Changed Testing Structure

The patches introduced previously don't work very well with MCP's md5
system, so they have been replaced with a runtime patcher which operates
in a very similar way to the static BTH installer. The build script has
been updated to reflect this. Also did some maintenance on the build
script, such as *attempting* to use a standard format and adding
task-describing comments. Also corrected BaseTransformer's
implementation of appliesTo, as previously it did not match
Transformer's specification.