In preparation for #1454

Among other things, in order to render private and relative aa mutations we need to group them similarly to how absolute aa mutations are grouped. This involves finding adjacent mutations and nuc context for these mutations.

Sadly, the code for grouping is quite complex and is not immediately reusable (it combines aa mutation search and grouping at the same time), so let's do some refactoring.

Let's start from factoring away structs and functions that will be unchanged, to clear up some space for the action, to minimize diffs  and to reduce scrolling.

Rather than carrying the 2 vecs for qry and ref sequences, lets group them into a class with meaningful methods. This prevents position lookup code from spreading everywhere, and removes extra param to pass into functions.

Let's make the free functions checking for certain conditions at certain positions into class methods.

These functions are useful for all kinds of mutation structs, so let's move some into the `AbstractMutation` trait. Turns out that most of these functions can have neat default implementations just from existing trait methods.

This is a nuc version of 5ee7936