Store Sequence sequence location in a shared_ptr class

This is a large (176 changes) patch, that moved most of the
information needed to store a sequence location into a class called
SeqSpan, which is designed to be solely managed as a shared_ptr.

This is one step in converting sequence annotations into being tree
of subsequences.

The hope is that the Sequence class doesn't store very much and
is mostly responsible for managing various collections of shared_ptrs
(which are a bit annoying to work with as local variables).

This also updated GlSequence to be a subclass of Sequence
(instead of holding a reference a shared_ptr<Sequence>)

Those changes required updating many random little function
calls.