minor tweaking to the assembler documentation/error checks
clean up warning comments
Change name of SVCandidateData to reflect it's coverage of potentially many candidates
give aligners a const invokation
finished 2 large (linked) refactorings:

1. Separate out the previous SVCandidateData into one class continaing data spanning muliple SVCandidates (SVCandidateSetData) and a one which is specific the current SVCandidate (used for assembly data)
2. Compartmentalize the entire assembly and alignment candidate refinement process to a new class: SVCandidateAssemblyRefiner