Don't use the the mdBook link preprocessor
#499
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This removes some pointless magic from the mdBook compilation and makes the links work consistently whether viewing the compiled book or the markdown sources.
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Closes #497
Instead of having mdBook convert
README.mdfiles in the docs intoindex.mdfiles, we just name the indexs properly. This keep linking consistent in both the markdown and rendered HTML, makes it easier to understand what's going on, and make sit clearer to someone looking at the docs via the github UI that it's not the convenient place to browse the documentation :)I also link the manual from the README.md in the docs dir.
Tests added for any new codeEntry added to UNRELEASED.md for any new functionality