Merge branch 'master' into assistant

Conflicts:
	Makefile

29 files changed, 195 insertions, 16 deletions

diff --git a/Makefile b/Makefile
index a6030efa1..8b9b35bdd 100644
--- a/Makefile
+++ b/Makefile
@@ -3,20 +3,29 @@ mans=git-annex.1 git-annex-shell.1
 sources=Build/SysConfig.hs Utility/Touch.hs Utility/Mounts.hs
 all=$(bins) $(mans) docs
 
+CFLAGS=-Wall
+
 OS:=$(shell uname | sed 's/[-_].*//')
 ifeq ($(OS),Linux)
-BASEFLAGS_OPTS+=-DWITH_INOTIFY -DWITH_DBUS
+BASEFLAGS_OPTS=-DWITH_INOTIFY -DWITH_DBUS
 clibs=Utility/libdiskfree.o Utility/libmounts.o
 else
-BASEFLAGS_OPTS+=-DWITH_KQUEUE
+# BSD system
+BASEFLAGS_OPTS=-DWITH_KQUEUE
 clibs=Utility/libdiskfree.o Utility/libmounts.o Utility/libkqueue.o
+ifeq ($(OS),Darwin)
+# Ensure OSX compiler builds for 32 bit when using 32 bit ghc
+GHCARCH:=$(shell ghc -e 'print System.Info.arch')
+ifeq ($(GHCARCH),i386)
+CFLAGS=-Wall -m32
+endif
+endif
 endif
 
 PREFIX=/usr
 IGNORE=-ignore-package monads-fd -ignore-package monads-tf
 BASEFLAGS=-threaded -Wall $(IGNORE) -outputdir tmp -IUtility -DWITH_ASSISTANT -DWITH_S3 $(BASEFLAGS_OPTS)
 GHCFLAGS=-O2 $(BASEFLAGS)
-CFLAGS=-Wall
 
