Gonk, Android, and the generic cross-compilation setup all were using a
different yet similar way to prefix the toolchain. The latter was even
wrong, since the target and target alias usually don't match actual
toolchain prefixes (which don't include the machine part of the target).
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.
