Fix Makefile dependency issue with files in vhdl/*

Fix Makefile dependency issue with files in vhdl/*

GHDL doesn't seem to have a way to specify the location of the object
file it writes, so right now they are all ending up in the root
directory. The Makefile rules did not reflect that, so make would
continually the files in fpga/*

Fix the rules to match what GHDL is doing.

Signed-off-by: Anton Blanchard <anton@linux.ibm.com>