 ifdef PROFILE
 GHCFLAGS=-prof -auto-all -rtsopts -caf-all -fforce-recomp $(BASEFLAGS)
diff --git a/doc/bugs/fat_support/comment_6_a3b6000330c9c376611c228d746a1d55._comment b/doc/bugs/fat_support/comment_6_a3b6000330c9c376611c228d746a1d55._comment
new file mode 100644
index 000000000..c7defd13e
--- /dev/null
+++ b/doc/bugs/fat_support/comment_6_a3b6000330c9c376611c228d746a1d55._comment
@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawkZRoTRyW3tox-FD2DQWxskgI6_tkEtHL4"
+ nickname="Ben"
+ subject="comment 6"
+ date="2012-07-23T16:11:52Z"
+ content="""
+The above would work fine for me but the files in my annex (e.g. .git/annex/objects/xx/yy/blah.ogg) don't have extensions like that, so my media player doesn't recognize them as media files. How do I get the files under \"objects\" to keep the extensions of the original files like in Joey's example?
+"""]]
diff --git a/doc/bugs/fat_support/comment_7_a0ac7f2c44efc8116940c7b94b35e9d0._comment b/doc/bugs/fat_support/comment_7_a0ac7f2c44efc8116940c7b94b35e9d0._comment
new file mode 100644
index 000000000..11668615e
--- /dev/null
+++ b/doc/bugs/fat_support/comment_7_a0ac7f2c44efc8116940c7b94b35e9d0._comment
@@ -0,0 +1,7 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ subject="comment 7"
+ date="2012-07-24T14:51:50Z"
+ content="""
+You can get the extensions by migrating to the SHA1E (or SHA256E) backend. 
+"""]]
diff --git a/doc/bugs/subtle_build_issue_on_OSX_10.7_and_Haskell_Platform___40__if_you_have_the_32bit_version_installed__41__.mdwn b/doc/bugs/subtle_build_issue_on_OSX_10.7_and_Haskell_Platform___40__if_you_have_the_32bit_version_installed__41__.mdwn
index 0414823f8..3a50256db 100644
--- a/doc/bugs/subtle_build_issue_on_OSX_10.7_and_Haskell_Platform___40__if_you_have_the_32bit_version_installed__41__.mdwn
+++ b/doc/bugs/subtle_build_issue_on_OSX_10.7_and_Haskell_Platform___40__if_you_have_the_32bit_version_installed__41__.mdwn
@@ -46,3 +46,5 @@ Or just telling users to use the 64bit version of the haskell platform?
 It may also be possible to get osx's c compiler to output a universal binary 
 to give you everything, but that be going down the _being too platform 
 specific route_.
+
+> [[done]], it'll detect this and force -m32. --[[Joey]]
diff --git a/doc/design/assistant/blog/day_40__dbus/comment_2_6799f2baf6a6ce14b1fa76a8402840c0._comment b/doc/design/assistant/blog/day_40__dbus/comment_2_6799f2baf6a6ce14b1fa76a8402840c0._comment
new file mode 100644
index 000000000..832be854a
--- /dev/null
+++ b/doc/design/assistant/blog/day_40__dbus/comment_2_6799f2baf6a6ce14b1fa76a8402840c0._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="hamish"
+ ip="203.0.139.24"
+ subject="dbus vs polling "
+ date="2012-07-22T07:13:37Z"
+ content="""
+I, too, am running a dbus but like to hand mount my filesystems.  However, I'd imagine that I am both a minority and that my minority could like the extra control, so perhaps even a \"re-read the mtab /now/\" command that can be manually run after something is  manually mounted would suffice
+
+Is it not possible to use inotify on the mtab?
+"""]]
diff --git a/doc/design/assistant/blog/day_40__dbus/comment_3_fa1d7444bdafcb990cacf2ace7ee6ef1._comment b/doc/design/assistant/blog/day_40__dbus/comment_3_fa1d7444bdafcb990cacf2ace7ee6ef1._comment
new file mode 100644
index 000000000..a372670b8
--- /dev/null
+++ b/doc/design/assistant/blog/day_40__dbus/comment_3_fa1d7444bdafcb990cacf2ace7ee6ef1._comment
@@ -0,0 +1,10 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ ip="4.154.4.169"
+ subject="comment 3"
+ date="2012-07-22T16:03:52Z"
+ content="""
+How did I not think about using my favorite hammer on this problem too? But, no, /proc/mounts cannot be watched with inotify it seems, and of course the BSDs don't seem to have a file at all.
+
+I think the dbus stuff is sorted out for manual users, see later blog entries.
+"""]]
diff --git a/doc/design/assistant/blog/day_42__the_answer.mdwn b/doc/design/assistant/blog/day_42__the_answer.mdwn
new file mode 100644
index 000000000..fd7c4ebb5
--- /dev/null
+++ b/doc/design/assistant/blog/day_42__the_answer.mdwn
@@ -0,0 +1,27 @@
+Made the MountWatcher update state for remotes located in a drive that
+gets mounted. This was tricky code. First I had to make remotes declare
+when they're located in a local directory. Then it has to rescan git
+configs of git remotes (because the git repo mounted at a mount point may
+change), and update all the state that a newly available remote can affect.
+
+And it works: I plug in a drive containing one of my git remotes, and the
+assistant automatically notices it and syncs the git repositories.
+
+---
+
+But, data isn't transferred yet. When a disconnected remote becomes
+connected, keys should be transferred in both directions to get back into
+sync.
+
+To that end, added Yet Another Thread; the TransferScanner thread
+will scan newly available remotes to find keys, and queue low priority
+transfers to get them fully in sync.
+
+(Later, this will probably also be used for network remotes that become
+available when moving between networks. I think network-manager sends
+dbus events it could use..)
+
+This new thread is missing a crucial peice, it doesn't yet have a way to
+find the keys that need to be transferred. Doing that efficiently (without
+scanning the whole git working copy) is Hard. I'm considering design
+possibilities..
diff --git a/doc/design/assistant/syncing.mdwn b/doc/design/assistant/syncing.mdwn
index 5f00cf606..cc23f786f 100644
--- a/doc/design/assistant/syncing.mdwn
+++ b/doc/design/assistant/syncing.mdwn
@@ -3,20 +3,59 @@ all the other git clones, at both the git level and the key/value level.
 
