..._version_upgrade_leaves_repo_unusable.mdwn | 20 ++++++++-----------
 1 file changed, 8 insertions(+), 12 deletions(-)

diff --git a/doc/bugs/backend_version_upgrade_leaves_repo_unusable.mdwn b/doc/bugs/backend_version_upgrade_leaves_repo_unusable.mdwn
index 7bbd02364f..64c18f202c 100644
--- a/doc/bugs/backend_version_upgrade_leaves_repo_unusable.mdwn
+++ b/doc/bugs/backend_version_upgrade_leaves_repo_unusable.mdwn
@@ -46,17 +46,13 @@ Running the copy job again, I am still getting the same error as above (as expec
 >>>
 >>> That's a v1 key, but a corrupt form of the key; it's missing the 
 >>> size and mtime fields that all WORM keys have in v1. And 
->>> the filename is itself a key, a v2 SHA512 key. My guess at what
->>> happened is that these were created when you did the `git annex copy`
->>> to the v1 bare repo.
+>>> the filename is itself a key, a v2 SHA512 key. These were
+>>> created when you did the `git annex copy to the v1 bare repo.
+>>> In v2, git-annex-shell takes a full key object, while in v1,
+>>> it takes a key name and a backend name. This incompatability
+>>> leads to the weird behavior seen.
 >>>
->>> So, assuming none of these are the only copy of your data
->>> (which you should check), the best thing to do is delete those
->>> keys, and re-run the copy now that it's upgraded. Not sure 
->>> it even makes sense to fix the crash. I should probably focus
->>> on fixing what let these mixed keys be created by the mixed-version
->>> copy.
->>>
->>> On second thought, you shouldn't delete anything. I'll simply
->>> make the v2 upgrade detect and work around this bug.
+>>> I had suggested you delete data.. don't. On second thought,
+>>> you shouldn't delete anything. I'll simply make the v2 upgrade
+>>> detect and work around this bug.
 >>> --[[Joey]]

From 016eea028086f2e8c1733ac77612f4397297d1a3 Mon Sep 17 00:00:00 2001
From: Joey Hess <joey@kitenet.net>
Date: Mon, 28 Mar 2011 09:27:28 -0400
Subject: [PATCH 05/15] Bugfix: Keys could be received into v1 annexes from v2
 annexes, via v1 git-annex-shell. This results in some oddly named keys in the
 v1 annex. Recognise and fix those keys when upgrading, instead of crashing.

---
 Upgrade/V1.hs                                 | 44 +++++++++++--------
 debian/changelog                              |  3 ++
 ..._version_upgrade_leaves_repo_unusable.mdwn |  3 ++
 3 files changed, 31 insertions(+), 19 deletions(-)

diff --git a/Upgrade/V1.hs b/Upgrade/V1.hs
index a876142220..4ce2612d60 100644
--- a/Upgrade/V1.hs
+++ b/Upgrade/V1.hs
@@ -16,6 +16,7 @@ import System.FilePath
 import Data.String.Utils
 import System.Posix.Types
 import Data.Maybe
+import Data.Char
 
 import Key
 import Content
@@ -79,12 +80,11 @@ upgrade = do
 moveContent :: Annex ()
 moveContent = do
 	showNote "moving content..."
-	keys <- getKeysPresent1
-	forM_ keys move
+	files <- getKeyFilesPresent1
+	forM_ files move
 	where
-		move k = do
-			g <- Annex.gitRepo
-			let f = gitAnnexObjectDir g </> keyFile1 k </> keyFile1 k
+		move f = do
+			let k = fileKey1 (takeFileName f)
 			let d = parentDir f
 			liftIO $ allowWrite d
 			liftIO $ allowWrite f
@@ -154,8 +154,15 @@ oldlog2key l =
 
 -- WORM backend keys: "WORM:mtime:size:filename"
 -- all the rest: "backend:key"
+--
+-- If the file looks like "WORM:XXX-...", then it was created by mixing
+-- v2 and v1; that infelicity is worked around by treating the value
+-- as the v2 key that it is.
 readKey1 :: String -> Key
-readKey1 v = Key { keyName = n , keyBackendName = b, keySize = s, keyMtime = t }
+readKey1 v = 
+	if mixup
+		then fromJust $ readKey $ join ":" $ tail bits
+		else Key { keyName = n , keyBackendName = b, keySize = s, keyMtime = t }
 	where
 		bits = split ":" v
 		b = head bits
@@ -166,7 +173,8 @@ readKey1 v = Key { keyName = n , keyBackendName = b, keySize = s, keyMtime = t }
 		s = if wormy
 			then Just (read (bits !! 2) :: Integer)
 			else Nothing
-		wormy = b == "WORM"
+		wormy = head bits == "WORM"
+		mixup = wormy && (isUpper $ head $ bits !! 1)
 
 showKey1 :: Key -> String
 showKey1 Key { keyName = n , keyBackendName = b, keySize = s, keyMtime = t } =
@@ -211,24 +219,22 @@ lookupFile1 file = do
 				skip = "skipping " ++ file ++ 
 					" (unknown backend " ++ bname ++ ")"
 
