Corrected unmigrated file links

Links were broken in combinations of many different ways:
 - Referencing arts.uwaterloo.ca
 - Referencing ctnserv
 - Using `?q=system/files`
 - Using `f/...`
 - Using `[inline:...]` syntax
 - Using `+` instead of `%20` in URLs
 - Line breaks at 80 chars

Fixed as many of these file link problems as I could find. Some different link issues will be deferred to a later commit.

@tcstewar Changed a broken link to a paper on terrystewart.ca
@studywolf Changed a broken link in your NOCH thesis in your [people's page](http://compneuro.uwaterloo.ca/people/travis-dewolf.html)
@drasmuss Changed a broken download link for your [RPM demo](http://compneuro.uwaterloo.ca/research/cognition/demo.html)