Take a look at the Demand Peripherals Baseboard4. It uses standard USB-serial for code download instead of JTAG and the development is even Makefile based. Hope this helps ....

If considering file-system as database, then consider application as database. The Run-Time-Access package makes your program's internal data structures appear as tables in a PostgreSQL DB. RTA is to a DB as /proc is to a file-system.
http://www.runtimeaccess.com/