Revert "Use superscript for citations"

This reverts commit 1808ead1cc987301691d49173493a2c16fa8fffd.
Fix cites in introduction
Reflect section swap in Thesis structure
Swap Summary and Related work chapters
Add talks to introduction
Reword paragraph about talks in the summary
Move cite back in introduction
work -> works grammar
Remove cite from Basic usage title
Remove cites from titles in 3pps
Fix cite and period orders