E3-186: Combine configure/E3 and configure/modules

The two configure directories had a lot of overlapping code. configure/E3 is used to build and install require itself, while configure/modules is used to build other e3 modules.

This MR combines all of these configure files into a single configure/E3 directory. The require-specific rules are then placed in a new directory, configure/module (note the lack of an 's'), the same as how other e3 modules are structured. There is also some assorted cleanup.