-getKeysPresent1 :: Annex [Key]
-getKeysPresent1  = do
+getKeyFilesPresent1 :: Annex [FilePath]
+getKeyFilesPresent1  = do
 	g <- Annex.gitRepo
-	getKeysPresent1' $ gitAnnexObjectDir g
-getKeysPresent1' :: FilePath -> Annex [Key]
-getKeysPresent1' dir = do
+	getKeyFilesPresent1' $ gitAnnexObjectDir g
+getKeyFilesPresent1' :: FilePath -> Annex [FilePath]
+getKeyFilesPresent1' dir = do
 	exists <- liftIO $ doesDirectoryExist dir
 	if (not exists)
 		then return []
 		else do
-			contents <- liftIO $ getDirectoryContents dir
-			files <- liftIO $ filterM present contents
-			return $ map fileKey1 files
+			dirs <- liftIO $ getDirectoryContents dir
+			let files = map (\d -> dir ++ "/" ++ d ++ "/" ++ takeFileName d) dirs
+			liftIO $ filterM present files
 	where
-		present d = do
-			liftIO $ putStrLn $ dir ++ "/" ++ d ++ "/"  ++ takeFileName d
-			result <- try $
-				getFileStatus $ dir ++ "/" ++ d ++ "/"  ++ takeFileName d
+		present f = do
+			result <- try $ getFileStatus f
 			case result of
 				Right s -> return $ isRegularFile s
 				Left _ -> return False
diff --git a/debian/changelog b/debian/changelog
index 2f532784d4..517cf59695 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -6,6 +6,9 @@ git-annex (0.20110326) UNRELEASED; urgency=low
   * Provide a less expensive version of `git annex copy --to`, enabled
     via --fast. This assumes that location tracking information is correct,
     rather than contacting the remote for every file.
+  * Bugfix: Keys could be received into v1 annexes from v2 annexes, via
+    v1 git-annex-shell. This results in some oddly named keys in the v1
+    annex. Recognise and fix those keys when upgrading, instead of crashing.
 
  -- Joey Hess <joeyh@debian.org>  Sat, 26 Mar 2011 14:36:16 -0400
 
diff --git a/doc/bugs/backend_version_upgrade_leaves_repo_unusable.mdwn b/doc/bugs/backend_version_upgrade_leaves_repo_unusable.mdwn
index 64c18f202c..1eebd9ecd4 100644
--- a/doc/bugs/backend_version_upgrade_leaves_repo_unusable.mdwn
+++ b/doc/bugs/backend_version_upgrade_leaves_repo_unusable.mdwn
@@ -56,3 +56,6 @@ Running the copy job again, I am still getting the same error as above (as expec
 >>> you shouldn't delete anything. I'll simply make the v2 upgrade
 >>> detect and work around this bug.
 >>> --[[Joey]]
+
+>>>> This should be fixed in current git. The scambled keys will be 
+>>>> fixed up on upgrade. Thanks for your patience! [[done]] --[[Joey]]

From 2933860847c8092cd2f447e29f3da8b00a15cb18 Mon Sep 17 00:00:00 2001
From: "http://christian.amsuess.com/chrysn" <chrysn@web>
Date: Mon, 28 Mar 2011 14:01:00 +0000
Subject: [PATCH 06/15] not actively pursuing this issue any more

---
 doc/forum/relying_on_git_for_numcopies.mdwn | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/doc/forum/relying_on_git_for_numcopies.mdwn b/doc/forum/relying_on_git_for_numcopies.mdwn
index b7ebba805a..37b46cf4e7 100644
--- a/doc/forum/relying_on_git_for_numcopies.mdwn
+++ b/doc/forum/relying_on_git_for_numcopies.mdwn
@@ -1,3 +1,5 @@
+**&lt;out-of-date-warning&gt;**The main problems this is supposed to solve are addressed in a different way with [[todo/hidden files]] and the `--fast` option introduced in [[batch check on remote when using copy]], so while this is not technically obsolete, the main reasons for it are gone. --[[chrysn]]**&lt;/out-of-date-warning&gt;**
+
 This is a rough sketch of a modification of git-annex to rely more on git commit semantics. It might be flawed due to my lack of understanding of git-annex internals. --[[chrysn]]
 
 Summary

From fc363b9ca39f264566ec9299358f201c348b792a Mon Sep 17 00:00:00 2001
From: 
 "https://www.google.com/accounts/o8/id?id=AItOawl9sYlePmv1xK-VvjBdN-5doOa_Xw-jH4U"
 <Richard@web>
Date: Mon, 28 Mar 2011 14:44:26 +0000
Subject: [PATCH 07/15]

---
 .../backend_version_upgrade_leaves_repo_unusable.mdwn | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/doc/bugs/backend_version_upgrade_leaves_repo_unusable.mdwn b/doc/bugs/backend_version_upgrade_leaves_repo_unusable.mdwn
index 1eebd9ecd4..122224a8f3 100644
--- a/doc/bugs/backend_version_upgrade_leaves_repo_unusable.mdwn
+++ b/doc/bugs/backend_version_upgrade_leaves_repo_unusable.mdwn
@@ -59,3 +59,14 @@ Running the copy job again, I am still getting the same error as above (as expec
 
 >>>> This should be fixed in current git. The scambled keys will be 
 >>>> fixed up on upgrade. Thanks for your patience! [[done]] --[[Joey]]
+
+>>>>> I should stop reading your answers via git; by the time I got to
+>>>>> "second thoughts", I had already deleted the files & directories
+>>>>> in question, upgraded the bare repo and was busy uploading from my
+>>>>> local repo. I agree that taking care of this in the upgrade code
+>>>>> is the cleanest approach, by the way.
+>>>>> No need to thank me for my patience; thank you for your quickness!
+>>>>> RichiH
+>>>>> 
+>>>>> PS: If I get a handle on the mtime issue in the SHA backend, git
+>>>>> annex will be pretty much perfect :)

