modified .gitignore

* allows .pdf because cache'd files are
  excluded
* excludes .Rprofile
updated .Rbuildignore

* a bunch of \.* files are excluded
* knitr cache'd chunks are excluded
* man-roxygen/ is excluded
rebuilt roxumentation

uses `system.file()` to access the full filepath to inst/final_project/final_paper/final_paper.pdf