Bug fixes:

- MMTK.NormalModes.Core.reduceToRange() didn't work correctly for
  VibrationalModes.
- MMTK.Subspace.RigidMotionSubspace could fail for some object collections.
- Various 64-bit issues.
- Crashes at termination of Python when running under Python 2.5.
- Molecule creation through MoleculeFactory didn't work.

Improvements:

- MMTK.PDB.PDBConfiguration accepts optional arguments for model and
  alternate code.
- The C modules are adapted to the new 64-bit features in Python 2.5.
- Installation on Linux makes CLAPACK code compile correctly with GCC 4.
- Improved handling of PDB residues with non-unique atom names.
- Trajectory files contain a netCDF attributes "Conventions" that identifies
  them as MMTK trajectories.