refactoring!: remove branch-base references

BREAKING CHANGE: move from branch-based references in the tuple to
the array-based. Also add a logical ID to all relational nodes and
keep it in all its child tuples.

Now, our reference coordination system in a tuple looks like:
- parent relational node logical ID (we don't know actual position
  in the nodes list, so use "secondary index")
- target - i.e. a position of the reffered node in the relational
  node's children list
- posirtion in the reffered relational child node output tuple