Delete garbage subdir.mk files

PHYS-24 #time 25m
Generate .d files properly for cleaning

PHYS-24 #time 10m
Get rid of objects.mk. Remove old subdir references
Move all building into single makefile

PHYS-24 #time 25m

I think?? this is working, but the output is totally screwy right now.
From looking at the output, I would expect everything to be completely
broken, but somehow it works...
Continue removing bits from makefile

PHYS-24 #time 25m
Merge branch 'nightly' into PHYS-25
Verify that unit tests work with new makefile

PHYS-25 #time 15m
Add test for updating dimensions of Simulation

PHYS-25 #time 10m