Fixed some errors in new topotools.py

write function wrote points in wrong order (should start at NW corner),
Z was flipped relative to Y, so plots upside down,
needed to fix read for topo_type==1 to flip Z,
added topo3writer.
Note that Z now has same dimensions as X,Y and indexed same as X,Y.
Y and Z are both flipped updown relative to what was used in 5.1.0 version.

Also added some tests in src/python/geoclaw/tests/test_new_topotools.py

@mandli, please check that I didn't mess something up, particularly if you had tests that seemed to be working.