cleaned up the dependecy scripts in the makefiles
fixed the bugs introduced by switching the periodic box to a matrix
Updated the ChangeLog, and Converted most of the SImInfo to use non-Isotropic boxes. wrapVector needs to be finished.
Most of the integrator and NVT seem to be working now.
bug fixes
Fixed a bug caused by my experimentation
final mods to try a fortran compiler
fixed some small things with simError.h
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Makefile fixes, directory re-org, autoconf fixes
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This commit was generated by cvs2svn to compensate for changes in r377, which included commits to RCS files with non-trunk default branches.