assist: operate on all files in working tree by default

Consistency with sync and internal consistency is more important than
consistency with the assistant, which is not itself consistent about
what it does when run in a subdirectory.

Note that with -C, it will still commit staged changes to files outside
the directory. Like sync does. Presumably if the user is manually
staging things, then running this command, they intend to build up a
commit.

Sponsored-by: unqueued on Patreon

Command/Assist.hs

@@ -22,11 +22,13 @@ cmd = withAnnexOptions [jobsOption, backendOption] $
 
 myseek :: Command.Sync.SyncOptions -> CommandSeek
 myseek o = startConcurrency transferStages $ do
-	-- Run before prepMerge so it adds only files in the current
-	-- directory and below, not new files elsewhere in the working
-	-- tree.
+	-- Changes to top of repository, so when this is run in a
+	-- subdirectory, it will still default to adding files anywhere in
+	-- the working tree.
+	Command.Sync.prepMerge
+
 	Command.Add.seek Command.Add.AddOptions
-		{ Command.Add.addThese = []
+		{ Command.Add.addThese = Command.Sync.contentOfOption o
 		, Command.Add.batchOption = NoBatch
 		, Command.Add.updateOnly = False
 		, Command.Add.largeFilesOverride = Nothing
@@ -37,5 +39,4 @@ myseek o = startConcurrency transferStages $ do
 	-- Flush added files to index so they will be committed.
 	Annex.Queue.flush
 
-	Command.Sync.prepMerge
 	Command.Sync.seek' o