7340: Fix bundle clean issue r=deivid-rodriguez a=deivid-rodriguez

### What was the end-user problem that led to this PR?

The problem was that `bundle clean` is crashing under some conditions.

### What was your diagnosis of the problem?

My diagnosis was that sometimes (when the bundle includes git sourced gems with extensions), it assumes that some paths exist, but they don't.

### What is your fix for the problem, implemented in this PR?

My fix is to ignore those paths.

### Why did you choose this fix out of the possible options?

I chose this fix because it fixes the issue.

Fixes #7338.

Co-authored-by: David Rodríguez <deivid.rodriguez@riseup.net>
(cherry picked from commit b007fde67c77c1f15f13b97eda186644c2a2be04)

https://github.com/bundler/bundler/commit/3766053507