Provide a more carefully filtered environment for subprocesses.

• More rigor in environment preparation for subprocesses: Add gmxapi.runtime.filtered_mpi_environ() and use by default for gmxapi.commandline_operation() (including solvate in test fixtures).
• Remove the env override in the test fixtures in conftest.py.
• Update documentation and do some linting.

Ref #4421 (closed), #4423 (closed), #4736 (closed)

Closes #4736 (closed)

See also https://gromacs.bioexcel.eu/t/gmxapi-runtimeerror-solvate-failed-in-spc-water-box-testing-fixture/6097