add --force-annex/--force-git

options make it easier to override annex.largefiles configuration
(and potentially safer as it avoids bugs like the smudge bug fixed
in the last release)

Deleted some old comments that were posted to the man page discussing such
options.

Updated docs that used -c annex.largefiles to use the options.

Note that addSmallOverridden was needed to avoid the clean filter running
on the file. It would be possible to make addFile also update the index
directly, rather than going via git add. However, it was not necessary,
and I want to avoid breaking on some edge case, particularly if the code in
addSmallOverridden has some oversight.

Also, when annex.addunlocked is set and annex.largefiles does not match a file,
git annex add --force-large works, but git status will then show the file
as added, with a unstaged modification. The unstaged modification adds the
file to git. This is identical behavior to using -c annex.largefiles=nothing
when annex.addunlocked is set. This does not prevent committing what was
intended to be added. I have not gotten to the bottom of why git thinks
the file is modified and runs it through the clean filter in this case.

Command/Add.hs

@@ -1,6 +1,6 @@
 {- git-annex command
  -
- - Copyright 2010-2017 Joey Hess <id@joeyh.name>
+ - Copyright 2010-2020 Joey Hess <id@joeyh.name>
  -
  - Licensed under the GNU AGPL version 3 or higher.
  -}
@@ -17,8 +17,12 @@ import qualified Database.Keys
 import Annex.FileMatcher
 import Annex.Link
 import Annex.Tmp
+import Annex.HashObject
 import Messages.Progress
+import Git.Types
 import Git.FilePath
+import qualified Git.UpdateIndex
+import Utility.FileMode
 import qualified Utility.RawFilePath as R
 
 cmd :: Command
@@ -32,6 +36,7 @@ data AddOptions = AddOptions
 	, includeDotFiles :: Bool
 	, batchOption :: BatchMode
 	, updateOnly :: Bool
+	, largeFilesOverride :: Maybe Bool
 	}
 
 optParser :: CmdParamsDesc -> Parser AddOptions
@@ -47,18 +52,31 @@ optParser desc = AddOptions
 		<> short 'u'
 		<> help "only update tracked files"
 		)
+	<*> (parseforcelarge <|> parseforcesmall)
+  where
+	parseforcelarge = flag Nothing (Just True)
+		( long "force-large"
+		<> help "add all files to annex, ignoring other configuration"
+		)
+	parseforcesmall = flag Nothing (Just False)
+		( long "force-small"
+		<> help "add all files to git, ignoring other configuration"
+		)
 
 seek :: AddOptions -> CommandSeek
 seek o = startConcurrency commandStages $ do
 	largematcher <- largeFilesMatcher
 	addunlockedmatcher <- addUnlockedMatcher
-	let gofile file = ifM (checkFileMatcher largematcher (fromRawFilePath file) <||> Annex.getState Annex.force)
-		( start file addunlockedmatcher
-		, ifM (annexAddSmallFiles <$> Annex.getGitConfig)
-			( startSmall file
-			, stop
+	let gofile file = case largeFilesOverride o of
+		Nothing -> ifM (checkFileMatcher largematcher (fromRawFilePath file) <||> Annex.getState Annex.force)
+			( start file addunlockedmatcher
+			, ifM (annexAddSmallFiles <$> Annex.getGitConfig)
+				( startSmall file
+				, stop
+				)
 			)
-		)
+		Just True -> start file addunlockedmatcher
+		Just False -> startSmallOverridden file
 	case batchOption o of
 		Batch fmt
 			| updateOnly o ->
@@ -82,6 +100,29 @@ addSmall file = do
 	showNote "non-large file; adding content to git repository"
 	addFile file
 
+startSmallOverridden :: RawFilePath -> CommandStart
+startSmallOverridden file = starting "add" (ActionItemWorkTreeFile file) $
+	next $ addSmallOverridden file
+
+addSmallOverridden :: RawFilePath -> Annex Bool
+addSmallOverridden file = do
+	showNote "adding content to git repository"
+	let file' = fromRawFilePath file
+	s <- liftIO $ getFileStatus file'
+	if isSymbolicLink s
+		then addFile file 
+		else do
+			-- Can't use addFile because the clean filter will
+			-- honor annex.largefiles and it has been overridden.
+			-- Instead, hash the file and add to the index.
+			sha <- hashFile file'
+			let ty = if isExecutable (fileMode s)
+				then TreeExecutable
+				else TreeFile
+			Annex.Queue.addUpdateIndex =<<
+				inRepo (Git.UpdateIndex.stageFile sha ty file')
+			return True
+
 addFile :: RawFilePath -> Annex Bool
 addFile file = do
 	ps <- forceParams