Expand clean-e2e Makefile target

[sirpaleet]

User Story

As a developer I would like to use flags to clean up the VM/local run of e2e scripts for easier local development.

Detailed Description

Expand on clean-e2e Makefile target, by adding flags so that the cleanup process described in README happens properly through the Makefile. Update README.

Anything else you would like to add:
Some previous discussion happened here: #2642

/kind feature

[Rozzii]

/triage accepted