Make sample_tri_multi_calculation depend on NDEBUG_DP, not NDEBUG.

Not doing this causes crashes if we #include "alignment-sums"
under #undef NDEBUG in a calling file, but -DNDEBUG in the
file that implements sample_tri_multi_calculation.
Fix calc_root_probability_unaligned( ).
Fix subA_index_aligned to avoid SEGFAULTs.
Simplify heated_lieklihood_unaligned_root( ).
Don't use cached likelihood values for Pr_unaligned( )!

This avoids using (a) using cached values (b) writing to
cached values.
Suppress an unused-variable warning.
Allow empty columns in subA index.
Stop removing empty columns from the subA index.
Create functions to monitor subA indices.
Fix unused-variable warning.
Fix Pr_unaligned_root( ).
Remove commented-out caching code.
Move comment.
Add sanity check.
Add more detailed comment.
Move #include "substitution.H" to the beginning of the file.
Allow reverting to the old behavior.
Start using Pr_unaligned( ) to evaluate SPR attachment locations.
Allow NDEBUG.