[master]

- Add some new files
	new file:   HybridSimulation/.gitignore
	modified:   HybridSimulation/HybridSimulation.sdf
	modified:   HybridSimulation/HybridSimulation.v11.suo
	new file:   HybridSimulation/HybridSimulation/.gitignore
	new file:   HybridSimulation/prework.bat
[master]

- Temporary
	renamed:    HybridSimulation/README.md -> README.md
[master]

- Fixed some bugs
	new file:   ../.gitmodules
	modified:   .gitignore
	deleted:    HybridSimulation.sdf
	modified:   HybridSimulation/.gitignore
	modified:   Makefile
	new file:   doc/Refs/Eigen.html
	new file:   include/Eigen
	modified:   prework.bat
	modified:   tools/cleaner.py
	modified:   tools/makefile.py
	modified:   tools/makelink.py
	deleted:    tools/mklnks.py
	new file:   tools/module.pyc
	new file:   ../Toolbox