Changing doc/manual/.gitignore to ignore *.dox~ auxiliary files.
Minor change to Simulation.h, editing documentation.

Conflicts:

	src/mcMd/simulation/Simulation.h
Small changes to user-modifiable makefiles.
Merge branch 'devel' of github.com:/dmorse/simpatico into devel
Editing of patterns.mk files.
Updated/edited doc/notes/util/OptionalParam
Editing doc/notes/util/OptionalParam
Modifying Util::Label to allow for optional labels.
Modifying Util::Begin to use a Label object. Add Label::clear().
Reversing commit of .ioUtil.h.swp
Adding *.swp to simpatico/.gitignore
Putting #ifdef INTER_BOND blocks in ddMd code.
New diagnostics added in DdMd and updated with upstream master branch