deps: Track `Bender.lock` file

[fischeti]

A new AXI patch release broke the Gitlab-CI, and bender automatically incremented the AXI version since we don't have a Bender.lock file tracked that locks the IP versions used. To prevent similar problems in the future and to give users of the snitch cluster a clear set of dependency versions I suggest to track the Bender.lock file.

Apart from that, this PR does also:

• Bump the AXI version
• Remove the Bender.local file, which is redundant now and is anyway more of a hack.
• Fixes some minor issues for VCS simulation that were somehow triggered only after updating the dependencies.

TODO:

• [ ] Use new AXI release (0.39.5) once it is published

[colluca]

Merging this to unblock development on other PRs. We can later bump the AXI version.