project-workflow chapter needs editing

[skaltman]

• Confusing when to make the makefile
• Embed example Makefile example in Make walkthrough
• Explain why you can edit files in RStudio that have nothing to do with R (like .bash_profile)
• explain how to use a GitHub template repo instead of using the RStudio project (also need to make a GitHub template repo)
• Add a better introduction for context
• remove references to the birds files / require the reader to take a look at the project-example repo
• Explain how to use use_git to setup GitHub repository