Removing finished items from TODO.
Have misc/analyze-source.pl check for C-style headers.
Enforcing naming conventions on adapter.h:
ArrayOfSequencesIterator -> array_of_sequences_iterator
DiskGeometry -> simdisk_geometry
RunsToBIDArrayAdaptor -> runs2bid_array_adaptor
RunsToBIDArrayAdaptor2 ->  runs2bid_array_adaptor2
TwoToOneDimArrayAdaptorBase -> two2one_dim_array_adapter_base
TwoToOneDimArrayColumnAdaptor -> two2one_dim_array_adapter_base
TwoToOneDimArrayRowAdaptor -> two2one_dim_array_row_adapter