Fixes a lingering sobek.ext bug.
Moves Cython source files to proper directories.

For maximum Cython compatibility (more specifically, so that Cython
modules can use extension types in other Cython modules), we need to
allow the Cython source to "live" at the module scope it wants to be
defined. Thus, things like sobek.glm should live at "sobek/glm.pyx", so
forth and so on. This patch begins that migration process.
Updates setup.py/.gitignore for Cython changes.

Updates setup and ignore files to follow the Cython rearrangement.