t3001, t7300: add testcase showcasing missed directory traversal

t3001, t7300: add testcase showcasing missed directory traversal

In the last commit, we added a testcase showing that the directory
traversal machinery sometimes traverses into directories unnecessarily.
Here we show that there are cases where it does the opposite: it does
not traverse into directories, despite those directories having
important files that need to be flagged.

Add a testcase showing that `git ls-files -o -i --directory` can omit
some of the files it should be listing, and another showing that `git
clean -fX` can fail to clean out some of the expected files.

Signed-off-by: Elijah Newren <newren@gmail.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>