Revise the internal workflow

[sfcheung]

Note

Many of the functions were initially developed to do simple tasks. Quick fixes were added as we encountered some special cases and the code became more and more difficult to maintain. They work for what they are designed for. It is just becoming more and more difficult to maintain them or to add new features.

We may need to inspect the code, especially the functions set_cfa_layout() and set_sem_layout(), and come up with a better workflow, with some common tasks factored out as internal helpers. The goal is not for adding new features, but to make the functions easier to maintain.