…d files

The issue happens only with the latest release 1.5.0.

* When the biome output is empty, the contents of the input file to format are used unchanged instead.
* When biome outputs warnings / errors to stderr, these are now logged. This includes warnings such as
  when biome ignores files. Otherwise people would be left wondering why certain files are not formatted.

I also added a test for this scenarion.

On another note, I mostly use Maven, so I always need to look up how to run tests via Gradle. I added
a short section to CONTRIBUTING.md that gives some example commands how to run tests for this project,
especially how to run only a single test.