Internal refactor of parser pipeline

[charlespwd]

• Renames (objective make the flow more obvious)
  • cst.ts -> stage-1-cst.ts,
  • ast.ts -> stage-2-ast.ts
• Add explainer comments at head of both files
• Make the CST responsible for setting .source on the nodes
  • Cleans up wiring of source argument in all the methods in stage-2-ast.ts