Initial commit of the CMJCU documentation
Merge pull request #138 from kjmoore/cmjcu-docs

CMJCU documentation, many thanks @kjmoore
Ignore system dependencies.  Fixes #140
Add files.
CN - Changed -MD gcc flag to -MMD so that system files are excluded from dependency list. The pathnames to these files in the .d files were screwy, resulting in an error when 'make clean' was issued.