From 1b6927995de5e25ec6c5c464c6444d2ba61ec748 Mon Sep 17 00:00:00 2001
From: Joey Hess <joey@kitenet.net>
Date: Mon, 28 Mar 2011 11:12:32 -0400
Subject: [PATCH 08/15] releasing version 0.20110328

---
 debian/changelog | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 517cf59695..7251ab6653 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,8 @@
-git-annex (0.20110326) UNRELEASED; urgency=low
+git-annex (0.20110328) experimental; urgency=low
 
   * annex.diskreserve can be given in arbitrary units (ie "0.5 gigabytes")
   * Generalized remotes handling, laying groundwork for remotes that are
-    not regular git remotes.
+    not regular git remotes. (Think Amazon S3.)
   * Provide a less expensive version of `git annex copy --to`, enabled
     via --fast. This assumes that location tracking information is correct,
     rather than contacting the remote for every file.
@@ -10,7 +10,7 @@ git-annex (0.20110326) UNRELEASED; urgency=low
     v1 git-annex-shell. This results in some oddly named keys in the v1
     annex. Recognise and fix those keys when upgrading, instead of crashing.
 
- -- Joey Hess <joeyh@debian.org>  Sat, 26 Mar 2011 14:36:16 -0400
+ -- Joey Hess <joeyh@debian.org>  Mon, 28 Mar 2011 10:47:29 -0400
 
 git-annex (0.20110325) experimental; urgency=low
 

From 659f0fe980b6bff6900037d9ae52024b989613e1 Mon Sep 17 00:00:00 2001
From: Joey Hess <joey@kitenet.net>
Date: Mon, 28 Mar 2011 11:13:15 -0400
Subject: [PATCH 09/15] add news item for git-annex 0.20110328

---
 doc/news/version_0.20110328.mdwn | 11 +++++++++++
 doc/news/version_0.24.mdwn       | 12 ------------
 2 files changed, 11 insertions(+), 12 deletions(-)
 create mode 100644 doc/news/version_0.20110328.mdwn
 delete mode 100644 doc/news/version_0.24.mdwn

diff --git a/doc/news/version_0.20110328.mdwn b/doc/news/version_0.20110328.mdwn
new file mode 100644
index 0000000000..512ce4647a
--- /dev/null
+++ b/doc/news/version_0.20110328.mdwn
@@ -0,0 +1,11 @@
+git-annex 0.20110328 released with [[!toggle text="these changes"]]
+[[!toggleable text="""
+   * annex.diskreserve can be given in arbitrary units (ie "0.5 gigabytes")
+   * Generalized remotes handling, laying groundwork for remotes that are
+     not regular git remotes. (Think Amazon S3.)
+   * Provide a less expensive version of `git annex copy --to`, enabled
+     via --fast. This assumes that location tracking information is correct,
+     rather than contacting the remote for every file.
+   * Bugfix: Keys could be received into v1 annexes from v2 annexes, via
+     v1 git-annex-shell. This results in some oddly named keys in the v1
+     annex. Recognise and fix those keys when upgrading, instead of crashing."""]]
\ No newline at end of file
diff --git a/doc/news/version_0.24.mdwn b/doc/news/version_0.24.mdwn
deleted file mode 100644
index 81b013a26f..0000000000
--- a/doc/news/version_0.24.mdwn
+++ /dev/null
@@ -1,12 +0,0 @@
-Branched the 0.24 series, which will be maintained for a while (in the
-stable branch in git) to support v1 git-annex repos, while main development
-moves to the 0.2011 series, with v2 git-annex repos.
-
-git-annex 0.24 released with [[!toggle text="these changes"]]
-[[!toggleable text="""
-* Add Suggests on graphviz. Closes: #[618039](http://bugs.debian.org/618039)
-* When adding files to the annex, the symlinks pointing at the annexed
-  content are made to have the same mtime as the original file.
-  While git does not preserve that information, this allows a tool
-  like metastore to be used with annexed files.
-  (Currently this is only done on systems supporting POSIX 200809.)"""]]

From b6d40c119a9982f05db4134e182e762cb1953697 Mon Sep 17 00:00:00 2001
From: 
 "https://www.google.com/accounts/o8/id?id=AItOawkSq2FDpK2n66QRUxtqqdbyDuwgbQmUWus"
 <Jimmy@web>
Date: Mon, 28 Mar 2011 15:13:54 +0000
Subject: [PATCH 10/15] Added a comment

