init: Fix bugs in submodule .git symlink fixup, that occurred when initializing in a subdirectory of a submodule and a submodule of a submodule.

Annex/Fixup.hs

@@ -90,8 +90,9 @@ fixupSubmodule r@(Repo { location = l@(Local { worktree = Just w, gitdir = d })
   where
 	dotgit = w </> ".git"
 	replacedotgit = whenM (doesFileExist dotgit) $ do
+		linktarget <- relPathDirToFile w d
 		nukeFile dotgit
-		createSymbolicLink (w </> d) dotgit
+		createSymbolicLink linktarget dotgit
 		maybe (error "unset core.worktree failed") (\_ -> return ())
 			=<< Git.Config.unset "core.worktree" r
 fixupSubmodule r _ = return r

debian/changelog

@@ -19,6 +19,9 @@ git-annex (6.20160127) UNRELEASED; urgency=medium
     expression.
   * Brought back the dbus and xmpp build flags, so build from source can be
     done without C libraries that may be hard to install.
+  * init: Fix bugs in submodule .git symlink fixup, that occurred when
+    initializing in a subdirectory of a submodule and a submodule of a
+    submodule.
 
  -- Joey Hess <id@joeyh.name>  Thu, 28 Jan 2016 13:53:09 -0400
 

doc/bugs/use_of_annex_in_submodule_replaces_.git_with_incorrect_symlink.mdwn

@@ -45,3 +45,5 @@ upgrade supported from repository versions: 0 1 2 4 5
 """]]
 
 [[!meta author=yoh]]
+
+> [[fixed|done]]

doc/bugs/use_of_annex_in_submodule_replaces_.git_with_incorrect_symlink/comment_3_7781f13c070a3c79f5b63d3172b0280a._comment

@@ -0,0 +1,8 @@
+[[!comment format=mdwn
+ username="joey"
+ subject="""comment 3"""
+ date="2016-02-08T18:27:32Z"
+ content="""
+Yeah, it was running git annex init in the subdir of the submodule that
+triggered the bug. Easy fix, also fixes init in submodules of submodules.
+"""]]