Output time for stress autocorrelation.
Added file doc/notes/makefiles
Added IntraStructureFactorGrid class
Removed spurious debug output statement
Working on user manual *.dox files (small corrections).
Merge pull request #13 from jglaser/intra_sq_grid

IntraStructureFactorGrid
Fixing SystemDiagnostic fatory and editing param file documentation.
Changes to ddMd and ddMd examples, working on dihedrals.
Adding separate potential energies to output of OutputEnergy.
Changes to ddMd tests to accomodate angles and dihedrals.

Minor changes to Exchanger (exchangeAtoms method made private) and
GroupStorage (changes in function documentation).
Editing ddMd code, added Setable nTotal in GroupSTorage, changing ExchangerForceTest.
Continuing debuggin and testing of ddMd dihedrals.
Fixed bug in DdMd::DihedralPotentialImp.h.

Energy is now conserved in DdMd with dihedrals.
Editing ddMd/TODO file.
Added MultiHarmonicDihedral to DdMd::DihedralFactory.cpp_r.
Add dihedral N=32 example for mdSim.
Flattened examples/ directory structure.
Small changes to documentation.
Merge branch 'master' of github.com:medapuram/simpatico

Conflicts:
	src/mcMd/diagnostics/mcSystem/McStressAutoCorr.cpp
Merge branch 'master' of git://github.com/dmorse/simpatico