---
 ..._174952fc3e3be12912e5fcfe78f2dd13._comment | 185 ++++++++++++++++++
 1 file changed, 185 insertions(+)
 create mode 100644 doc/bugs/git-annex_directory_hashing_problems_on_osx/comment_2_174952fc3e3be12912e5fcfe78f2dd13._comment

diff --git a/doc/bugs/git-annex_directory_hashing_problems_on_osx/comment_2_174952fc3e3be12912e5fcfe78f2dd13._comment b/doc/bugs/git-annex_directory_hashing_problems_on_osx/comment_2_174952fc3e3be12912e5fcfe78f2dd13._comment
new file mode 100644
index 0000000000..6e6e5dc6be
--- /dev/null
+++ b/doc/bugs/git-annex_directory_hashing_problems_on_osx/comment_2_174952fc3e3be12912e5fcfe78f2dd13._comment
@@ -0,0 +1,185 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkSq2FDpK2n66QRUxtqqdbyDuwgbQmUWus"
+ nickname="Jimmy"
+ subject="comment 2"
+ date="2011-03-28T15:09:45Z"
+ content="""
+I think I know how I got myself into this mess... I was on my mac workstation and I had just pulled in a change set from another repo on a linux workstation after I had a made a bunch of moves. here's a bit of a log of what happened...
+
+
+<pre>
+jtang@x00:~/sources $ git pull cports-devel master
+Warning: untrusted X11 forwarding setup failed: xauth key data not generated
+Warning: No xauth data; using fake authentication data for X11 forwarding.
+remote: Counting objects: 4195, done.
+remote: Compressing objects: 100% (1135/1135), done.
+remote: Total 2582 (delta 866), reused 2576 (delta 860)
+Receiving objects: 100% (2582/2582), 229.42 KiB | 111 KiB/s, done.
+Resolving deltas: 100% (866/866), completed with 9 local objects.
+From cports-devel:/home/people/jtang/sources
+ * branch            master     -> FETCH_HEAD
+Updating 319df99..ab0a98c
+error: Your local changes to the following files would be overwritten by merge:
+	.git-annex/09/5X/WORM-s361516678-m1301310614--l_fcompxe_intel64_2011.2.137.tgz.log
+	.git-annex/43/2g/WORM-s19509673-m1301310496--l_fcompxe_2011.2.137_redist.tgz.log
+	.git-annex/4J/qF/WORM-s18891115-m1301310934--w_flm_p_1.0.011_ia64.zip.log
+	.git-annex/87/w1/WORM-s12212473-m1301310909--w_flm_p_1.0.011_ia32.zip.log
+	.git-annex/99/Jq/WORM-s194345957-m1301310926--l_mkl_10.3.2.137_ia32.log
+	.git-annex/99/kf/WORM-s9784531-m1301311680--l_ccompxe_2011.2.137_redist.log
+	.git-annex/FF/f3/WORM-s93033394-m1301311706--l_gen_ipp_7.0.2.137.log
+	.git-annex/MF/xZ/WORM-s515140733-m1301310936--l_cprof_p_11.1.075.log
+	.git-annex/XW/X8/WORM-s355559731-m1301310797--l_mkl_10.3.2.137.log
+	.git-annex/fJ/mZ/WORM-s1372886477-m1301313368--l_cproc_p_11.1.075.log
+	.git-annex/j7/Q9/WORM-s44423202-m1301310622--l_cprof_p_11.1.075_redist.log
+	.git-annex/k4/K7/WORM-s239539070-m1301310760--l_mkl_10.3.2.137_intel64.log
+	.git-annex/kz/01/WORM-s279573314-m1301310783--l_cprof_p_11.1.075_ia32.log
+	.git-annex/p6/Kq/WORM-s31199343-m1301311829--l_cproc_p_11.1.075_redist.log
+	.git-annex/pz/J5/WORM-s626995277-m1301312301--l_ccompxe_ia32_2011.2.137.log
+	.git-annex/v3/kX/WORM-s339693045-m1301310851--l_cprof_p_11.1.075_intel64.log
+Please, commit your changes or stash them before you can merge.
+error: Your local changes to the following files would be overwritten by merge:
+	.git-annex/12/3W/WORM-s3058814-m1276699694--Botan-1.8.9.tgz.log
+	.git-annex/1G/qV/WORM-s9122-m1251558854--Array-Compare-2.01.tar.gz.log
+	.git-annex/3W/W5/WORM-s231523-m1270740744--DBD-Pg-2.17.1.tar.gz.log
+	.git-annex/3x/PX/WORM-s380310-m1293025187--HTSeq-0.4.7.tar.gz.log
+	.git-annex/45/gk/WORM-s67337-m1248732018--ExtUtils-Install-1.54.tar.gz.log
+	.git-annex/4J/7Q/WORM-s8608-m1224694862--Algorithm-Munkres-0.08.tar.gz.log
+	.git-annex/4g/XQ/WORM-s89208-m1278682033--HTML-Parser-3.66.tar.gz.log
+	.git-annex/54/jw/WORM-s300163-m1226422051--AcePerl-1.92.tar.gz.log
+	.git-annex/63/kj/WORM-s1213460-m1262942058--DBD-SQLite-1.29.tar.gz.log
+	.git-annex/6Z/42/WORM-s4074-m943766010--File-Sync-0.09.tar.gz.log
+	.git-annex/8F/M5/WORM-s6989-m1263161127--Digest-HMAC-1.02.tar.gz.log
+	.git-annex/G2/FK/WORM-s3309-m1163872981--Bundle-BioPerl-2.1.8.tar.gz.log
