annex.skipunknown with transition plan

Added annex.skipunknown git config, that can be set to false to change the
behavior of commands like `git annex get foo*`, to not skip over files/dirs
that are not checked into git and are explicitly listed in the command
line.

Significant complexity was needed to handle git-annex add, which uses some
git ls-files calls, but needs to not use --error-unmatch because of course
the files are not known to git.

annex.skipunknown is planned to change to default to false in a
git-annex release in early 2022. There's a todo for that.

Annex/AutoMerge.hs

@@ -120,7 +120,7 @@ resolveMerge us them inoverlay = do
 	void $ liftIO cleanup
 
 	unless inoverlay $ do
-		(deleted, cleanup2) <- inRepo (LsFiles.deleted [top])
+		(deleted, cleanup2) <- inRepo (LsFiles.deleted [] [top])
 		unless (null deleted) $
 			Annex.Queue.addCommand "rm"
 				[Param "--quiet", Param "-f", Param "--"]
@@ -130,7 +130,8 @@ resolveMerge us them inoverlay = do
 	when merged $ do
 		Annex.Queue.flush
 		unless inoverlay $ do
-			unstagedmap <- inodeMap $ inRepo $ LsFiles.notInRepo False [top]
+			unstagedmap <- inodeMap $ inRepo $
+				LsFiles.notInRepo [] False [top]
 			cleanConflictCruft mergedks' mergedfs' unstagedmap
 		showLongNote "Merge conflict was automatically resolved; you may want to examine the result."
 	return merged

Assistant/Threads/SanityChecker.hs

@@ -152,7 +152,7 @@ dailyCheck urlrenderer = do
 	batchmaker <- liftIO getBatchCommandMaker
 
 	-- Find old unstaged symlinks, and add them to git.
-	(unstaged, cleanup) <- liftIO $ Git.LsFiles.notInRepo False ["."] g
+	(unstaged, cleanup) <- liftIO $ Git.LsFiles.notInRepo [] False ["."] g
 	now <- liftIO getPOSIXTime
 	forM_ unstaged $ \file -> do
 		let file' = fromRawFilePath file

Assistant/Threads/TransferScanner.hs

@@ -128,7 +128,7 @@ expensiveScan urlrenderer rs = batch <~> do
 		<$> filterM inUnwantedGroup us
 
 	g <- liftAnnex gitRepo
-	(files, cleanup) <- liftIO $ LsFiles.inRepo [] g
+	(files, cleanup) <- liftIO $ LsFiles.inRepo [] [] g
 	removablers <- scan unwantedrs files
 	void $ liftIO cleanup
 

Assistant/Threads/Watcher.hs

@@ -136,7 +136,7 @@ startupScan scanner = do
 		-- Notice any files that were deleted before
 		-- watching was started.
 		top <- liftAnnex $ fromRepo Git.repoPath
-		(fs, cleanup) <- liftAnnex $ inRepo $ LsFiles.deleted [top]
+		(fs, cleanup) <- liftAnnex $ inRepo $ LsFiles.deleted [] [top]
 		forM_ fs $ \f -> do
 			let f' = fromRawFilePath f
 			liftAnnex $ onDel' f'
@@ -362,7 +362,7 @@ onDel' file = do
 onDelDir :: Handler
 onDelDir dir _ = do
 	debug ["directory deleted", dir]
-	(fs, clean) <- liftAnnex $ inRepo $ LsFiles.deleted [toRawFilePath dir]
+	(fs, clean) <- liftAnnex $ inRepo $ LsFiles.deleted [] [toRawFilePath dir]
 	let fs' = map fromRawFilePath fs
 
 	liftAnnex $ mapM_ onDel' fs'

CHANGELOG

@@ -1,5 +1,12 @@
 git-annex (8.20200523) UNRELEASED; urgency=medium
 
+  * Added annex.skipunknown git config, that can be set to false to change
+    the behavior of commands like `git annex get foo*`, to not skip
+    over files/dirs that are not checked into git and are explicitly listed in
+    the command line.
+  * annex.skipunknown is planned to change to default to false in a
+    git-annex release in early 2022. If you prefer the current behavior,
+    you can explicitly set it to true.
   * Try to enable special remotes configured with autoenable=yes
     when git-annex auto-initialization happens in a new clone of an
     existing repo. Previously, git-annex init had to be explicitly run to
@@ -14,7 +21,7 @@ git-annex (8.20200523) UNRELEASED; urgency=medium
     sync -J --content is used with an export remote.
   * export: Let concurrent transfers be done with -J or annex.jobs.
   * move --to, copy --to, mirror --to: When concurrency is enabled, run
-    cleanup actions in separate job pool from uploads.
+    cleanup actions in separate job pool from uploads. 
 
  -- Joey Hess <id@joeyh.name>  Tue, 26 May 2020 10:20:52 -0400
 

CmdLine/Seek.hs

@@ -4,7 +4,7 @@
  - the values a user passes to a command, and prepare actions operating
  - on them.
  -
- - Copyright 2010-2018 Joey Hess <id@joeyh.name>
+ - Copyright 2010-2020 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU AGPL version 3 or higher.
  -}
@@ -35,13 +35,13 @@ import Annex.InodeSentinal
 import qualified Database.Keys
 import qualified Utility.RawFilePath as R
 
-withFilesInGit :: (RawFilePath -> CommandSeek) -> [WorkTreeItem] -> CommandSeek
-withFilesInGit a l = seekActions $ prepFiltered a $
-	seekHelper LsFiles.inRepo l
+withFilesInGit :: WarnUnmatchWhen -> (RawFilePath -> CommandSeek) -> [WorkTreeItem] -> CommandSeek
+withFilesInGit ww a l = seekActions $ prepFiltered a $
+	seekHelper ww LsFiles.inRepo l
 
