fix process and FD leak

Fix process and file descriptor leak that was exposed when git-annex was
built with ghc 8.2.1. Apparently ghc has changed its behavior of GC
of open file handles that are pipes to running processes. That
broke git-annex test on OSX due to running out of FDs.

Audited for all uses of Annex.new and made stopCoProcesses be called
once it's done with the state. Fixed several places that might have
leaked in other situations than running the test suite.

This commit was sponsored by Ewen McNeill.

Remote/Git.hs

@@ -59,7 +59,7 @@ import Annex.Path
 import Creds
 import Messages.Progress
 import Types.NumCopies
-import Annex.Concurrent
+import Annex.Action
 
 import Control.Concurrent
 import Control.Concurrent.MSampleVar
@@ -311,11 +311,12 @@ tryGitConfigRead autoinit r
 	 - it if allowed. However, if that fails, still return the read
 	 - git config. -}
 	readlocalannexconfig = do
-		s <- Annex.new r
-		Annex.eval s $ do
+		let check = do
 			Annex.BranchState.disableUpdate
 			void $ tryNonAsync $ ensureInitialized
 			Annex.getState Annex.repo
+		s <- Annex.new r
+		Annex.eval s $ check `finally` stopCoProcesses
 		
 	configlistfields = if autoinit
 		then [(Fields.autoInit, "1")]
@@ -611,7 +612,7 @@ repairRemote r a = return $ do
 	Annex.eval s $ do
 		Annex.BranchState.disableUpdate
 		ensureInitialized
-		a
+		a `finally` stopCoProcesses
 
 {- Runs an action from the perspective of a local remote.
  -
@@ -632,7 +633,7 @@ onLocal r a = do
 	go st = do
 		curro <- Annex.getState Annex.output
 		(ret, st') <- liftIO $ Annex.run (st { Annex.output = curro }) $
-			stopCoProcesses `after` a
+			a `finally` stopCoProcesses
 		cache st'
 		return ret