Initialize default index groups for C++ tools

If an index file is not explicitly provided, initialize default
index groups using the old analyse() method for the new C++ tools.
This is better than nothing, and keeps the default groups in sync.

Also some clean-up for related code in
TrajectoryAnalysisCommandLineRunner.

Temporary fix for #921.

Change-Id: I4f9d2586a0446302ce0a2d9326d2fd4c85b02ef0