 ## immediate action items
 
-* At startup, and possibly periodically, look for files we have that
-  location tracking indicates remotes do not, and enqueue Uploads for
-  them. Also, enqueue Downloads for any files we're missing.
+* At startup, and possibly periodically, or when the network connection
+  changes, or some heuristic suggests that a remote was disconnected from
+  us for a while, queue remotes for processing by the TransferScanner,
+  to queue Transfers of files it or we're missing.
 * After git sync, identify content that we don't have that is now available
-  on remotes, and transfer. But first, need to ensure that when a remote
+  on remotes, and transfer. (Needed when we have a uni-directional connection
+  to a remote, so it won't be uploading content to us.) 
+  But first, need to ensure that when a remote
   receives content, and updates its location log, it syncs that update
   out.
-* When MountWatcher detects a newly mounted drive, rescan git remotes
-  in order to get ones on the drive, and do a git sync and file transfers
-  to sync any repositories on it.
+
+## TransferScanner
+
+The TransferScanner thread needs to find keys that need to be Uploaded
+to a remote, or Downloaded from it.
+
+How to find the keys to transfer? I'd like to avoid potentially
+expensive traversals of the whole git working copy if I can.
+
+One way would be to do a git diff between the (unmerged) git-annex branches
+of the git repo, and its remote. Parse that for lines that add a key to
+either, and queue transfers. That should work fairly efficiently when the
+remote is a git repository. Indeed, git-annex already does such a diff
+when it's doing a union merge of data into the git-annex branch. It
+might even be possible to have the union merge and scan use the same
+git diff data.
+
+But that approach has several problems:
+
+1. The list of keys it would generate wouldn't have associated git
+   filenames, so the UI couldn't show the user what files were being
+   transferred.
+2. Worse, without filenames, any later features to exclude
+   files/directories from being transferred wouldn't work.
+3. Looking at a git diff of the git-annex branches would find keys
+   that were added to either side while the two repos were disconnected.
+   But if the two repos' keys were not fully in sync before they
+   disconnected (which is quite possible; transfers could be incomplete),
+   the diff would not show those older out of sync keys.
+
+The remote could also be a special remote. In this case, I have to either
+traverse the git working copy, or perhaps traverse the whole git-annex
+branch (which would have the same problems with filesnames not being
+available).
+
+If a traversal is done, should check all remotes, not just
+one. Probably worth handling the case where a remote is connected
+while in the middle of such a scan, so part of the scan needs to be
+redone to check it.
 
 ## longer-term TODO
 
-* Test MountWatcher on Gnome (should work ok) and LXDE (dunno).
+* Test MountWatcher on LXDE.
 * git-annex needs a simple speed control knob, which can be plumbed
   through to, at least, rsync. A good job for an hour in an
   airport somewhere.
diff --git a/doc/design/assistant/syncing/comment_1_c70156174ff19b503978d623bd2df36f._comment b/doc/design/assistant/syncing/comment_1_c70156174ff19b503978d623bd2df36f._comment
new file mode 100644
index 000000000..019490e61
--- /dev/null
+++ b/doc/design/assistant/syncing/comment_1_c70156174ff19b503978d623bd2df36f._comment
@@ -0,0 +1,19 @@
+[[!comment format=mdwn
+ username="https://www.google.com/accounts/o8/id?id=AItOawk4YX0PWICfWGRLuncCPufMPDctT7KAYJA"
+ nickname="betabrain"
+ subject="selective data syncing"
+ date="2012-07-24T15:27:08Z"
+ content="""
+How will the assistant know which files' data to distribute between the repos?
+
+I'm using git-annex and it's numcopies attribute to maintain a redundant archive spread over different computers and usb drives. Not all drives should get a copy of everything, e.g. the usb drive I take to work should not automatically get a copy of family pictures.
+
+How about .gitattributes?
+
+* \* annex.auto-sync-data = false # don't automatically sync the data
+* archive/ annex.auto-push-repos = NAS # everything added to archive/ in any repo goes automatically to the NAS remote.
+* work/ annex.auto-synced-repos = LAPTOP WORKUSB # everything added to work/ in LAPTOP or WORKUSB gets synced to WORKUSB and LAPTOP
+* work/ annex.auto-push-repos = LAPTOP WORKUSB # stuff added to work/ anywhere gets synced to LAPTOP and WORKUSB
+* important/ annex.auto-sync-data = true # push data to all repos
+* webserver_logs/ annex.remote.WEBSERVER.auto-push-repos = S3 # only the assistant running in WEBSERVER pushes webserver_logs/ to S3 remote
+"""]]
diff --git a/doc/install.mdwn b/doc/install.mdwn
index 4eb7b179b..54d6ecb6b 100644
--- a/doc/install.mdwn
+++ b/doc/install.mdwn
@@ -9,8 +9,8 @@
 * [[ArchLinux]]
 * [[NixOS]]
 * [[Gentoo]]
-* Windows: [[sorry, not possible yet|todo/windows_support]]
 * [[ScientificLinux5]] - This should cover RHEL5 clones such as CentOS5 and so on
+* Windows: [[sorry, not possible yet|todo/windows_support]]
 
