t5403.1 and adding a file that belongs to a submodule

A part of t5403.1 is like this

touch a b; git commit -am1
git clone ./. clone2
GIT_DIR=clone2/.git git add clone2/b

The last command troubles me because clone2/.git is valid, I don't
think it should add "clone2/b" to clone2/.git/index. This is likely
due to common prefix optimization in read_directory, where it skips
checking .git at the first level (clone2). If we turn that command to
"git add a clone2/b" (common prefix would be ""), the second argument
is silently dropped (seems like a bug to me). Should t5403.1 be
rewritten to avoid that construct?
-- 
Duy