-withFilesInGitNonRecursive :: String -> (RawFilePath -> CommandSeek) -> [WorkTreeItem] -> CommandSeek
-withFilesInGitNonRecursive needforce a l = ifM (Annex.getState Annex.force)
-	( withFilesInGit a l
+withFilesInGitNonRecursive :: WarnUnmatchWhen -> String -> (RawFilePath -> CommandSeek) -> [WorkTreeItem] -> CommandSeek
+withFilesInGitNonRecursive ww needforce a l = ifM (Annex.getState Annex.force)
+	( withFilesInGit ww a l
 	, if null l
 		then giveup needforce
 		else seekActions $ prepFiltered a (getfiles [] l)
@@ -49,7 +49,8 @@ withFilesInGitNonRecursive needforce a l = ifM (Annex.getState Annex.force)
   where
 	getfiles c [] = return (reverse c)
 	getfiles c ((WorkTreeItem p):ps) = do
-		(fs, cleanup) <- inRepo $ LsFiles.inRepo [toRawFilePath p]
+		os <- seekOptions ww
+		(fs, cleanup) <- inRepo $ LsFiles.inRepo os [toRawFilePath p]
 		case fs of
 			[f] -> do
 				void $ liftIO $ cleanup
@@ -66,7 +67,7 @@ withFilesNotInGit  a l = go =<< seek
 		force <- Annex.getState Annex.force
 		g <- gitRepo
 		liftIO $ Git.Command.leaveZombie
-			<$> LsFiles.notInRepo force (map (\(WorkTreeItem f) -> toRawFilePath f) l) g
+			<$> LsFiles.notInRepo [] force (map (\(WorkTreeItem f) -> toRawFilePath f) l) g
 	go fs = seekActions $ prepFiltered a $
 		return $ concat $ segmentPaths (map (\(WorkTreeItem f) -> toRawFilePath f) l) fs
 
@@ -104,7 +105,7 @@ withPairs a params = seekActions $ return $ map a $ pairs [] params
 
 withFilesToBeCommitted :: (RawFilePath -> CommandSeek) -> [WorkTreeItem] -> CommandSeek
 withFilesToBeCommitted a l = seekActions $ prepFiltered a $
-	seekHelper LsFiles.stagedNotDeleted l
+	seekHelper WarnUnmatchWorkTreeItems (const LsFiles.stagedNotDeleted) l
 
 isOldUnlocked :: RawFilePath -> Annex Bool
 isOldUnlocked f = liftIO (notSymlink f) <&&> 
@@ -112,12 +113,12 @@ isOldUnlocked f = liftIO (notSymlink f) <&&>
 
 {- unlocked pointer files that are staged, and whose content has not been
  - modified-}
-withUnmodifiedUnlockedPointers :: (RawFilePath -> CommandSeek) -> [WorkTreeItem] -> CommandSeek
-withUnmodifiedUnlockedPointers a l = seekActions $
+withUnmodifiedUnlockedPointers :: WarnUnmatchWhen -> (RawFilePath -> CommandSeek) -> [WorkTreeItem] -> CommandSeek
+withUnmodifiedUnlockedPointers ww a l = seekActions $
 	prepFiltered a unlockedfiles
   where
 	unlockedfiles = filterM isUnmodifiedUnlocked 
-		=<< seekHelper LsFiles.typeChangedStaged l
+		=<< seekHelper ww (const LsFiles.typeChangedStaged) l
 
 isUnmodifiedUnlocked :: RawFilePath -> Annex Bool
 isUnmodifiedUnlocked f = catKeyFile f >>= \case
@@ -125,9 +126,9 @@ isUnmodifiedUnlocked f = catKeyFile f >>= \case
 	Just k -> sameInodeCache f =<< Database.Keys.getInodeCaches k
 
 {- Finds files that may be modified. -}
-withFilesMaybeModified :: (RawFilePath -> CommandSeek) -> [WorkTreeItem] -> CommandSeek
-withFilesMaybeModified a params = seekActions $
-	prepFiltered a $ seekHelper LsFiles.modified params
+withFilesMaybeModified :: WarnUnmatchWhen -> (RawFilePath -> CommandSeek) -> [WorkTreeItem] -> CommandSeek
+withFilesMaybeModified ww a params = seekActions $
+	prepFiltered a $ seekHelper ww LsFiles.modified params
 
 withKeys :: (Key -> CommandSeek) -> CmdParams -> CommandSeek
 withKeys a l = seekActions $ return $ map (a . parse) l
@@ -228,13 +229,25 @@ prepFiltered a fs = do
 seekActions :: Annex [CommandSeek] -> Annex ()
 seekActions gen = sequence_ =<< gen
 
-seekHelper :: ([RawFilePath] -> Git.Repo -> IO ([RawFilePath], IO Bool)) -> [WorkTreeItem] -> Annex [RawFilePath]
-seekHelper a l = inRepo $ \g ->
-	concat . concat <$> forM (segmentXargsOrdered l')
-		(runSegmentPaths (\fs -> Git.Command.leaveZombie <$> a fs g) . map toRawFilePath)
+seekHelper :: WarnUnmatchWhen -> ([LsFiles.Options] -> [RawFilePath] -> Git.Repo -> IO ([RawFilePath], IO Bool)) -> [WorkTreeItem] -> Annex [RawFilePath]
+seekHelper ww a l = do
+	os <- seekOptions ww
+	inRepo $ \g ->
+		concat . concat <$> forM (segmentXargsOrdered l')
+			(runSegmentPaths (\fs -> Git.Command.leaveZombie <$> a os fs g) . map toRawFilePath)
   where
 	l' = map (\(WorkTreeItem f) -> f) l
 
+data WarnUnmatchWhen = WarnUnmatchLsFiles | WarnUnmatchWorkTreeItems
+
+seekOptions :: WarnUnmatchWhen -> Annex [LsFiles.Options]
+seekOptions WarnUnmatchLsFiles =
+	ifM (annexSkipUnknown <$> Annex.getGitConfig)
+		( return [] 
+		, return [LsFiles.ErrorUnmatch]
+		)
+seekOptions WarnUnmatchWorkTreeItems = return []
+
 -- An item in the work tree, which may be a file or a directory.
 newtype WorkTreeItem = WorkTreeItem FilePath
 
