Revisions to NGramIndexer

- change u'mark singles' setting to u'mark_singles'
- update tests to reflect that revision
- remove :obj: from docs, since it made confusing cross-refs

(cherry picked from commit fc53a120f5574a10b08c923cb912bc8cf8fa07d8)
Adjust WorkflowManager's Part-Combination Handling

- fixes huge bug where not all part combos were included
- updated WorkflowManager's Integration EXPECTED_2 Value
- added new integration test where I did count everything by hand
- makes LilyPond easier

(cherry picked from commit 6aa5f1c0e524b5b3280938e403b4f21cd7754084)