+	.git-annex/Gk/XF/WORM-s23572243-m1279546902--EMBOSS-6.3.1.tar.gz.log
+	.git-annex/Jk/X6/WORM-s566429-m1279309002--DBI-1.612.tar.gz.log
+	.git-annex/K6/fV/WORM-s1561451-m1240055295--Convert-Binary-C-0.74.tar.gz.log
+	.git-annex/KM/4q/WORM-s146959-m1268515086--Graph-0.94.tar.gz.log
+	.git-annex/MF/m2/WORM-s425766-m1212514609--Data-Stag-0.11.tar.gz.log
+	.git-annex/QJ/P6/WORM-s1045868-m1282215033--9base-6.tar.gz.log
+	.git-annex/Qm/WG/WORM-s39078-m1278163547--Digest-SHA1-2.13.tar.gz.log
+	.git-annex/Wq/Fj/WORM-s45680640-m1297862101--BclConverter-1.7.1.tar.log
+	.git-annex/Wq/Wm/WORM-s263536640-m1295025537--CASAVA_v1.7.0.tar.log
+	.git-annex/XW/qm/WORM-s36609-m1276050470--Bio-ASN1-EntrezGene-1.10-withoutworldwriteables.tar.gz.log
+	.git-annex/f7/g0/WORM-s40872-m1278273227--ExtUtils-ParseXS-2.2206.tar.gz.log
+	.git-annex/j3/JF/WORM-s11753-m1232427595--Clone-0.31.tar.gz.log
+	.git-annex/kX/9g/WORM-s84690-m1229117599--GraphViz-2.04.tar.gz.log
+	.git-annex/km/z5/WORM-s44634-m1275505134--Authen-SASL-2.15.tar.gz.log
+	.git-annex/kw/J3/WORM-s132396-m1278780649--DBD-mysql-4.016.tar.gz.log
+	.git-annex/p5/1P/WORM-s53736-m1278673485--Archive-Tar-1.64.tar.gz.log
+	.git-annex/wv/zG/WORM-s30584-m1268774021--ExtUtils-CBuilder-0.2703.tar.gz.log
+	.git-annex/x5/7v/WORM-s10462526-m1254242591--BioPerl-1.6.1.tar.gz.log
+Please, commit your changes or stash them before you can merge.
+error: The following untracked working tree files would be overwritten by merge:
+	.git-annex/1g/X3/WORM-s309910751-m1301311322--l_fcompxe_ia32_2011.2.137.tgz.log
+	.git-annex/3w/Xf/WORM-s805764902-m1301312756--l_cproc_p_11.1.075_intel64.log
+	.git-annex/9Q/Wz/WORM-s1234430253-m1301311891--l_ccompxe_2011.2.137.log
+	.git-annex/FQ/4z/WORM-s318168323-m1301310848--l_cprof_p_11.1.075_ia64.log
+	.git-annex/FV/0P/WORM-s710135470-m1301311835--l_ccompxe_intel64_2011.2.137.log
+	.git-annex/Jx/qM/WORM-s599386592-m1301310731--l_fcompxe_2011.2.137.tgz.log
+	.git-annex/KX/w1/WORM-s35976002-m1301312193--l_tbb_3.0.6.174.log
+	.git-annex/Vw/jK/WORM-s15795178-m1301310913--w_flm_p_1.0.011_intel64.zip.log
+	.git-annex/jK/zK/WORM-s374617670-m1301312705--l_ipp_7.0.2.137_intel64.log
+	.git-annex/vK/kv/WORM-s584342291-m1301312669--l_cproc_p_11.1.075_ia64.log
+	.git-annex/vw/v1/WORM-s736986678-m1301312794--l_cproc_p_11.1.075_ia32.log
+	.git-annex/zq/7X/WORM-s343075585-m1301312233--l_ipp_7.0.2.137_ia32.log
+Please move or remove them before you can merge.
+Aborting
+1|jtang@x00:~/sources $ git status
+# On branch master
+# Your branch is ahead of 'origin/master' by 2 commits.
+#
+# Changes to be committed:
+#   (use \"git reset HEAD <file>...\" to unstage)
+#
+#	modified:   .git-annex/09/5X/WORM-s361516678-m1301310614--l_fcompxe_intel64_2011.2.137.tgz.log
+#	modified:   .git-annex/43/2g/WORM-s19509673-m1301310496--l_fcompxe_2011.2.137_redist.tgz.log
+#	modified:   .git-annex/4J/qF/WORM-s18891115-m1301310934--w_flm_p_1.0.011_ia64.zip.log
+#	modified:   .git-annex/87/w1/WORM-s12212473-m1301310909--w_flm_p_1.0.011_ia32.zip.log
+#	modified:   .git-annex/99/Jq/WORM-s194345957-m1301310926--l_mkl_10.3.2.137_ia32.log
+#	modified:   .git-annex/99/kf/WORM-s9784531-m1301311680--l_ccompxe_2011.2.137_redist.log
+#	modified:   .git-annex/FF/f3/WORM-s93033394-m1301311706--l_gen_ipp_7.0.2.137.log
+#	modified:   .git-annex/MF/xZ/WORM-s515140733-m1301310936--l_cprof_p_11.1.075.log
+#	modified:   .git-annex/XW/X8/WORM-s355559731-m1301310797--l_mkl_10.3.2.137.log
+#	modified:   .git-annex/fJ/mZ/WORM-s1372886477-m1301313368--l_cproc_p_11.1.075.log
+#	modified:   .git-annex/j7/Q9/WORM-s44423202-m1301310622--l_cprof_p_11.1.075_redist.log
+#	modified:   .git-annex/k4/K7/WORM-s239539070-m1301310760--l_mkl_10.3.2.137_intel64.log
+#	modified:   .git-annex/kz/01/WORM-s279573314-m1301310783--l_cprof_p_11.1.075_ia32.log
+#	modified:   .git-annex/p6/Kq/WORM-s31199343-m1301311829--l_cproc_p_11.1.075_redist.log
+#	modified:   .git-annex/pz/J5/WORM-s626995277-m1301312301--l_ccompxe_ia32_2011.2.137.log
