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+If a submodule isn't toplevel, git-annex breaks
+
+**What steps will reproduce the problem?**
+
+Make two non-empty repositories:
+
+    mkdir submod
+    cd submod
+    git init
+    touch README && git add README
+    git commit -a -m "first import of submodule"
+    cd ..
+
+    mkdir test
+    cd test
+    git init
+    touch README && git add README
+    git commit -a -m "first import of master"
+
+Add first repository as a non-toplevel submodule:
+
+    git submodule add ../submod lib/submod
+    
+Setup git-annex for the submodule inside the other repository:
+
+    cd lib/submod
+    git annex init
+
+**What is the expected output? What do you see instead?**
+
+Expected:
+
+    init  ok
+    (Recording state in git...)
+
+Got:
+
+    init  fatal: Could not switch to '../../../../lib': No such file or directory
+    git-annex: git config [Param "annex.uuid",Param "55D974D1-73E8-489E-B454-03D164664C82"] failed
+
+
+**What version of git-annex are you using? On what operating system?**
+
+3.20121011 compiled from git on Mac OS X 10.8
+
+
+**Please provide any additional information below.**
+
+* git-annex read the path from the "worktree" variable in the git config.
+* The git config for a submodule is storen in the main repository, e.g. "../../.git/modules/lib/submod/config"
+* The path in that config is relative to the config file: "worktree = ../../../../lib/submod"
+* Git-annex expect the path to be relative to the current directory, which is why it fails.
+
+
+