Fixed some hyperlinks
Updating parameter documentation
Updating parameter documentation
new --coverageExclude to trim files from the coverage reports
Merge pull request #39 from dmitris/master

fixed miscellaneous bad links
Merge pull request #37 from drewfish/coverage-exclude

new --coverageExclude to trim files from the coverage reports
Merge pull request #32 from klamping/master

Fixed some of the incorrect hyperlinks listed in Issue #30
more broken links fixed, broken images and TODOs are commented out