Stubs and Build System

A number of changes were made in order to simplify the build system and compartmentalize associated code.

* the repo directory structure now looks like the following

```
/
  cli/
  doc/
  src/
  stubs/
  tests/
   ...
```

* the top-level CMakeLists has been moved to the root directory
* each subdirectory has an associated CMakeLists file specifically for its constituents
* test module directory structure has been flattened
* stubs are now compiled into a separate library, cyclusstubs
* stub tests are incorporated into the unit test driver
* model test files are now installed to share rather cyclus/include
* CyclusUnitTestDriver is renamed cyclus_unit_tests (@zwelchWI, this will likely affect you)

closes #606 and closes #602 and closes #559