 ## Using cabal
 
diff --git a/doc/install/Fedora.mdwn b/doc/install/Fedora.mdwn
index 73e9f9a5d..c1905e01b 100644
--- a/doc/install/Fedora.mdwn
+++ b/doc/install/Fedora.mdwn
@@ -1,4 +1,10 @@
-Installation recipe for Fedora 14 thruough 17.
+git-annex is recently finding its way into Fedora.
+
+* [Status of getting a Fedora package](https://bugzilla.redhat.com/show_bug.cgi?id=662259)
+* [Koji build for F17](http://koji.fedoraproject.org/koji/buildinfo?buildID=328654)
+* [Koji build for F16](http://koji.fedoraproject.org/koji/buildinfo?buildID=328656)
+
+Installation recipe for Fedora 14 thruough 15.
 
 <pre>
 sudo yum install ghc cabal-install pcre-devel
@@ -15,6 +21,3 @@ cabal install --bindir=$HOME/bin
 Note: You can't just use `cabal install git-annex`, because Fedora does
 not yet ship ghc 7.4.
 
-* [Status of getting a Fedora package](https://bugzilla.redhat.com/show_bug.cgi?id=662259)a
-* [Koji build for F17](http://koji.fedoraproject.org/koji/buildinfo?buildID=328654)
-* [Koji build for F16](http://koji.fedoraproject.org/koji/buildinfo?buildID=328656)
diff --git a/doc/install/OSX/comment_2_25552ff2942048fafe97d653757f1ad6._comment b/doc/install/OSX/comment_2_25552ff2942048fafe97d653757f1ad6._comment
new file mode 100644
index 000000000..62ee10910
--- /dev/null
+++ b/doc/install/OSX/comment_2_25552ff2942048fafe97d653757f1ad6._comment
@@ -0,0 +1,7 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ subject="comment 2"
+ date="2012-07-24T15:09:29Z"
+ content="""
+I've moved some outdated comments about installing on OSX to [[old_comments]].
+"""]]
diff --git a/doc/install/OSX/old_comments.mdwn b/doc/install/OSX/old_comments.mdwn
new file mode 100644
index 000000000..ccb6785fd
--- /dev/null
+++ b/doc/install/OSX/old_comments.mdwn
@@ -0,0 +1 @@
+Moved a bunch of outdated comments here, AFAIK all these issues are fixed.
diff --git a/doc/install/OSX/comment_10_798000aab19af2944b6e44dbc550c6fe._comment b/doc/install/OSX/old_comments/comment_10_798000aab19af2944b6e44dbc550c6fe._comment
index 675a90eee..675a90eee 100644
--- a/doc/install/OSX/comment_10_798000aab19af2944b6e44dbc550c6fe._comment
+++ b/doc/install/OSX/old_comments/comment_10_798000aab19af2944b6e44dbc550c6fe._comment
diff --git a/doc/install/OSX/comment_11_707a1a27a15b2de8dfc8d1a30420ab4c._comment b/doc/install/OSX/old_comments/comment_11_707a1a27a15b2de8dfc8d1a30420ab4c._comment
index 69a4f9128..69a4f9128 100644
--- a/doc/install/OSX/comment_11_707a1a27a15b2de8dfc8d1a30420ab4c._comment
+++ b/doc/install/OSX/old_comments/comment_11_707a1a27a15b2de8dfc8d1a30420ab4c._comment
diff --git a/doc/install/OSX/comment_12_60d13f2c8e008af1041bea565a392c83._comment b/doc/install/OSX/old_comments/comment_12_60d13f2c8e008af1041bea565a392c83._comment
index e2e85aaa9..e2e85aaa9 100644
--- a/doc/install/OSX/comment_12_60d13f2c8e008af1041bea565a392c83._comment
+++ b/doc/install/OSX/old_comments/comment_12_60d13f2c8e008af1041bea565a392c83._comment
