Removed R/ prefix from roxygenate dependencies

This is a maintenance change. Roxygenate dependencies were prefixed by 'R/'. This is unnecessary and can interfere with Roxygenate's collate process. Only needed when making documentation for the project so shouldn't effect end users. Tested it with roxygen2-3.0.0. Don't know if it breaks backwards compatibility with earlier versions of roxygen2.

Ran `source('roxygenate.R')` to rebuild project man pages. Removed some leading tabs in man pages. This looks to be how the newest version of roxygen2 works. Tried `Rd2roxygen::rab('.', build = F)` to see if that would bring documentation back to original state but no luck.

Newest version of roxygen2 also changes the order in Collate slightly. Before files that did not have dependencies were listed alphabetically. Now it is reverse alphabetical.

These are minor issues and I think should just be merged into the project.