@@ -243,30 +256,42 @@ newtype WorkTreeItem = WorkTreeItem FilePath
 -- seeking for such files.
 newtype AllowHidden = AllowHidden Bool
 
--- Many git commands like ls-files seek work tree items matching some criteria,
--- and silently skip over anything that does not exist. But users expect
--- an error message when one of the files they provided as a command-line
--- parameter doesn't exist, so this checks that each exists.
---
+-- git ls-files without --error-unmatch seeks work tree items matching
+-- some criteria, and silently skips over anything that does not exist.
+
 -- Also, when two directories are symlinked, referring to a file
--- inside the symlinked directory will be silently skipped by git commands
--- like ls-files. But, the user would be surprised for it to be skipped, so
--- check if the parent directories are symlinks.
-workTreeItems :: CmdParams -> Annex [WorkTreeItem]
+-- inside the symlinked directory will be silently skipped by
+-- git ls-files without --error-unmatch. 
+--
+-- Sometimes a command needs to use git-lsfiles that way, perhaps repeatedly.
+-- But users expect an error message when one of the files they provided
+-- as a command-line parameter doesn't exist, so this checks that each
+-- exists when run with WarnUnmatchWorkTreeItems.
+--
+-- Note that, unlike --error-unmatch, using this does not warn
+-- about command-line parameters that exist, but are not checked into git.
+workTreeItems :: WarnUnmatchWhen -> CmdParams -> Annex [WorkTreeItem]
 workTreeItems = workTreeItems' (AllowHidden False)
 
-workTreeItems' :: AllowHidden -> CmdParams -> Annex [WorkTreeItem]
-workTreeItems' (AllowHidden allowhidden) ps = do
-	currbranch <- getCurrentBranch
-	forM_ ps $ \p -> do
-		relf <- liftIO $ relPathCwdToFile p
-		ifM (not <$> (exists p <||> hidden currbranch relf))
-			( prob (p ++ " not found")
-			, whenM (viasymlink (upFrom relf)) $
-				prob (p ++ " is beyond a symbolic link")
-			)
-	return (map (WorkTreeItem) ps)
+workTreeItems' :: AllowHidden -> WarnUnmatchWhen -> CmdParams -> Annex [WorkTreeItem]
+workTreeItems' (AllowHidden allowhidden) ww ps = do
+	case ww of
+		WarnUnmatchWorkTreeItems -> runcheck
+		WarnUnmatchLsFiles -> 
+			whenM (annexSkipUnknown <$> Annex.getGitConfig)
+				runcheck
+	return (map WorkTreeItem ps)
   where
+	runcheck = do
+		currbranch <- getCurrentBranch
+		forM_ ps $ \p -> do
+			relf <- liftIO $ relPathCwdToFile p
+			ifM (not <$> (exists p <||> hidden currbranch relf))
+				( prob (p ++ " not found")
+				, whenM (viasymlink (upFrom relf)) $
+					prob (p ++ " is beyond a symbolic link")
+				)
+	
 	exists p = isJust <$> liftIO (catchMaybeIO $ getSymbolicLinkStatus p)
 
 	viasymlink Nothing = return False

Command/Add.hs

@@ -82,10 +82,15 @@ seek o = startConcurrency commandStages $ do
 				giveup "--update --batch is not supported"
 			| otherwise -> batchFilesMatching fmt (gofile . toRawFilePath)
 		NoBatch -> do
-			l <- workTreeItems (addThese o)
-			let go a = a (commandAction . gofile) l
+			-- Avoid git ls-files complaining about files that
+			-- are not known to git yet, since this will add
+			-- them. Instead, have workTreeItems warn about other
+			-- problems, like files that don't exist.
+			let ww = WarnUnmatchWorkTreeItems
+			l <- workTreeItems ww (addThese o)
+			let go a = a ww (commandAction . gofile) l
 			unless (updateOnly o) $
-				go withFilesNotInGit
+				go (const withFilesNotInGit)
 			go withFilesMaybeModified
 			go withUnmodifiedUnlockedPointers
 

Command/Copy.hs

@@ -51,8 +51,10 @@ seek o = startConcurrency commandStages $ do
 		NoBatch -> withKeyOptions
 			(keyOptions o) (autoMode o)
 			(commandAction . Command.Move.startKey (fromToOptions o) Command.Move.RemoveNever)
-			(withFilesInGit $ commandAction . go)
-			=<< workTreeItems (copyFiles o)
+			(withFilesInGit ww $ commandAction . go)
+			=<< workTreeItems ww (copyFiles o)
+  where
+	ww = WarnUnmatchLsFiles
 
 {- A copy is just a move that does not delete the source file.
  - However, auto mode avoids unnecessary copies, and avoids getting or

Command/Drop.hs

@@ -57,10 +57,11 @@ seek o = startConcurrency commandStages $
 		Batch fmt -> batchFilesMatching fmt (go . toRawFilePath)
 		NoBatch -> withKeyOptions (keyOptions o) (autoMode o)
 			(commandAction . startKeys o)
-			(withFilesInGit (commandAction . go))
-			=<< workTreeItems (dropFiles o)
+			(withFilesInGit ww (commandAction . go))
+			=<< workTreeItems ww (dropFiles o)
   where
 	go = whenAnnexed $ start o
+	ww = WarnUnmatchLsFiles
 
 start :: DropOptions -> RawFilePath -> Key -> CommandStart
 start o file key = start' o key afile ai

Command/Find.hs

@@ -57,11 +57,12 @@ seek :: FindOptions -> CommandSeek
 seek o = case batchOption o of
 	NoBatch -> withKeyOptions (keyOptions o) False
 		(commandAction . startKeys o)
-		(withFilesInGit (commandAction . go))
-		=<< workTreeItems (findThese o)
+		(withFilesInGit ww (commandAction . go))
+		=<< workTreeItems ww (findThese o)
 	Batch fmt -> batchFilesMatching fmt (go . toRawFilePath)
   where
 	go = whenAnnexed $ start o
+	ww = WarnUnmatchLsFiles
 
