What steps will reproduce the problem?
Delete the last repository in the current repository (where it says: warning type in "yes please do as i say"). Then try running git annex webapp

What is the expected output? What do you see instead?
Webapp starts. git-annex: Not in a git repository.

What version of git-annex are you using? On what operating system?
4.20130417. Debian wheezy/testing

Please provide any additional information below.
See also ?git-annex: Not in a git repository. where the same error message occurs