Consistent approach for whole-program tests

Consistent approach for whole-program tests

All tests that essentially execute one command-line program as the test
are now using CommandLineTestBase, which makes them much simpler, easier
to read, and a better source for copy-pasting new tests.  Move the
functionality of IntegrationTestFixture to a helper class that can be
used in any kind of test and not excluding other types of useful
fixtures from tests that need that functionality.

Tests that execute mdrun are not changed here to keep the scope limited.

Change-Id: Ic49593d6e27c48be43021e4fc9b1fcd685d43ffd