 -- only files inAnnex are shown, unless the user has requested
 -- others via a limit

Command/Fix.hs

@@ -32,9 +32,11 @@ cmd = noCommit $ withGlobalOptions [annexedMatchingOptions] $
 
 seek :: CmdParams -> CommandSeek
 seek ps = unlessM crippledFileSystem $ do 
-	withFilesInGit
+	withFilesInGit ww
 		(commandAction . (whenAnnexed $ start FixAll))
-		=<< workTreeItems ps
+		=<< workTreeItems ww ps
+  where
+	ww = WarnUnmatchLsFiles
 
 data FixWhat = FixSymlinks | FixAll
 

Command/Fsck.hs

@@ -94,10 +94,12 @@ seek o = startConcurrency commandStages $ do
 	i <- prepIncremental u (incrementalOpt o)
 	withKeyOptions (keyOptions o) False
 		(\kai -> commandAction . startKey from i kai =<< getNumCopies)
-		(withFilesInGit $ commandAction . (whenAnnexed (start from i)))
-		=<< workTreeItems (fsckFiles o)
+		(withFilesInGit ww $ commandAction . (whenAnnexed (start from i)))
+		=<< workTreeItems ww (fsckFiles o)
 	cleanupIncremental i
 	void $ tryIO $ recordActivity Fsck u
+  where
+	ww = WarnUnmatchLsFiles
 
 checkDeadRepo :: UUID -> Annex ()
 checkDeadRepo u =

Command/Get.hs

@@ -45,8 +45,10 @@ seek o = startConcurrency downloadStages $ do
 		Batch fmt -> batchFilesMatching fmt (go . toRawFilePath)
 		NoBatch -> withKeyOptions (keyOptions o) (autoMode o)
 			(commandAction . startKeys from)
-			(withFilesInGit (commandAction . go))
-			=<< workTreeItems (getFiles o)
+			(withFilesInGit ww (commandAction . go))
+			=<< workTreeItems ww (getFiles o)
+  where
+	ww = WarnUnmatchLsFiles
 
 start :: GetOptions -> Maybe Remote -> RawFilePath -> Key -> CommandStart
 start o from file key = start' expensivecheck from key afile ai

Command/Inprogress.hs

@@ -38,9 +38,11 @@ seek o = do
 			| otherwise -> commandAction stop
 		_ -> do
 			let s = S.fromList ts
-			withFilesInGit
+			withFilesInGit ww
 				(commandAction . (whenAnnexed (start s)))
-				=<< workTreeItems (inprogressFiles o)
+				=<< workTreeItems ww (inprogressFiles o)
+  where
+	ww = WarnUnmatchLsFiles
 
 start :: S.Set Key -> RawFilePath -> Key -> CommandStart
 start s _file k

Command/List.hs

@@ -44,9 +44,10 @@ seek :: ListOptions -> CommandSeek
 seek o = do
 	list <- getList o
 	printHeader list
-	withFilesInGit
-		(commandAction . (whenAnnexed $ start list))
-		=<< workTreeItems (listThese o)
+	withFilesInGit ww (commandAction . (whenAnnexed $ start list))
+		=<< workTreeItems ww (listThese o)
+  where
+	ww = WarnUnmatchLsFiles
 
 getList :: ListOptions -> Annex [(UUID, RemoteName, TrustLevel)]
 getList o

Command/Lock.hs

@@ -30,8 +30,10 @@ cmd = withGlobalOptions [jsonOptions, annexedMatchingOptions] $
 
 seek :: CmdParams -> CommandSeek
 seek ps = do
-	l <- workTreeItems ps
-	withFilesInGit (commandAction . (whenAnnexed startNew)) l
+	l <- workTreeItems ww ps
+	withFilesInGit ww (commandAction . (whenAnnexed startNew)) l
+  where
+	ww = WarnUnmatchLsFiles
 
 startNew :: RawFilePath -> Key -> CommandStart
 startNew file key = ifM (isJust <$> isAnnexLink file)

Command/Log.hs

@@ -86,11 +86,13 @@ seek o = do
 	zone <- liftIO getCurrentTimeZone
 	let outputter = mkOutputter m zone o
 	case (logFiles o, allOption o) of
-		(fs, False) -> withFilesInGit
+		(fs, False) -> withFilesInGit ww
 			(commandAction . (whenAnnexed $ start o outputter)) 
-			=<< workTreeItems fs
+			=<< workTreeItems ww fs
 		([], True) -> commandAction (startAll o outputter)
 		(_, True) -> giveup "Cannot specify both files and --all"
+  where
+	ww = WarnUnmatchLsFiles
 
 start :: LogOptions -> (FilePath -> Outputter) -> RawFilePath -> Key -> CommandStart
 start o outputter file key = do

Command/LookupKey.hs

@@ -31,7 +31,7 @@ run _ file = seekSingleGitFile file >>= \case
 -- But, this plumbing command does not recurse through directories.
 seekSingleGitFile :: FilePath -> Annex (Maybe RawFilePath)
 seekSingleGitFile file = do
-	(l, cleanup) <- inRepo (Git.LsFiles.inRepo [toRawFilePath file])
+	(l, cleanup) <- inRepo (Git.LsFiles.inRepo [] [toRawFilePath file])
 	r <- case l of
 		(f:[]) | takeFileName (fromRawFilePath f) == takeFileName file ->
 			return (Just f)

