First batch of refactoring.
Finished initial refactoring in database package.
A bunch on atoms.
More commenting and refactoring in atom package.
Work on the atom package.
Modifications to atom and kernel packages.
Collapsed two Atom statuses to one.
Started to update inference application.
Updated AtomManager interface.
Updates to AtomManager interface and AtomStatus.
More atom changes and app. reorganization.
Documented more of the database package.
Removed some unnecessary code.
Changed some database interfaces.
Updated Atom events.
Switched back to database as source of Atoms.
Started splitting up the AtomManager again.
Changed Atom statuses to subclasses.
Worked more on Atom class tree.
Added AtomEventFramework.