org for separate compilation + more

[yakra]

• Commits thru eb1db56 on Dec. 22 work on organizing the Makefile and C++ code for separate compilation, per C++ code organization for separate compilation #378. It may not be our final destination, but it's a step ahead of what's in master right now.
• Closemove colocation list sorting into WaypointQuadtree::sort yakra/DataProcessing#89. Both C++ and Python.
• Comment out WaypointQuadtree.tmg. It may have helped make sure I was on the right track when siteupdate.cpp was first crawling out of the muck, but has long outlived its usefulness. It may take 0.1s on Ubuntu or FreeBSD, but wastes 10-20s on CentOS depending on which machine.
• CloseWaypointQuadtree::points -- forward_list -> list #327.

[jteresco]

Meant to bring this in before tonight's update, but then realized I hadn't when the update was about 80% done.

[yakra]

Nothing Earth-shattering on the Python side. We just save 0.7s Sorting colocated point lists.