Command/MetaData.hs

@@ -75,15 +75,16 @@ seek :: MetaDataOptions -> CommandSeek
 seek o = case batchOption o of
 	NoBatch -> do
 		c <- liftIO currentVectorClock
+		let ww = WarnUnmatchLsFiles
 		let seeker = case getSet o of
-			Get _ -> withFilesInGit
-			GetAll -> withFilesInGit
-			Set _ -> withFilesInGitNonRecursive
+			Get _ -> withFilesInGit ww
+			GetAll -> withFilesInGit ww
+			Set _ -> withFilesInGitNonRecursive ww
 				"Not recursively setting metadata. Use --force to do that."
 		withKeyOptions (keyOptions o) False
 			(commandAction . startKeys c o)
 			(seeker (commandAction . (whenAnnexed (start c o))))
-			=<< workTreeItems (forFiles o)
+			=<< workTreeItems ww (forFiles o)
 	Batch fmt -> withMessageState $ \s -> case outputType s of
 		JSONOutput _ -> ifM limited
 			( giveup "combining --batch with file matching options is not currently supported"

Command/Migrate.hs

@@ -26,7 +26,10 @@ cmd = withGlobalOptions [annexedMatchingOptions] $
 		paramPaths (withParams seek)
 
 seek :: CmdParams -> CommandSeek
-seek = withFilesInGit (commandAction . (whenAnnexed start)) <=< workTreeItems
+seek = withFilesInGit ww (commandAction . (whenAnnexed start))
+	<=< workTreeItems ww
+  where
+	ww = WarnUnmatchLsFiles
 
 start :: RawFilePath -> Key -> CommandStart
 start file key = do

Command/Mirror.hs

@@ -44,12 +44,13 @@ seek :: MirrorOptions -> CommandSeek
 seek o = startConcurrency stages $ 
 	withKeyOptions (keyOptions o) False
 		(commandAction . startKey o (AssociatedFile Nothing))
-		(withFilesInGit (commandAction . (whenAnnexed $ start o)))
-		=<< workTreeItems (mirrorFiles o)
+		(withFilesInGit ww (commandAction . (whenAnnexed $ start o)))
+		=<< workTreeItems ww (mirrorFiles o)
   where
 	stages = case fromToOptions o of
 		FromRemote _ -> downloadStages
 		ToRemote _ -> commandStages
+	ww = WarnUnmatchLsFiles
 
 start :: MirrorOptions -> RawFilePath -> Key -> CommandStart
 start o file k = startKey o afile (k, ai)

Command/Move.hs

@@ -60,13 +60,14 @@ seek o = startConcurrency stages $ do
 		Batch fmt -> batchFilesMatching fmt (go . toRawFilePath)
 		NoBatch -> withKeyOptions (keyOptions o) False
 			(commandAction . startKey (fromToOptions o) (removeWhen o))
-			(withFilesInGit (commandAction . go))
-			=<< workTreeItems (moveFiles o)
+			(withFilesInGit ww (commandAction . go))
+			=<< workTreeItems ww (moveFiles o)
   where
 	stages = case fromToOptions o of
 		Right (FromRemote _) -> downloadStages
 		Right (ToRemote _) -> commandStages
 		Left ToHere -> downloadStages
+	ww = WarnUnmatchLsFiles
 
 start :: FromToHereOptions -> RemoveWhen -> RawFilePath -> Key -> CommandStart
 start fromto removewhen f k = start' fromto removewhen afile k ai

Command/Multicast.hs

@@ -129,7 +129,9 @@ send ups fs = do
 	-- expensive.
 	starting "sending files" (ActionItemOther Nothing) $
 		withTmpFile "send" $ \t h -> do
-			fs' <- seekHelper LsFiles.inRepo =<< workTreeItems fs
+			let ww = WarnUnmatchLsFiles
+			fs' <- seekHelper ww LsFiles.inRepo
+				=<< workTreeItems ww fs
 			matcher <- Limit.getMatcher
 			let addlist f o = whenM (matcher $ MatchingFile $ FileInfo f f) $
 				liftIO $ hPutStrLn h o

Command/PreCommit.hs

@@ -32,7 +32,8 @@ cmd = command "pre-commit" SectionPlumbing
 
 seek :: CmdParams -> CommandSeek
 seek ps = do
-	l <- workTreeItems ps
+	let ww = WarnUnmatchWorkTreeItems
+	l <- workTreeItems ww ps
 	-- fix symlinks to files being committed
 	flip withFilesToBeCommitted l $ \f -> commandAction $
 		maybe stop (Command.Fix.start Command.Fix.FixSymlinks f)

Command/Sync.hs

@@ -636,11 +636,11 @@ seekSyncContent o rs currbranch = do
 		Just WantAllKeys -> Just <$> genBloomFilter (seekworktree mvar [])
 		_ -> case currbranch of
                 	(Just origbranch, Just adj) | adjustmentHidesFiles adj -> do
-				l <- workTreeItems' (AllowHidden True) (contentOfOption o)
+				l <- workTreeItems' (AllowHidden True) ww (contentOfOption o)
 				seekincludinghidden origbranch mvar l (const noop)
 				pure Nothing
 			_ -> do
-				l <- workTreeItems (contentOfOption o)
+				l <- workTreeItems ww (contentOfOption o)
 				seekworktree mvar l (const noop)
 				pure Nothing
 	withKeyOptions' (keyOptions o) False
@@ -651,13 +651,15 @@ seekSyncContent o rs currbranch = do
 	liftIO $ not <$> isEmptyMVar mvar
   where
 	seekworktree mvar l bloomfeeder = 
-		seekHelper LsFiles.inRepo l
+		seekHelper ww LsFiles.inRepo l
 			>>= gofiles bloomfeeder mvar
 
 	seekincludinghidden origbranch mvar l bloomfeeder = 
-		seekHelper (LsFiles.inRepoOrBranch origbranch) l 
+		seekHelper ww (LsFiles.inRepoOrBranch origbranch) l 
 			>>= gofiles bloomfeeder mvar
 
+	ww = WarnUnmatchLsFiles
+
 	gofiles bloomfeeder mvar = mapM_ $ \f ->
 		ifAnnexed f
 			(go (Right bloomfeeder) mvar (AssociatedFile (Just f)))

