Minor refactoring of generate.sh

[oliverkwebb]

I hope to get the build infrastructure in a flexible enough state eventually so that the book can be compiled into different formats (mainly, PDF and single-page HMTL)

Changes Made:

• Remove significant whitespace in generate.sh
• Give generate.sh executable permissions
• Re-run generate.sh, pushing a few previous changes to the generated html
• sed command | sed command -> sed "command; command", unnecessary $ in shell math

P.S. Right now, the filenames for the chapters are being stored in a simple text file, and the titles for the chapters are being extracted using sed, if that file was a YAML file, which stored the filenames and titles in a list, and the templating could use it to reference the previous/next chapters (with pandoc's $for$). It would remove the need for most of the shell code here (at the cost of the file being harder to parse)