Reorganize the directory layout

To allow subprojects other than math, the build system and directory
layout is changed: all math related code, tools and tests are under
the math directory now, new subprojects should be similarly self-
contained.

The top level Makefile design is still kept, but the subproject build
directories provide their own Dir.mk with the build rules for the
subproject. The user interface of config.mk is kept for now, in the
future subproject specific flags and make variables may be added for
finer grained control.