Rename virtualbox VMs

- ls.db -> vm-ship (intented to contain only dockerized components)
- ls.ext -> vm-ext (will move into vm-ship when it's dockerized)
- ls.test -> vm-test
- ls.devops -> vm-devops
- All hostnames are now the same as VM names
- Also removed quite a bit of trailing whitespace (sorry for the noise)
- Gliffy diagram not updated to reflect name changes
Update to latest available koha-common package