Smoldyn

- Fixed some very minor bugs and added several runtime commands.

- Small improvements to Libmoleculizer and a few minor bug fixes.

- Improved CMake build system and fixed a few minor bugs. Added rudimentary filament code.

- Added molecular drift relative to surface coordinates and settable precision
for numerical output. Improved simulation of molecules with excluded volume
so rebound is not to fixed distance but equals prior overlap. Also, changed
code from C to C++, changed build system from AutoTools to CMake, improved
internal error handling, and coordinated development with VCell team.

- Finished rule-based modeling with Libmoleculizer, added partial wildcard
support, and enabled excluded volume reactions with periodic boundaries.

- Fixed minor bugs and improved Ubuntu installation.