Correct links in README.md

[danieldegroot2]

This PR changes the following:

• Corrects GitHub section link for 'building vc-deps dependencies'.
• Changes Doxygen link to GitHub repo link.
  (Alternatively, change to direct HTTPS link; .org HTTP link redirects to https://www.doxygen.nl/.)
• Changes William Brent Seales et al. (2016) link from HTTP link redirects to HTTPS to direct HTTPS link.
  (the share link for this page is also the direct link.)
• Trims redundant trailing spaces (also double ones)
• Removes 'the' from 'the Vesuvius Challenge' link display text, as it is not directly part of the name.