Bug 1254410 - Include app-specific configure files according to...

Bug 1254410 - Include app-specific configure files according to --enable-application/--enable-project. r=chmanchester

Because --enable-application is the current way to do things, transpose
it to configure.py, but since --enable-application=js doesn't make
sense, make it an alias of a new --enable-project option.

This only partially moves --enable-application out of old-configure.in
because there are a lot of other things intertwined with it.