Command/Unannex.hs

@@ -23,7 +23,10 @@ cmd = withGlobalOptions [annexedMatchingOptions] $
 		paramPaths (withParams seek)
 
 seek :: CmdParams -> CommandSeek
-seek ps = (withFilesInGit $ commandAction . whenAnnexed start) =<< workTreeItems ps
+seek ps = (withFilesInGit ww $ commandAction . whenAnnexed start)
+	=<< workTreeItems ww ps
+  where
+	ww = WarnUnmatchLsFiles
 
 start :: RawFilePath -> Key -> CommandStart
 start file key = stopUnless (inAnnex key) $

Command/Undo.hs

@@ -27,7 +27,7 @@ seek :: CmdParams -> CommandSeek
 seek ps = do
 	-- Safety first; avoid any undo that would touch files that are not
 	-- in the index.
-	(fs, cleanup) <- inRepo $ LsFiles.notInRepo False (map toRawFilePath ps)
+	(fs, cleanup) <- inRepo $ LsFiles.notInRepo [] False (map toRawFilePath ps)
 	unless (null fs) $
 		giveup $ "Cannot undo changes to files that are not checked into git: " ++ unwords (map fromRawFilePath fs)
 	void $ liftIO $ cleanup

Command/Uninit.hs

@@ -41,11 +41,13 @@ check = do
 
 seek :: CmdParams -> CommandSeek
 seek ps = do
-	l <- workTreeItems ps
+	l <- workTreeItems ww ps
 	withFilesNotInGit (commandAction . whenAnnexed (startCheckIncomplete . fromRawFilePath)) l
 	Annex.changeState $ \s -> s { Annex.fast = True }
-	withFilesInGit (commandAction . whenAnnexed Command.Unannex.start) l
+	withFilesInGit ww (commandAction . whenAnnexed Command.Unannex.start) l
 	finish
+  where
+	ww = WarnUnmatchLsFiles
 
 {- git annex symlinks that are not checked into git could be left by an
  - interrupted add. -}

Command/Unlock.hs

@@ -27,7 +27,10 @@ mkcmd n d = withGlobalOptions [jsonOptions, annexedMatchingOptions] $
 	command n SectionCommon d paramPaths (withParams seek)
 
 seek :: CmdParams -> CommandSeek
-seek ps = withFilesInGit (commandAction . whenAnnexed start) =<< workTreeItems ps
+seek ps = withFilesInGit ww (commandAction . whenAnnexed start)
+	=<< workTreeItems ww ps
+  where
+	ww = WarnUnmatchLsFiles
 
 start :: RawFilePath -> Key -> CommandStart
 start file key = ifM (isJust <$> isAnnexLink file)

Command/Unused.hs

@@ -210,9 +210,9 @@ withKeysReferenced' mdir initial a = do
 			( return ([], return True)
 			, do
 				top <- fromRepo Git.repoPath
-				inRepo $ LsFiles.allFiles [top]
+				inRepo $ LsFiles.allFiles [] [top]
 			)
-		Just dir -> inRepo $ LsFiles.inRepo [toRawFilePath dir]
+		Just dir -> inRepo $ LsFiles.inRepo [] [toRawFilePath dir]
 	go v [] = return v
 	go v (f:fs) = do
 		mk <- lookupFile f

Command/View.hs

@@ -101,7 +101,7 @@ checkoutViewBranch view mkbranch = do
 		 - removed.) -}
 		top <- liftIO . absPath . fromRawFilePath =<< fromRepo Git.repoPath
 		(l, cleanup) <- inRepo $
-			LsFiles.notInRepoIncludingEmptyDirectories False
+			LsFiles.notInRepoIncludingEmptyDirectories [] False
 				[toRawFilePath top]
 		forM_ l (removeemptydir top)
 		liftIO $ void cleanup

Command/Whereis.hs

@@ -57,8 +57,10 @@ seek o = do
 		NoBatch -> 
 			withKeyOptions (keyOptions o) False
 				(commandAction . startKeys o m)
-				(withFilesInGit (commandAction . go))
-				=<< workTreeItems (whereisFiles o)
+				(withFilesInGit ww (commandAction . go))
+				=<< workTreeItems ww (whereisFiles o)
+  where
+	ww = WarnUnmatchLsFiles
 
 start :: WhereisOptions -> M.Map UUID Remote -> RawFilePath -> Key -> CommandStart
 start o remotemap file key = 

Git/LsFiles.hs

@@ -1,11 +1,12 @@
 {- git ls-files interface
  -
- - Copyright 2010-2019 Joey Hess <id@joeyh.name>
+ - Copyright 2010-2020 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU AGPL version 3 or higher.
  -}
 
 module Git.LsFiles (
+	Options(..),
 	inRepo,
 	inRepoOrBranch,
 	notInRepo,
@@ -13,10 +14,8 @@ module Git.LsFiles (
 	allFiles,
 	deleted,
 	modified,
-	modifiedOthers,
 	staged,
 	stagedNotDeleted,
-	stagedOthersDetails,
 	stagedDetails,
 	typeChanged,
 	typeChangedStaged,
@@ -63,101 +62,63 @@ guardSafeForLsFiles r a
 	| safeForLsFiles r = a
 	| otherwise = error $ "git ls-files is unsafe to run on repository " ++ repoDescribe r
 
+data Options = ErrorUnmatch
+
 {- Lists files that are checked into git's index at the specified paths.
  - With no paths, all files are listed.
  -}
-inRepo :: [RawFilePath] -> Repo -> IO ([RawFilePath], IO Bool)
-inRepo = inRepo' [] 
+inRepo :: [Options] -> [RawFilePath] -> Repo -> IO ([RawFilePath], IO Bool)
+inRepo = inRepo' [Param "--cached"] 
 
-inRepo' :: [CommandParam] -> [RawFilePath] -> Repo -> IO ([RawFilePath], IO Bool)
-inRepo' ps l repo = guardSafeForLsFiles repo $ pipeNullSplit' params repo
+inRepo' :: [CommandParam] -> [Options] -> [RawFilePath] -> Repo -> IO ([RawFilePath], IO Bool)
+inRepo' ps os l repo = guardSafeForLsFiles repo $ pipeNullSplit' params repo
   where
 	params = 
 		Param "ls-files" :
-		Param "--cached" :
 		Param "-z" :
-		ps ++
+		map op os ++ ps ++
 		(Param "--" : map (File . fromRawFilePath) l)
+	op ErrorUnmatch = Param "--error-unmatch" 
 
