Reorgainizig the repository to use pyproject.toml

[Iximiel]

I did a few things:

• I migrated to a pure pyproject.toml for package info, but it still uses setuptools for installation
  • If you are familiar with tox, I propose no changes, otherwise I would suggest to migrate from setuptools+tox to hatch for building the package and organizing the tests, since it is more flexible than tox on setting up things/setting up the wheels for distribution and so on
• Every setting now is in the pyproject.toml for compactness and ease of navigation
• I removed one of the two testHeader tests since they were 1:1 identical, is that ok? It is maybe better to invert the file in which I have deleted on of the two?
• I changed how the code is organized, moving the package to src and the tests to tests, so that the base dir is the "tools, examples and maintenance" directory and src acts as the sink for the code to be distributed
• Now the coverage is more accurate: it does not says 100% coverage for the tests and 0% for PlumedToHTML but returns the actual coverage for the package
• I added a few extra tools to tox t
  • DO not run tox as now but tox -e tests because you will run the extra checks and the extra checks do not pass
  • ruff check simply suggest good practices and suggest to remove things like unused imports (and potential bugs)
  • ruff format formats
  • I did not apply the formatting and the suggestion from ruff with this PR, those will be useful for maintenance, but those are not the point here, and they will be in a next PR
• I add some extra tags and classifiers for pypi, do you like them?