rework copy_git_files() to use a git clone

rework copy_git_files() to use a git clone

Using a git clone allows to solve some problems:
    - It allows to copy git submodules without having to fallback to
      --use-git-files=no since git-ls-files doesn't recurse submodules
    - It allows build systems that rely on git describe or similar to
      tag the build: this is more important when projects use
      git modules and they want to tag the git revision of each
      submodule.
    - It uses less disk space when using output as directory since
      when passing a local directory git will use hard links

Some additional handling for files that were modified (or added with
git -A) was put in place to allow tests to be performed before
committing.

In addition the call to git ls-files was fixed in the following cases:
    - When mkosi is called with -C option: it was calling ls-files inside
      the caller directory, not inside the src dir.
    - When mkosi is called with --git-files=others and .gitignore
      doesn't contain an entry for '.mkosi-*': it would try to copy the
      temporary directory we created and fail