+#	modified:   .git-annex/v3/kX/WORM-s339693045-m1301310851--l_cprof_p_11.1.075_intel64.log
+#
+# Changes not staged for commit:
+#   (use \"git add <file>...\" to update what will be committed)
+#   (use \"git checkout -- <file>...\" to discard changes in working directory)
+#
+#	modified:   .git-annex/12/3W/WORM-s3058814-m1276699694--Botan-1.8.9.tgz.log
+#	modified:   .git-annex/1G/qV/WORM-s9122-m1251558854--Array-Compare-2.01.tar.gz.log
+#	modified:   .git-annex/3W/W5/WORM-s231523-m1270740744--DBD-Pg-2.17.1.tar.gz.log
+#	modified:   .git-annex/3x/PX/WORM-s380310-m1293025187--HTSeq-0.4.7.tar.gz.log
+#	modified:   .git-annex/45/gk/WORM-s67337-m1248732018--ExtUtils-Install-1.54.tar.gz.log
+#	modified:   .git-annex/4J/7Q/WORM-s8608-m1224694862--Algorithm-Munkres-0.08.tar.gz.log
+#	modified:   .git-annex/4g/XQ/WORM-s89208-m1278682033--HTML-Parser-3.66.tar.gz.log
+#	modified:   .git-annex/54/jw/WORM-s300163-m1226422051--AcePerl-1.92.tar.gz.log
+#	modified:   .git-annex/63/kj/WORM-s1213460-m1262942058--DBD-SQLite-1.29.tar.gz.log
+#	modified:   .git-annex/6Z/42/WORM-s4074-m943766010--File-Sync-0.09.tar.gz.log
+#	modified:   .git-annex/8F/M5/WORM-s6989-m1263161127--Digest-HMAC-1.02.tar.gz.log
+#	modified:   .git-annex/G2/FK/WORM-s3309-m1163872981--Bundle-BioPerl-2.1.8.tar.gz.log
+#	modified:   .git-annex/Gk/XF/WORM-s23572243-m1279546902--EMBOSS-6.3.1.tar.gz.log
+#	modified:   .git-annex/Jk/X6/WORM-s566429-m1279309002--DBI-1.612.tar.gz.log
+#	modified:   .git-annex/K6/fV/WORM-s1561451-m1240055295--Convert-Binary-C-0.74.tar.gz.log
+#	modified:   .git-annex/KM/4q/WORM-s146959-m1268515086--Graph-0.94.tar.gz.log
+#	modified:   .git-annex/MF/m2/WORM-s425766-m1212514609--Data-Stag-0.11.tar.gz.log
+#	modified:   .git-annex/QJ/P6/WORM-s1045868-m1282215033--9base-6.tar.gz.log
+#	modified:   .git-annex/Qm/WG/WORM-s39078-m1278163547--Digest-SHA1-2.13.tar.gz.log
+#	modified:   .git-annex/Wq/Fj/WORM-s45680640-m1297862101--BclConverter-1.7.1.tar.log
+#	modified:   .git-annex/Wq/Wm/WORM-s263536640-m1295025537--CASAVA_v1.7.0.tar.log
+#	modified:   .git-annex/XW/qm/WORM-s36609-m1276050470--Bio-ASN1-EntrezGene-1.10-withoutworldwriteables.tar.gz.log
+#	modified:   .git-annex/Zq/7X/WORM-s343075585-m1301312233--l_ipp_7.0.2.137_ia32.log
+#	modified:   .git-annex/f7/g0/WORM-s40872-m1278273227--ExtUtils-ParseXS-2.2206.tar.gz.log
+#	modified:   .git-annex/j3/JF/WORM-s11753-m1232427595--Clone-0.31.tar.gz.log
+#	modified:   .git-annex/kX/9g/WORM-s84690-m1229117599--GraphViz-2.04.tar.gz.log
+#	modified:   .git-annex/km/z5/WORM-s44634-m1275505134--Authen-SASL-2.15.tar.gz.log
+#	modified:   .git-annex/kw/J3/WORM-s132396-m1278780649--DBD-mysql-4.016.tar.gz.log
+#	modified:   .git-annex/p5/1P/WORM-s53736-m1278673485--Archive-Tar-1.64.tar.gz.log
+#	modified:   .git-annex/wv/zG/WORM-s30584-m1268774021--ExtUtils-CBuilder-0.2703.tar.gz.log
+#	modified:   .git-annex/x5/7v/WORM-s10462526-m1254242591--BioPerl-1.6.1.tar.gz.log
+#
+# Untracked files:
+#   (use \"git add <file>...\" to include in what will be committed)
+#
+#	.git-annex/1G/X3/
+#	.git-annex/3W/Xf/
+#	.git-annex/9q/Wz/
+#	.git-annex/Fq/4z/
+#	.git-annex/Jk/zK/
+#	.git-annex/Kx/w1/
+#	.git-annex/VK/kv/
+#	.git-annex/fv/0P/
+#	.git-annex/jX/qM/
+#	.git-annex/vW/jK/
+#	.git-annex/vW/v1/
+jtang@x00:~/sources $ git commit -a -m \"snap\"
+[master 45f254a] snap
+ 47 files changed, 64 insertions(+), 30 deletions(-)
+jtang@x00:~/sources $ git status
+# On branch master
+# Your branch is ahead of 'origin/master' by 3 commits.
+#
+# Untracked files:
+#   (use \"git add <file>...\" to include in what will be committed)
+#
+#	.git-annex/1G/X3/
+#	.git-annex/3W/Xf/
+#	.git-annex/9q/Wz/
+#	.git-annex/Fq/4z/
+#	.git-annex/Jk/zK/
+#	.git-annex/Kx/w1/
+#	.git-annex/VK/kv/
+#	.git-annex/fv/0P/
+#	.git-annex/jX/qM/
+#	.git-annex/vW/jK/
+#	.git-annex/vW/v1/
+nothing added to commit but untracked files present (use \"git add\" to track)
+jtang@x00:~/sources $ git pull
+</pre>
+"""]]

