fix handling of sub modules in git rely on ls-files --recurse-submodules, there since end of 2016

Summary: before this fix, submodules lead to duplicate files in the file tree for a project

Test Plan:
test e.g.

https://github.com/christoph-cullmann/cullmann.io

without patch: duplicated files, missing sub-modules

with patch: no duplicates + sub-module files are there

Subscribers: kwrite-devel

Tags: Kate

Differential Revision: https://phabricator.kde.org/D20343