Prep for new semester / general book updates

[aerenchyma]

All updates in this PR are things that are not specific to a class:

• Arranging assignments in a sub-folder so they can be used by a given course or someone using the book, but don't appear in the public book (we could change this, but it seems like it might get confusing ultimately, especially if someone wanted to refer to the public book for their own course that doesn't use the Runestone grading)

• Reorganizing exercises vs extra exercises so they increase in difficulty, as previously discussed

• A few exercise clarity edits; I removed exercises that I noticed were not working or were confusing in class or that needed more concept edits, and improved various phrasing in some of the extra exercises developed last summer.

• There are a number of individual commits that come from the extra/exercises swap & renaming files and file titles

• I also added a whole section of hidden files to the TOC so if this is cloned directly, you get a bunch of resource files that could be used eg for a class or a discussion section, etc, but they're hidden from the TOC until a user changes that so it's not confusing how they fit into the book, and you still get no build warnings with the current Components

cc @soney just in case

[aerenchyma]

Oh, and I've commented out everything in the former directives_home.rst file which is now inside the assignment_files folder -- the updates to the assignment directive and possibly other changes cause it to break, but I wanted to maintain the information in it, so it's stored away in that assignment_files folder if it's wanted to clone / change / uncomment / use any of it.