From 8db6b4f655096d141af5b8a25cf76826c02d9fdd Mon Sep 17 00:00:00 2001
From: Joey Hess <joey@kitenet.net>
Date: Mon, 28 Mar 2011 11:16:36 -0400
Subject: [PATCH 11/15] response

---
 ...has_issues_with_git_when_staging__47__commiting_logs.mdwn | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/doc/bugs/git-annex_has_issues_with_git_when_staging__47__commiting_logs.mdwn b/doc/bugs/git-annex_has_issues_with_git_when_staging__47__commiting_logs.mdwn
index b7944b418c..554cfa41e2 100644
--- a/doc/bugs/git-annex_has_issues_with_git_when_staging__47__commiting_logs.mdwn
+++ b/doc/bugs/git-annex_has_issues_with_git_when_staging__47__commiting_logs.mdwn
@@ -16,3 +16,8 @@ For now it's just a bit of extra work for me when it does occur but it does not
 >>> be some error message? --[[Joey]] 
 
 >>>> there were no error messages at all
+
+>>>>> Can I see a transcript? I'm having difficulty getting my head around
+>>>>> what git is doing. Sounds like the files could just not be `git
+>>>>> added` yet, but I get the impression from other things that you say
+>>>>> that it's not so simple. --[[Joey]] 

From 73b4fe5d61e492fe537f04d3971f25970b7ebf3f Mon Sep 17 00:00:00 2001
From: 
 "https://www.google.com/accounts/o8/id?id=AItOawl9sYlePmv1xK-VvjBdN-5doOa_Xw-jH4U"
 <Richard@web>
Date: Mon, 28 Mar 2011 15:20:59 +0000
Subject: [PATCH 12/15]

---
 doc/forum/wishlist:_git_backend_for_git-annex.mdwn | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 doc/forum/wishlist:_git_backend_for_git-annex.mdwn

diff --git a/doc/forum/wishlist:_git_backend_for_git-annex.mdwn b/doc/forum/wishlist:_git_backend_for_git-annex.mdwn
new file mode 100644
index 0000000000..63ae83097e
--- /dev/null
+++ b/doc/forum/wishlist:_git_backend_for_git-annex.mdwn
@@ -0,0 +1,7 @@
+Preamble: Obviously, the core feature of git-annex is the ability to keep a subset of files in a local repo. The main trade-off is that you don't get version tracking.
+
+Use case: On my laptop, I might not have enough disk space to store everything. Not so for my main box nor my backup server. And I would _really_ like to have proper version tracking for many of my files. Thus...
+
+Wish: ...why not use git as a version backend? That way, I could just push all my stuff to the central instance(s) and have the best of both worlds. Depending on what backend is used in the local repos, it might make sense to define a list of supported client backends with pre-computed keys.
+
+-- RichiH

From 70d4df79ee1ada9a773d03579a86b798f3e1ff1d Mon Sep 17 00:00:00 2001
From: "http://joey.kitenet.net/" <joey@web>
Date: Mon, 28 Mar 2011 15:25:18 +0000
Subject: [PATCH 13/15] Added a comment

---
 ...3_a18ada7ac74c63be5753fdb2fe68dae5._comment | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 doc/bugs/git-annex_directory_hashing_problems_on_osx/comment_3_a18ada7ac74c63be5753fdb2fe68dae5._comment

diff --git a/doc/bugs/git-annex_directory_hashing_problems_on_osx/comment_3_a18ada7ac74c63be5753fdb2fe68dae5._comment b/doc/bugs/git-annex_directory_hashing_problems_on_osx/comment_3_a18ada7ac74c63be5753fdb2fe68dae5._comment
new file mode 100644
index 0000000000..4c2f609d9c
--- /dev/null
+++ b/doc/bugs/git-annex_directory_hashing_problems_on_osx/comment_3_a18ada7ac74c63be5753fdb2fe68dae5._comment
@@ -0,0 +1,18 @@
+[[!comment format=mdwn
+ username="http://joey.kitenet.net/"
+ nickname="joey"
+ subject="comment 3"
+ date="2011-03-28T15:25:18Z"
+ content="""
+So, there is evidence here of a circumstance caused by the [[other_bug|git-annex_has_issues_with_git_when_staging__47__commiting_logs]], as I suspected.
+
+I don't think that manual `git commit -a` caused the problem. I suspect it was a subsequent `git add` that caused git to follow the wrong case paths and add the files in the wrong place. Ie, when you run \"git add .git-annex\", it recurses into `.git-annex/Gm/`, and adds files using that case, that were previously added from `.git-annex/GM/`.
+
+For completeness, can you verify this repo's core.ignorecase setting?
+
+---
+
+I hate that you are stuck using loop filesystems to work around this bug. If my guess is correct, you don't need to, as long as you avoid manually running \"git add .git-annex\". I take this bug seriously. While I'm currently very involved in adding Amazon S3 support to git-annex (which will take days more of solid work), I do plan to make a look filesystem of my own, probably vfat, so I can try and reproduce this on a case-insensative filesystem. If you could confirm my above hypothesis, that would speed things up for me.
+
+It's possible I will have to tweak the hash directories. Hopefully if so, I will only tweak them for *new* keys; if I had to do a v3 backend just to fix this stupid thing, I'd murder myself -- upgrading all my offline disks from v1 to v2 took me many days.
+"""]]

