when all you have is a zombie, everything looks like a shotgun

Actually, let's do a targeted fix of the actual forkProcess that was not
waited on. The global reap is moved back to the end, after the long-running
git processes actually exit.

CmdLine.hs

@@ -85,9 +85,7 @@ tryRun' :: Integer -> Annex.AnnexState -> [Annex Bool] -> IO ()
 tryRun' errnum state (a:as) = do
 	result <- try $ Annex.run state $ do
 		AnnexQueue.flushWhenFull
-		r <- a
-		liftIO Git.reap
-		return r
+		a
 	case result of
 		Left err -> do
 			Annex.eval state $ do
@@ -106,4 +104,5 @@ startup = return True
 shutdown :: Annex Bool
 shutdown = do
 	saveState
+	liftIO Git.reap -- zombies from long-running git processes
 	return True

Crypto.hs

@@ -218,7 +218,7 @@ gpgCipherHandle params c a b = do
 
 	params' <- gpgParams $ passphrase ++ params
 	(pid, fromh, toh) <- hPipeBoth "gpg" params'
-	_ <- forkProcess $ do
+	pid2 <- forkProcess $ do
 		L.hPut toh =<< a
 		hClose toh
 		exitSuccess
@@ -227,6 +227,7 @@ gpgCipherHandle params c a b = do
 
 	-- cleanup
 	forceSuccess pid
+	_ <- getProcessStatus True False pid2
 	closeFd frompipe
 	return ret