Standardize handling of environment variables, java properties and so on between `test`,`run`, `script` (maybe others?) - and then document it properly

[oyvindberg]

          I'd like a follow-up task where we standardize handling of environment variables, java properties and so on between `test`,`run`, `script` (maybe others?) - and then document it properly

Originally posted by @oyvindberg in #394 (comment)