 {- Files that are checked into the index or have been committed to a
  - branch. -}
-inRepoOrBranch :: Branch -> [RawFilePath] -> Repo -> IO ([RawFilePath], IO Bool)
-inRepoOrBranch b = inRepo' [Param $ "--with-tree=" ++ fromRef b]
+inRepoOrBranch :: Branch -> [Options] -> [RawFilePath] -> Repo -> IO ([RawFilePath], IO Bool)
+inRepoOrBranch b = inRepo'
+	[ Param "--cached"
+	, Param ("--with-tree=" ++ fromRef b)
+	]
 
 {- Scans for files at the specified locations that are not checked into git. -}
-notInRepo :: Bool -> [RawFilePath] -> Repo -> IO ([RawFilePath], IO Bool)
+notInRepo :: [Options] -> Bool -> [RawFilePath] -> Repo -> IO ([RawFilePath], IO Bool)
 notInRepo = notInRepo' []
 
-notInRepo' :: [CommandParam] -> Bool -> [RawFilePath] -> Repo -> IO ([RawFilePath], IO Bool)
-notInRepo' ps include_ignored l repo = guardSafeForLsFiles repo $
-	pipeNullSplit' params repo
+notInRepo' :: [CommandParam] -> [Options] -> Bool -> [RawFilePath] -> Repo -> IO ([RawFilePath], IO Bool)
+notInRepo' ps os include_ignored = 
+	inRepo' (Param "--others" : ps ++ exclude) os
   where
-	params = concat
-		[ [ Param "ls-files", Param "--others"]
-		, ps
-		, exclude
-		, [ Param "-z", Param "--" ]
-		, map (File . fromRawFilePath) l
-		]
 	exclude
 		| include_ignored = []
 		| otherwise = [Param "--exclude-standard"]
 
 {- Scans for files at the specified locations that are not checked into
  - git. Empty directories are included in the result. -}
-notInRepoIncludingEmptyDirectories :: Bool -> [RawFilePath] -> Repo -> IO ([RawFilePath], IO Bool)
+notInRepoIncludingEmptyDirectories :: [Options] -> Bool -> [RawFilePath] -> Repo -> IO ([RawFilePath], IO Bool)
 notInRepoIncludingEmptyDirectories = notInRepo' [Param "--directory"]
 
 {- Finds all files in the specified locations, whether checked into git or
  - not. -}
-allFiles :: [RawFilePath] -> Repo -> IO ([RawFilePath], IO Bool)
-allFiles l repo = guardSafeForLsFiles repo $ pipeNullSplit' params repo
-  where
-	params =
-		Param "ls-files" :
-		Param "--cached" :
-		Param "--others" :
-		Param "-z" :
-		Param "--" :
-		map (File . fromRawFilePath) l
+allFiles :: [Options] -> [RawFilePath] -> Repo -> IO ([RawFilePath], IO Bool)
+allFiles = inRepo' [Param "--cached", Param "--others"]
 
 {- Returns a list of files in the specified locations that have been
  - deleted. -}
-deleted :: [RawFilePath] -> Repo -> IO ([RawFilePath], IO Bool)
-deleted l repo = guardSafeForLsFiles repo $ pipeNullSplit' params repo
-  where
-	params =
-		Param "ls-files" :
-		Param "--deleted" :
-		Param "-z" :
-		Param "--" :
-		map (File . fromRawFilePath) l
+deleted :: [Options] -> [RawFilePath] -> Repo -> IO ([RawFilePath], IO Bool)
+deleted = inRepo' [Param "--deleted"]
 
 {- Returns a list of files in the specified locations that have been
  - modified. -}
-modified :: [RawFilePath] -> Repo -> IO ([RawFilePath], IO Bool)
-modified l repo = guardSafeForLsFiles repo $ pipeNullSplit' params repo
-  where
-	params = 
-		Param "ls-files" :
-		Param "--modified" :
-		Param "-z" :
-		Param "--" :
-		map (File . fromRawFilePath) l
-
-{- Files that have been modified or are not checked into git (and are not
- - ignored). -}
-modifiedOthers :: [RawFilePath] -> Repo -> IO ([RawFilePath], IO Bool)
-modifiedOthers l repo = guardSafeForLsFiles repo $ pipeNullSplit' params repo
-  where
-	params = 
-		Param "ls-files" :
-		Param "--modified" :
-		Param "--others" :
-		Param "--exclude-standard" :
-		Param "-z" :
-		Param "--" :
-		map (File . fromRawFilePath) l
+modified :: [Options] -> [RawFilePath] -> Repo -> IO ([RawFilePath], IO Bool)
+modified = inRepo' [Param "--modified"]
 
 {- Returns a list of all files that are staged for commit. -}
 staged :: [RawFilePath] -> Repo -> IO ([RawFilePath], IO Bool)
@@ -177,11 +138,6 @@ staged' ps l repo = guardSafeForLsFiles repo $
 
 type StagedDetails = (RawFilePath, Maybe Sha, Maybe FileMode)
 
-{- Returns details about files that are staged in the index,
- - as well as files not yet in git. Skips ignored files. -}
-stagedOthersDetails :: [RawFilePath] -> Repo -> IO ([StagedDetails], IO Bool)
-stagedOthersDetails = stagedDetails' [Param "--others", Param "--exclude-standard"]
-
 {- Returns details about all files that are staged in the index. -}
 stagedDetails :: [RawFilePath] -> Repo -> IO ([StagedDetails], IO Bool)
 stagedDetails = stagedDetails' []

NEWS

@@ -1,3 +1,14 @@
+git-annex (8.20200523) UNRELEASED; urgency=medium
+
+  Transition notice: Commands like `git-annex get foo*` silently skip over
+  files that are not checked into git. Since that can be surprising in many
+  cases, the behavior will change to erroring out when one of the listed
+  files is not checked into git. This change is planned for a git-annex
+  release in early 2022. If you would like to keep the current
+  behavior, use git config to set annex.skipunknown to true.
+
+ -- Joey Hess <id@joeyh.name>  Thu, 28 May 2020 13:23:40 -0400
+
 git-annex (8.20200226) upstream; urgency=medium
   
   This version of git-annex uses repository version 8 for all repositories.

