Going forward cbin/.cbin will only be used if necessary and not by
default. This removes a step for most tools when used and better
aligns with the new auto_repairs and auto_setup scripts.
* Script work is brought into better focus
* New layout will be used to better package the python scripts
* No hidden folders (they will be hidden at build time)
* All building should be done under setup/
* Avoids ambiguous .bin/.cbin folders at root of project