diff --git a/doc/install/OSX/comment_13_a6f48c87c2d6eabe379d6e10a6cac453._comment b/doc/install/OSX/old_comments/comment_13_a6f48c87c2d6eabe379d6e10a6cac453._comment
index e5ce62b13..e5ce62b13 100644
--- a/doc/install/OSX/comment_13_a6f48c87c2d6eabe379d6e10a6cac453._comment
+++ b/doc/install/OSX/old_comments/comment_13_a6f48c87c2d6eabe379d6e10a6cac453._comment
diff --git a/doc/install/OSX/comment_14_6ef2ddb7b11ce6ad54578ae118ed346e._comment b/doc/install/OSX/old_comments/comment_14_6ef2ddb7b11ce6ad54578ae118ed346e._comment
index 35e0bb6ed..35e0bb6ed 100644
--- a/doc/install/OSX/comment_14_6ef2ddb7b11ce6ad54578ae118ed346e._comment
+++ b/doc/install/OSX/old_comments/comment_14_6ef2ddb7b11ce6ad54578ae118ed346e._comment
diff --git a/doc/install/OSX/comment_15_6fd1fad5b6d9f36620e5a0e99edd2f89._comment b/doc/install/OSX/old_comments/comment_15_6fd1fad5b6d9f36620e5a0e99edd2f89._comment
index 0005328c4..0005328c4 100644
--- a/doc/install/OSX/comment_15_6fd1fad5b6d9f36620e5a0e99edd2f89._comment
+++ b/doc/install/OSX/old_comments/comment_15_6fd1fad5b6d9f36620e5a0e99edd2f89._comment
diff --git a/doc/install/OSX/old_comments/comment_16_af6fe3540032cdf4400478de87771058._comment b/doc/install/OSX/old_comments/comment_16_af6fe3540032cdf4400478de87771058._comment
new file mode 100644
index 000000000..5da4b22c6
--- /dev/null
+++ b/doc/install/OSX/old_comments/comment_16_af6fe3540032cdf4400478de87771058._comment
@@ -0,0 +1,30 @@
+[[!comment format=mdwn
+ username="https://a-or-b.myopenid.com/"
+ ip="203.45.2.230"
+ subject="Compiling git-annex on OSX (with 32 bit Haskell)"
+ date="2012-07-24T03:26:45Z"
+ content="""
+I came across an issue when following the instructions here:
+     <http://git-annex.branchable.com/install/OSX/>
+
+I'm compiling the 'assistant' branch (522f568450a005ae81b24f63bb37e75320b51219).
+
+
+The pre-compiled version of Haskell for OSX recommends the 32 bit installer, however git-annex compiles
+
+>  Utility/libdiskfree.o Utility/libkqueue.o Utility/libmounts.o
+
+as 64 bit. The 'make' command fails on linking 32- and 64-bit code.
+
+So... I made a small change to the Makefile
+
+>  CFLAGS=-Wall
+
+becomes
+
+>  CFLAGS=-Wall -m32
+
+I don't know if there is an easy way to programmatically check for this, or even if you'd want to spend time doing it, but it might help someone else out.
+
+<https://gist.github.com/3167798>
+"""]]
diff --git a/doc/install/OSX/old_comments/comment_17_8d3a0596db67108041728b20f2790f31._comment b/doc/install/OSX/old_comments/comment_17_8d3a0596db67108041728b20f2790f31._comment
new file mode 100644
index 000000000..782f2fd75
--- /dev/null
+++ b/doc/install/OSX/old_comments/comment_17_8d3a0596db67108041728b20f2790f31._comment
@@ -0,0 +1,7 @@
+[[!comment format=mdwn
+ username="http://joeyh.name/"
+ subject="comment 17"
+ date="2012-07-24T15:03:49Z"
+ content="""
+The instructions say to use cabal for a reason -- it's more likely to work. But I have made the Makefile detect the mismatched GHC and C compiler and force the C compiler to 32 bit.
