better fix for zombie problem, which turns out to be a zombie ssh started by rsync

When rsyncProgress pipes rsync's stdout, this turns out to cause a ssh
process started by rsync to be left behind as a zombie. I don't know why,
but my recent zombie reaping cleanup was correct, it's just that this other
zombie, that's not directly started by git-annex, was no longer reaped
due to changes in the cleanup. Make rsyncProgress reap the zombie started
by rsync, as a workaround.

FWIW, the process tree looks like this. It seems like the rsync child
is for some reason starting but not waiting on this extra ssh process.
Ssh connection caching may be involved -- disabling it seemed to change
the shape of the tree, but did not eliminate the zombie.

 9378 pts/14   S+     0:00  |           \_ rsync -p --progress --inplace -4 -e 'ssh' '-S' ...
 9379 pts/14   S+     0:00  |           |   \_ ssh ...
 9380 pts/14   S+     0:00  |           |   \_ rsync -p --progress --inplace -4 -e 'ssh' '-S' ...
 9381 pts/14   Z+     0:00  |           \_ [ssh] <defunct>

6 files changed, 25 insertions, 21 deletions

diff --git a/CmdLine.hs b/CmdLine.hs
index 331c363e4..66bf5b882 100644
--- a/CmdLine.hs
+++ b/CmdLine.hs
@@ -117,5 +117,6 @@ shutdown :: Bool -> Annex Bool
 shutdown nocommit = do
 	saveState nocommit
 	sequence_ =<< M.elems <$> Annex.getState Annex.cleanup
+	liftIO reapZombies -- zombies from long-running git processes
 	sshCleanup -- ssh connection caching
 	return True
diff --git a/Command.hs b/Command.hs
index 145ad5003..8e7bf9758 100644
--- a/Command.hs
+++ b/Command.hs
@@ -39,7 +39,6 @@ import Usage as ReExported
 import Logs.Trust
 import Config
 import Annex.CheckAttr
-import qualified Git.Command
 
 {- Generates a normal command -}
 command :: String -> String -> [CommandSeek] -> String -> Command
@@ -84,14 +83,11 @@ doCommand = start
 	where
 		start   = stage $ maybe skip perform
 		perform = stage $ maybe failure cleanup
-		cleanup = stage $ end
+		cleanup = stage $ status
 		stage = (=<<)
 		skip = return True
 		failure = showEndFail >> return False
-		end r = do
-			-- zombies from long-running git processes
-			liftIO Git.Command.reap
-			showEndResult r >> return r
+		status r = showEndResult r >> return r
 
 {- Modifies an action to only act on files that are already annexed,
  - and passes the key and backend on to it. -}
diff --git a/Command/Log.hs b/Command/Log.hs
index c3ce67986..09d22b2ef 100644
--- a/Command/Log.hs
+++ b/Command/Log.hs
@@ -70,7 +70,7 @@ start :: M.Map UUID String -> TimeZone -> [CommandParam] -> Bool ->
 start m zone os gource file (key, _) = do
 	showLog output =<< readLog <$> getLog key os
 	-- getLog produces a zombie; reap it
-	liftIO Git.Command.reap
+	liftIO reapZombies
 	stop
 	where
 		output
diff --git a/Git/Command.hs b/Git/Command.hs
index 5f2dd47b0..37df44713 100644
--- a/Git/Command.hs
+++ b/Git/Command.hs
@@ -7,7 +7,6 @@
 
 module Git.Command where
 
-import System.Posix.Process (getAnyProcessStatus)
 import System.Process (std_out, env)
 
 import Common
@@ -97,17 +96,6 @@ pipeNullSplitZombie params repo = leaveZombie <$> pipeNullSplit params repo
 leaveZombie :: (a, IO Bool) -> a
 leaveZombie = fst
 
-{- Reaps any zombie git processes. 
- -
- - Warning: Not thread safe. Anything that was expecting to wait
- - on a process and get back an exit status is going to be confused
- - if this reap gets there first. -}
-reap :: IO ()
-reap = do
-	-- throws an exception when there are no child processes
-	catchDefaultIO Nothing (getAnyProcessStatus False True)
-		>>= maybe noop (const reap)
-
 {- Runs a git command as a coprocess. -}
 gitCoProcessStart :: [CommandParam] -> Repo -> IO CoProcess.CoProcessHandle
 gitCoProcessStart params repo = CoProcess.start "git" (toCommand $ gitCommandLine params repo) (gitEnv repo)
diff --git a/Utility/Misc.hs b/Utility/Misc.hs
index f03504040..7c81f56fd 100644
--- a/Utility/Misc.hs
+++ b/Utility/Misc.hs
@@ -12,6 +12,9 @@ import Control.Monad
 import Foreign
 import Data.Char
 import Control.Applicative
+import System.Posix.Process (getAnyProcessStatus)
+
+import Utility.Exception
 
 {- A version of hgetContents that is not lazy. Ensures file is 
  - all read before it gets closed. -}
@@ -96,3 +99,14 @@ hGetSomeString h sz = do
 	where
 		peekbytes :: Int -> Ptr Word8 -> IO [Word8]
 		peekbytes len buf = mapM (peekElemOff buf) [0..pred len]
+
+{- Reaps any zombie git processes. 
+ -
+ - Warning: Not thread safe. Anything that was expecting to wait
+ - on a process and get back an exit status is going to be confused
+ - if this reap gets there first. -}
+reapZombies :: IO ()
+reapZombies = do
+	-- throws an exception when there are no child processes
+	catchDefaultIO Nothing (getAnyProcessStatus False True)
+		>>= maybe (return ()) (const reapZombies)
diff --git a/Utility/Rsync.hs b/Utility/Rsync.hs
index f8e19eb57..68d27550c 100644
--- a/Utility/Rsync.hs
+++ b/Utility/Rsync.hs
@@ -53,8 +53,13 @@ rsync = boolSystem "rsync"
  - The params must enable rsync's --progress mode for this to work.
  -}
 rsyncProgress :: (Integer -> IO ()) -> [CommandParam] -> IO Bool
-rsyncProgress callback params = 
-	withHandle StdoutHandle createProcessSuccess p (feedprogress 0 [])
+rsyncProgress callback params = do
+	r <- withHandle StdoutHandle createProcessSuccess p (feedprogress 0 [])
+	{- For an unknown reason, piping rsync's output like this does
+	 - causes it to run a second ssh process, which it neglects to wait
+	 - on. Reap the resulting zombie. -}
+	reapZombies
+	return r
 	where
 		p = proc "rsync" (toCommand params)
 		feedprogress prev buf h = do