Merge pull request #803 from RosettaCommons/rhiju/remove_placeholder_residue_types
*Removing last exponential blow up in ResidueTypeSet*
Reduces setup time for FA_STANDARD residue type set from 1.1 seconds to 0.40 seconds on my machine. Allows activation of all available patches (e.g., ones currently under command-line control; see https://github.com/RosettaCommons/main/pull/756) and new 'metapatches' (see https://github.com/RosettaCommons/main/pull/844) without blowup of setup time & memory.
All Rosetta modes now compatible with refactored ResidueTypeSet and accessor function, including adducts; and lots of code cleanup.
Only tests that change are integration tests:
+ _fiber_diffraction_fad_, _fold_and_dock_ (cosmetic, tracer debug now registers instantiation of D-AA residue types)
+ _inverse_rotamer_remodel_ (broken before at SequenceMapping)
+ _mm_params_ now loops through D-AA residue types, though does not actually check mm parameters for those-- could do so.
+ _dna_interface_design_ changes at late stage; tracked down to a difference in a random number in a SmallMin move -- all the 'physics' of the simulation, including number of adduct rotamers used in design, appears preserved up to that point and later -- may be a sign of a memory leak.
+ _number_of_residuetypes_ now does not report on total number of residue types, which is no longer computed, but on the components of ResidueTypeSet, e.g.:
```
apps.pilot.doug.number_of_residuetypes: The FA_STANDARD ResidueTypeSet contains 364 base ResidueTypes, 71 Patches, and 0 custom ResidueTypes
```
instead of
```
apps.pilot.doug.number_of_residuetypes: The FA_STANDARD ResidueTypeSet contains 42632 ResidueTypes
```