+"""]]
diff --git a/doc/install/OSX/comment_2_0327c64b15249596add635d26f4ce67f._comment b/doc/install/OSX/old_comments/comment_2_0327c64b15249596add635d26f4ce67f._comment
index 5768d8b93..5768d8b93 100644
--- a/doc/install/OSX/comment_2_0327c64b15249596add635d26f4ce67f._comment
+++ b/doc/install/OSX/old_comments/comment_2_0327c64b15249596add635d26f4ce67f._comment
diff --git a/doc/install/OSX/comment_3_47c682a779812dda77601c24a619923c._comment b/doc/install/OSX/old_comments/comment_3_47c682a779812dda77601c24a619923c._comment
index 251375cbe..251375cbe 100644
--- a/doc/install/OSX/comment_3_47c682a779812dda77601c24a619923c._comment
+++ b/doc/install/OSX/old_comments/comment_3_47c682a779812dda77601c24a619923c._comment
diff --git a/doc/install/OSX/comment_4_e6109a964064a2a799768a370e57801d._comment b/doc/install/OSX/old_comments/comment_4_e6109a964064a2a799768a370e57801d._comment
index be3ba2be4..be3ba2be4 100644
--- a/doc/install/OSX/comment_4_e6109a964064a2a799768a370e57801d._comment
+++ b/doc/install/OSX/old_comments/comment_4_e6109a964064a2a799768a370e57801d._comment
diff --git a/doc/install/OSX/comment_5_50777853f808d57b957f8ce9a0f84b3d._comment b/doc/install/OSX/old_comments/comment_5_50777853f808d57b957f8ce9a0f84b3d._comment
index eca176178..eca176178 100644
--- a/doc/install/OSX/comment_5_50777853f808d57b957f8ce9a0f84b3d._comment
+++ b/doc/install/OSX/old_comments/comment_5_50777853f808d57b957f8ce9a0f84b3d._comment
diff --git a/doc/install/OSX/comment_6_18a8df794aa0ddd294dbf17d3d4c7fe2._comment b/doc/install/OSX/old_comments/comment_6_18a8df794aa0ddd294dbf17d3d4c7fe2._comment
index 5cb813776..5cb813776 100644
--- a/doc/install/OSX/comment_6_18a8df794aa0ddd294dbf17d3d4c7fe2._comment
+++ b/doc/install/OSX/old_comments/comment_6_18a8df794aa0ddd294dbf17d3d4c7fe2._comment
diff --git a/doc/install/OSX/comment_7_2ce7acab15403d3f993cec94ec7f3bc6._comment b/doc/install/OSX/old_comments/comment_7_2ce7acab15403d3f993cec94ec7f3bc6._comment
index 32093ee51..32093ee51 100644
--- a/doc/install/OSX/comment_7_2ce7acab15403d3f993cec94ec7f3bc6._comment
+++ b/doc/install/OSX/old_comments/comment_7_2ce7acab15403d3f993cec94ec7f3bc6._comment
diff --git a/doc/install/OSX/comment_8_a93ad4b67c5df4243268bcf32562f6be._comment b/doc/install/OSX/old_comments/comment_8_a93ad4b67c5df4243268bcf32562f6be._comment
index cd128a6f1..cd128a6f1 100644
--- a/doc/install/OSX/comment_8_a93ad4b67c5df4243268bcf32562f6be._comment
+++ b/doc/install/OSX/old_comments/comment_8_a93ad4b67c5df4243268bcf32562f6be._comment
diff --git a/doc/install/OSX/comment_9_ae3ed5345bc84f57e44251d2e6c39342._comment b/doc/install/OSX/old_comments/comment_9_ae3ed5345bc84f57e44251d2e6c39342._comment
index 70fbc6c3c..70fbc6c3c 100644
--- a/doc/install/OSX/comment_9_ae3ed5345bc84f57e44251d2e6c39342._comment
+++ b/doc/install/OSX/old_comments/comment_9_ae3ed5345bc84f57e44251d2e6c39342._comment