Travis: general updates to the Travis scripts

* exclude pull-requests from updating dox fixes #140
* eliminate `sh` from the callout to scripts so env variables are passed in
* used env variables from travis scripts on sub-scripts instead of passing parameters around
* eliminate unnecessary if's from travis.yml and move them to sub-scripts
* use $CC instead of $TOOLSET as they were exactly the same and $CC is already set up by the environment
Merge pull request #141 from broadinstitute/mc_website_dox_update

Travis: general updates to the Travis scripts