Fix critical bug in clean-up script

This release fixes a critical bug in the script that cleans up miscellaneous files generated by LaTeX when building to PDF.

As pointed out in this issue, the old regex could inadvertently delete files that happened to have partly similar filenames to the files the clean-up script was meant to remove... 😱 This is now fixed!

Bug fixes

• fixed critical bug in clean-up script

New functionality

• added functionality to control link highlighting with either coloured text or borders around hyperlinks directly from index.Rmd
• added ability to set width of the university logo on the title page from index.Rmd

Minor changes

• the abbreviations file is now an R Markdown instead of Tex file
• changed default to not include separate abstract page
• bibliography settings have been moved further up in index.Rmd