Types/GitConfig.hs

@@ -123,6 +123,7 @@ data GitConfig = GitConfig
 	, annexCacheCreds :: Bool
 	, annexAutoUpgradeRepository :: Bool
 	, annexCommitMode :: CommitMode
+	, annexSkipUnknown :: Bool
 	, coreSymlinks :: Bool
 	, coreSharedRepository :: SharedRepository
 	, receiveDenyCurrentBranch :: DenyCurrentBranch
@@ -214,6 +215,7 @@ extractGitConfig configsource r = GitConfig
 	, annexCommitMode = if getbool (annexConfig "allowsign") False
 		then ManualCommit
 		else AutomaticCommit
+	, annexSkipUnknown = getbool (annexConfig "skipunknown") True
 	, coreSymlinks = getbool "core.symlinks" True
 	, coreSharedRepository = getSharedRepository r
 	, receiveDenyCurrentBranch = getDenyCurrentBranch r

Upgrade/V1.hs

@@ -85,7 +85,7 @@ updateSymlinks :: Annex ()
 updateSymlinks = do
 	showAction "updating symlinks"
 	top <- fromRepo Git.repoPath
-	(files, cleanup) <- inRepo $ LsFiles.inRepo [top]
+	(files, cleanup) <- inRepo $ LsFiles.inRepo [] [top]
 	forM_ files (fixlink . fromRawFilePath)
 	void $ liftIO cleanup
   where

doc/bugs/annex_metadata___40__not_--batch__39__ed__41___is_not_aware_of_files_added_via_addurls_--batch.mdwn

@@ -35,3 +35,12 @@ P.S.  It might be a related observation that git-annex metadata does exit with n
 [[!tag projects/datalad]]
 
 [[!meta title="silently skipping files that are not in git or not annexed is sometimes surprising to some"]]
+
+> annex.skipunknown false will make git-annex error out in this situation.
+> That will become the default in a couple of years, but can be set already
+> by those who don't like the behavior of skipping. 
+> 
+> In the case of addurl --batch though, do see my first comment for a way to
+> avoid any errors.
+> 
+> [[done]] --[[Joey]]

doc/bugs/annex_metadata___40__not_--batch__39__ed__41___is_not_aware_of_files_added_via_addurls_--batch/comment_2_c479f19eb55dce35364eea30d0b727b7._comment

@@ -27,7 +27,8 @@ temp file that is not in git, then they would have to change scripts
 and workflows.
 
 Implementing it may be as simple as passing --error-unmatch to git
-ls-files.
+ls-files. (And disable git-annex's code that checks for parameters that are
+not existing files.)
 
 It could be an option, but I don't really consider an option as fixing the
 surprising behavior. And once you know git-annex behaves this way, I think

doc/bugs/annex_metadata___40__not_--batch__39__ed__41___is_not_aware_of_files_added_via_addurls_--batch/comment_3_f694e35efa09aa60daf17d63270968af._comment

@@ -0,0 +1,17 @@
+[[!comment format=mdwn
+ username="joey"
+ subject="""comment 3"""
+ date="2020-05-28T19:49:58Z"
+ content="""
+Implemented annex.skipunknown git config, that will make it error out when
+given a file that git doesn't know about.
+
+Not default yet, will be in a couple of years.
+[[todo/complete_annex.skipunknown_transition_in_2022]]
+
+As to git-annex skipping non-annexed files, I'm leaning toward keeping it
+the way it is, and it's not really the subject of this bug report, except
+maybe that it's not entirely consistent with the annex.skipunknown
+behavior for non-git files. If users complain about it, I'll consider it
+again.
+"""]]

doc/bugs/unlock_should_warn_if_file_isn__39__t_in_repo.mdwn

@@ -51,3 +51,7 @@ It would be nice if git-annex could give an error to explain why the unlock fail
 ### Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders)
 
 git-annex is amazing, I use it all the time. Thanks!
+
+> annex.skipunknown false will make git-annex error out in this situation.
+> That will become the default in a couple of years, but can be set already
+> by those who don't like the behavior of skipping. [[done]] --[[Joey]]

doc/git-annex.mdwn

@@ -880,6 +880,28 @@ Like other git commands, git-annex is configured via `.git/config`.
 
   The default reserve is 1 megabyte.
 
+* `annex.skipunknown`
+
+  Set to true to make commands like "git-annex get" silently skip over
+  items that are listed in the command line, but are not checked into git.
+
+  Set to false to make it an error for commands like "git-annex get"
+  to be asked to operate on files that are not checked into git.
+
+  The default is currently true, but is planned to change to false in a
+  release in 2022.
+
+  Note that, when annex.skipunknown is false, a command like "git-annex get ."
+  will fail if no files in the current directory are checked into git,
+  but a command like "git-annex get" will not fail, because the current
+  directory is not listed, but is implicit. Commands like "git-annex get foo/"
+  will fail if no files in the directory are checked into git, but if
+  at least one file is, it will ignore other files that are not. This is
+  all the same as the behavior of "git-ls files --error-unmatch".
+  
+  Also note that git-annex skips files that are checked into git, but are
+  not annexed files, this setting does not affect that.
+
 * `annex.largefiles`
 
   Used to configure which files are large enough to be added to the annex.

doc/todo/complete_annex.skipunknown_transition_in_2022.mdwn

@@ -0,0 +1,4 @@
+annex.skipunknown should be changed to default to false in early 2022.
+This transition was started in mid 2020 and there should have been plenty
+of time for people to learn about it and either set their preferred
+behavior or change workflows for the new behavior.