Create ExclusionBlocks
Moves exclusion modification functionality to the topology module, as
it is not functionality unique to preproceessing.
Renamed t_block2 to ExclusionBlocks, since that is the only use we
currently have for it, and any new use should be using std::vectors
anyway.
Used an assertion for an error that can only triggered by coding bug.
This fixes the broken mdrun-only configuration, found in post-submit
Jenkins testing.
Fixes #2690
Change-Id: I2d0916bc3be1c20d44e1c4e07b53488f2b6971a3