cmdlinerunner.cpp: use ICommandLineOptionsModule

cmdlinerunner.cpp: use ICommandLineOptionsModule

Make TrajectoryAnalysisCommandLineRunner a subclass of
ICommandLineOptionsModule for unification reasons. Resolve duplications
issues with run/writeHelp.
This should ease implementing of Python based trajectory tools later,
along with more refactoring and generalizations.

IOptionsContainer interface was extended with addGroup and addManager
methods from Options class, thus untying runner from Options itself.

Former support for batches was removed in favor of upcoming
implementation.