fully support core.symlinks=false in all relevant symlink handling code

Refactored annex link code into nice clean new library.

Audited and dealt with calls to createSymbolicLink.
Remaining calls are all safe, because:

Annex/Link.hs:  ( liftIO $ createSymbolicLink linktarget file
  only when core.symlinks=true
Assistant/WebApp/Configurators/Local.hs:                createSymbolicLink link link
  test if symlinks can be made
Command/Fix.hs: liftIO $ createSymbolicLink link file
  command only works in indirect mode
Command/FromKey.hs:     liftIO $ createSymbolicLink link file
  command only works in indirect mode
Command/Indirect.hs:                    liftIO $ createSymbolicLink l f
  refuses to run if core.symlinks=false
Init.hs:                createSymbolicLink f f2
  test if symlinks can be made
Remote/Directory.hs:    go [file] = catchBoolIO $ createSymbolicLink file f >> return True
  fast key linking; catches failure to make symlink and falls back to copy
Remote/Git.hs:          liftIO $ catchBoolIO $ createSymbolicLink loc file >> return True
  ditto
Upgrade/V1.hs:                          liftIO $ createSymbolicLink link f
  v1 repos could not be on a filesystem w/o symlinks

Audited and dealt with calls to readSymbolicLink.
Remaining calls are all safe, because:

Annex/Link.hs:		( liftIO $ catchMaybeIO $ readSymbolicLink file
  only when core.symlinks=true
Assistant/Threads/Watcher.hs:		ifM ((==) (Just link) <$> liftIO (catchMaybeIO $ readSymbolicLink file))
  code that fixes real symlinks when inotify sees them
  It's ok to not fix psdueo-symlinks.
Assistant/Threads/Watcher.hs:		mlink <- liftIO (catchMaybeIO $ readSymbolicLink file)
  ditto
Command/Fix.hs:	stopUnless ((/=) (Just link) <$> liftIO (catchMaybeIO $ readSymbolicLink file)) $ do
  command only works in indirect mode
Upgrade/V1.hs:	getsymlink = takeFileName <$> readSymbolicLink file
  v1 repos could not be on a filesystem w/o symlinks

Audited and dealt with calls to isSymbolicLink.
(Typically used with getSymbolicLinkStatus, but that is just used because
getFileStatus is not as robust; it also works on pseudolinks.)
Remaining calls are all safe, because:

Assistant/Threads/SanityChecker.hs:                             | isSymbolicLink s -> addsymlink file ms
  only handles staging of symlinks that were somehow not staged
  (might need to be updated to support pseudolinks, but this is
  only a belt-and-suspenders check anyway, and I've never seen the code run)
Command/Add.hs:         if isSymbolicLink s || not (isRegularFile s)
  avoids adding symlinks to the annex, so not relevant
Command/Indirect.hs:                            | isSymbolicLink s -> void $ flip whenAnnexed f $
  only allowed on systems that support symlinks
Command/Indirect.hs:            whenM (liftIO $ not . isSymbolicLink <$> getSymbolicLinkStatus f) $ do
  ditto
Seek.hs:notSymlink f = liftIO $ not . isSymbolicLink <$> getSymbolicLinkStatus f
  used to find unlocked files, only relevant in indirect mode
Utility/FSEvents.hs:                    | Files.isSymbolicLink s = runhook addSymlinkHook $ Just s
Utility/FSEvents.hs:                                            | Files.isSymbolicLink s ->
Utility/INotify.hs:                             | Files.isSymbolicLink s ->
Utility/INotify.hs:                     checkfiletype Files.isSymbolicLink addSymlinkHook f
Utility/Kqueue.hs:              | Files.isSymbolicLink s = callhook addSymlinkHook (Just s) change
  all above are lower-level, not relevant

Audited and dealt with calls to isSymLink.
Remaining calls are all safe, because:

Annex/Direct.hs:			| isSymLink (getmode item) =
  This is looking at git diff-tree objects, not files on disk
Command/Unused.hs:		| isSymLink (LsTree.mode l) = do
  This is looking at git ls-tree, not file on disk
Utility/FileMode.hs:isSymLink :: FileMode -> Bool
Utility/FileMode.hs:isSymLink = checkMode symbolicLinkMode
  low-level

Done!!

Command/Add.hs

@@ -12,22 +12,20 @@ module Command.Add where
 import Common.Annex
 import Annex.Exception
 import Command
-import qualified Annex
-import qualified Annex.Queue
 import Types.KeySource
 import Backend
 import Logs.Location
 import Annex.Content
 import Annex.Content.Direct
 import Annex.Perms
+import Annex.Link
+import qualified Annex
+import qualified Annex.Queue
 #ifndef WITH_ANDROID
 import Utility.Touch
 #endif
 import Utility.FileMode
 import Config
-import qualified Git.HashObject
-import qualified Git.UpdateIndex
-import Git.Types
 import Utility.InodeCache
 
 def :: [Command]
@@ -159,7 +157,7 @@ undo file key e = do
 link :: FilePath -> Key -> Bool -> Annex String
 link file key hascontent = handle (undo file key) $ do
 	l <- calcGitLink file key
-	liftIO $ createSymbolicLink l file
+	makeAnnexLink l file
 
 #ifndef WITH_ANDROID
 	when hascontent $ do
@@ -173,23 +171,35 @@ link file key hascontent = handle (undo file key) $ do
 	return l
 
 {- Note: Several other commands call this, and expect it to 
- - create the symlink and add it. -}
+ - create the link and add it.
+ - 
+ - In direct mode, when we have the content of the file, it's left as-is,
+ - and we just stage a symlink to git.
+ - 
+ - Otherwise, as long as the filesystem supports symlinks, we use
+ - git add, rather than directly staging the symlink to git.
+ - Using git add is best because it allows the queuing to work
+ - and is faster (staging the symlink runs hash-object commands each time).
+ - Also, using git add allows it to skip gitignored files, unless forced
+ - to include them.
+ -}
 cleanup :: FilePath -> Key -> Bool -> CommandCleanup
 cleanup file key hascontent = do
 	when hascontent $
 		logStatus key InfoPresent
 	ifM (isDirect <&&> pure hascontent)
-		( do
-			l <- calcGitLink file key
-			sha <- inRepo $ Git.HashObject.hashObject BlobObject l
-			Annex.Queue.addUpdateIndex =<<
-				inRepo (Git.UpdateIndex.stageSymlink file sha)
-		, do
-			_ <- link file key hascontent
-			params <- ifM (Annex.getState Annex.force)
-				( return [Param "-f"]
-				, return []
-				)
-			Annex.Queue.addCommand "add" (params++[Param "--"]) [file]
+		( stageSymlink file =<< hashSymlink =<< calcGitLink file key
+		, ifM (coreSymlinks <$> Annex.getGitConfig)
+			( do
+				_ <- link file key hascontent
+				params <- ifM (Annex.getState Annex.force)
+					( return [Param "-f"]
+					, return []
+					)
+				Annex.Queue.addCommand "add" (params++[Param "--"]) [file]
+			, do
+				l <- link file key hascontent
+				addAnnexLink l file
+			)
 		)
 	return True