From dd4004c43b95389440d9eadbcefc72dd726269b9 Mon Sep 17 00:00:00 2001
From: Joey Hess <joey@kitenet.net>
Date: Mon, 28 Mar 2011 11:28:34 -0400
Subject: [PATCH 14/15] wording

---
 .../comment_3_a18ada7ac74c63be5753fdb2fe68dae5._comment       | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/bugs/git-annex_directory_hashing_problems_on_osx/comment_3_a18ada7ac74c63be5753fdb2fe68dae5._comment b/doc/bugs/git-annex_directory_hashing_problems_on_osx/comment_3_a18ada7ac74c63be5753fdb2fe68dae5._comment
index 4c2f609d9c..00988ab58c 100644
--- a/doc/bugs/git-annex_directory_hashing_problems_on_osx/comment_3_a18ada7ac74c63be5753fdb2fe68dae5._comment
+++ b/doc/bugs/git-annex_directory_hashing_problems_on_osx/comment_3_a18ada7ac74c63be5753fdb2fe68dae5._comment
@@ -12,7 +12,7 @@ For completeness, can you verify this repo's core.ignorecase setting?
 
 ---
 
-I hate that you are stuck using loop filesystems to work around this bug. If my guess is correct, you don't need to, as long as you avoid manually running \"git add .git-annex\". I take this bug seriously. While I'm currently very involved in adding Amazon S3 support to git-annex (which will take days more of solid work), I do plan to make a look filesystem of my own, probably vfat, so I can try and reproduce this on a case-insensative filesystem. If you could confirm my above hypothesis, that would speed things up for me.
+I hate that you are stuck using loop filesystems to work around this bug. If my guess is correct, you don't need to, as long as you avoid manually running \"git add .git-annex\". I take this bug seriously. While I'm currently very involved in adding Amazon S3 support to git-annex (which will take days more of solid work), I do plan to make a loop filesystem of my own, probably vfat, so I can try and reproduce this on a case-insensative filesystem. If you could confirm my above hypothesis, that would speed things up for me.
 
-It's possible I will have to tweak the hash directories. Hopefully if so, I will only tweak them for *new* keys; if I had to do a v3 backend just to fix this stupid thing, I'd murder myself -- upgrading all my offline disks from v1 to v2 took me many days.
+It's possible I will have to tweak the hash directories. Hopefully if so, I will only tweak them for *new* keys; if I had to do a v3 backend just to fix this stupid thing, I'd be sad -- upgrading all my offline disks from v1 to v2 took me many days.
 """]]

From cf99575d74d2a68004efa152ea9e7ac1c2866935 Mon Sep 17 00:00:00 2001
From: Joey Hess <joey@kitenet.net>
Date: Mon, 28 Mar 2011 12:09:47 -0400
Subject: [PATCH 15/15] update

---
 Makefile                                                  | 1 +
 ..._issues_with_git_when_staging__47__commiting_logs.mdwn | 8 +++++++-
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index e1aaf8ec37..8e16645034 100644
--- a/Makefile
+++ b/Makefile
@@ -58,6 +58,7 @@ docs: $(mans)
 		--no-usedirs --disable-plugin=openid --plugin=sidebar \
 		--underlaydir=/dev/null --disable-plugin=shortcut \
 		--disable-plugin=smiley \
+		--plugin=comments --set comments_pagespec="*" \
 		--exclude='news/.*'
 
 clean:
diff --git a/doc/bugs/git-annex_has_issues_with_git_when_staging__47__commiting_logs.mdwn b/doc/bugs/git-annex_has_issues_with_git_when_staging__47__commiting_logs.mdwn
index 554cfa41e2..774ca6a16c 100644
--- a/doc/bugs/git-annex_has_issues_with_git_when_staging__47__commiting_logs.mdwn
+++ b/doc/bugs/git-annex_has_issues_with_git_when_staging__47__commiting_logs.mdwn
@@ -7,7 +7,13 @@ For now it's just a bit of extra work for me when it does occur but it does not
 > What do you mean when you say that git "got wedged"? It hung somehow?
 >
 > If git-annex runs concurrently with another git command that locks
-> the repository its git add of log files can fail.
+> the repository, its git add of log files can fail.
+> 
+> Update: Also, of course, if you are running a "got annex get" or
+> similar, and ctrl-c it after it has gotten some files, it can
+> end up with unstaged or in some cases un-added log files that git-annex
+> wrote -- since git-annex only stages log files in git on shutdown, and
+> ctrl-c bypasses that.
 > --[[Joey]] 
 
 >> It "got wedged" as in git doesn't let me commit anything, even though it tells me that there is stuff to be committed in the staging area.