Make the AnnotationSet constructor take an array of indexes

Before, it took an array of objects and translated those to indexes
using the store. Literally every caller outside of the test suite got
an array of indexes from the linear model, translated those to objects,
then passed them into the AnnotationSet constructor which translated
them right back to indexes.

The previous behavior was kind of ridiculous on its face, but the
reason we found it is because Inez was investigating the performance
degradation when bolding a line and found that half of it was due
to the hundreds of ve.getHash() calls caused by this behavior.

Change-Id: I38df8ae9f6392849dacf477ea2f804283c964417
Merge "Make the AnnotationSet constructor take an array of indexes"