Support compiler modules

The current API does not make the use of compiler level modules easy (all the flags need to be passed via `defs`). It would be nice to have first class module support which set at least `rename_prefix_namespace`, `module_wrapper` and `module`. Additionally, automatically counting the number of files in each module and hiding that complexity from the user would be ideal.

Start by examining how compiler flags are currently passed through defs. Trace how rename_prefix_namespace, module_wrapper, and module reach the compiler, then determine how module file counts could be derived and exposed. Done means users have first-class module support without manually supplying these flags or managing the file-count complexity.

Written by the indexing model from the issue text.