[BUG] Failure in case a file added to git does not exist

[Martoon-00]

Description

We rely on git ls-files to get the list of files to check, but some of the files could be removed after being added to git, this should be handled.

To Reproduce

1. touch doc.md
2. git add doc.md
3. rm doc.md
4. xrefcheck

This results in xrefcheck run failing.

Expected behavior

All tracked md files except for doc.md are checked.

I suppose we should treat doc.md as if it never existed, but it's discussible.

Environment

• Ubuntu
• Recent master (50e4e3b)