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.
Fixed bad regression data in tests/dtopo1 after checking the results agree with regression data at commit 3ff3c90.
changed depth to topo in topotools for clarity
changed bathy to topo for clarity
changed 'project' to 'interp' for clarity since it's really interpolation onto a grid not projection that is done for unstructured grids
Modified Topography class so that __init__ does not require path and read has several new arguments to allow specifying path, topo_type,  unstructured when calling the read method.
Fixed several bugs in Topography and perhaps fixed crop method, but not yet completely tested.  See RJL: comments for concerns
Fixed (?) Topography to set .X and .Y based on .x and .y if available.  Added test of cropping with plot.
Improved test_new_topotools.py by adding assertions and test of crop function
Merge pull request #90 from rjleveque/topotools_fix_xyz

Fixed some errors in new topotools.py