clean: preserve nested git worktree in subdirectories

remove_dir_recursively() has a check to avoid removing the directory it
was asked to remove without recursing into it and report success when the
directory is the top level of a working tree of a nested git repository,
to protect such a repository from "clean -f" (without double -f). If a
working tree of a nested git repository is in a subdirectory of a toplevel
project, however, this protection did not apply by mistake; we forgot to
pass the REMOVE_DIR_KEEP_NESTED_GIT down to the recursive removal
codepath.

This requires us to also teach the higher level not to remove the
directory it is asked to remove, when the recursed invocation did not
remove the directory it was asked to remove due to a nested git
repository, as it is not an error to leave the parent directories of such
a nested repository.

Signed-off-by: Junio C Hamano <gitster@pobox.com>

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