Annotated Registering & Displaying Menus by Joseph Dickson (joseph-dickson.com)
wp_nav_menu( array( 'theme_location' => 'footer-menu' ) ); 
Typo? I suspect Joseph may have transposed the ‘footer-menu’ an ‘header-menu’ in these two sections.
I imagine that header-menu belongs in the header.php section.
Annotated An Open Letter to Marc Andreessen and Rap Genius by dwhly dwhly (Hypothesis)
The lessons of Twitter and Facebook, other Internet-scale basic service layers that most of us use, are instructive here. After the honeymoon period is over, and disruptive returns need to be generated to pay off limited partners or satisfy public shareholders, the tensions that these monetization efforts create ultimately seem to separate the motivations of management from those of users and the broader ecosystem. How will Rap Genius–and Marc Andreessen–navigate these questions? 
This is probably the question of the past two decades which many companies are only beginning to realize.

Annotated Tuesday 19 May, 2020 by John NaughtonJohn Naughton (Memex 1.1)

Interestingly, I’ve found that Kindle is useful in this respect. I buy Kindle versions of books that I need for work, and highlight passages and bookmark pages as I go. And when I’ve finished the software obligingly has a collection of all the passages I’ve highlighted. 

John, you should spend a minute or two to learn about Hypothes.is as an online tool for doing this. It’s a free account or you can self-host the software yourself if you like. There are also functionalities to have public, private, or group annotations.

I often pull my own annotations to my personal website similar to your own Memex and publish them there (example: https://boffosocko.com/kind/annotation/)

Incidentally you can also annotate documents stored locally on your computer, but viewed through a browser as well as collaboratively annotating with others.

Annotated edit (indieweb.org)
An edit (AKA diff, change) is a special type of reply that indicates a set of suggested changes to the post it is replying to. A collection of (presumably related) suggested edits in open source is often called a patch or pull request.
In part out of laziness and lack of an easy way to implement a workflow and mark up, I will post content (bookmarks or notes) to my website and (pseudo-)syndicate all or portions of it to the IndieWeb wiki as either edits or as links to See Also sections of pages. “Pseudo” because the content isn’t always a 1 to 1 match.

To document the change, I’ll include a syndication link on my website to the permalink for the edit on the wiki. Having subscribed to feeds of wiki changes/edits before the user interfaces are far less than useful/ideal, so having a better contextual bookmark on my website makes more sense for readers while somewhat reformatting things for the readers of the wiki (a related but somewhat different context) works better for that, but still provides bi-directional links and references.

Perhaps I’ll create an edit post kind in the future? For the moment I’ll just post some (like this one) as an annotation? Small steps…

Example bookmark of a commonplace book: https://boffosocko.com/2020/03/14/neils-noodlemaps/
with a syndication link to the diff of the addition to the example on the IndieWeb wiki: https://indieweb.org/wiki/index.php?title=commonplace_book&oldid=69042

Annotated Dear Bob, by Jeff Jarvis (BuzzMachine)

I learned long ago in my career that shorter is harder. When I started Entertainment Weekly, I decreed that long reviews usually waste readers' time with critics showing off. Shorter can be smarter.

One doesn't measure comprehensiveness with a clock or a ruler. Longer is not deeper.

I was particularly struck by two quotes in the comments which are very similar to a popular saying by Blaise Pascal.

Are these truisms proven out on a daily basis by Twitter?

Annotated Blogroll by Dan MacKinlay (danmackinlay.name)
ITBio – Chris Aldrich (feed)
Hey, wait! He’s not only following me, but a very distinct subset of my posts! 🙂

This is the first time I’ve ever seen someone indicate that they’ve done this in the wild.

I’ll also admit that this is a really great looking blogroll too! I’m going to have to mine it for the bunch of feeds that I’m not already following. 

Annotated The Dan MacKinlay family of variably-well-considered enterprises by Dan MacKinlayDan MacKinlay (danmackinlay.name)
A statistician is the exact same thing as a data scientist or machine learning researcher with the differences that there are qualifications needed to be a statistician, and that we are snarkier.
Annotated How to Highlight the Internet by Andrew Courter (Medium)
Screenshots are disposable, but highlights are forever.
Highlighting this sentence on the Highly blog (on Medium) ironically using Hypothes.is. I’m syndicating a copy over to my own website because I know that most social services are not long for this world. The only highlights that live forever are the ones you keep on your own website or another location that you own and control.

RIP Highly.
Viva IndieWeb!

Annotated Unequal Scenes - USA (unequalscenes.com)

"Some inequality of income and wealth is inevitable, if not necessary. If an economy is to function well, people need incentives to work hard and innovate.The pertinent question is not whether income and wealth inequality is good or bad. It is at what point do these inequalities become so great as to pose a serious threat to our economy, our ideal of equal opportunity and our democracy."
—Robert Reich

An important observation. What might create such a tipping point? Is there a way to look back at these things historically to determine the most common factors that would create such tipping points?
Annotated Economy, Society and Public Policy (core-econ.org)
Economy, Society and Public Policy (an open textbook)
David Brancaccio and the kind folks at Marketplace are doing a public virtual bookclub with this book as their text for twelve weeks through the Spring of 2020.

Given the complexity of the subject and the public nature, I might suggest that they consider using the opensource and free Hypothes.is platform as an academic discussion tool for allowing everyone to highlight, annotate, and respond to the text and conversations?

I suspect the Hypothesis team would be happy to do a quick run through of their platform as well as potentially creating a private group if they preferred.

This link is an example of an annotation on the text.

Annotated FACT CHECK: Did Mark Twain Pen This Quote On Kindness? by Aryssa Damron (checkyourfact.com)

Christian Nestell Bovee often receives credit for the quote. “Kindness: a language which the dumb can speak and the deaf can understand,” he wrote in his 1857 book “Thoughts, Feelings, and Fancies.”

black and white photo of Mark Twain

Annotated An Outline for Using Hypothesis for Owning your Annotations and Highlights by Chris AldrichChris Aldrich (boffosocko.com)

Create an IFTTT.com recipe to port your Hypothesis RSS feed into WordPress posts. Generally chose an “If RSS, then WordPress” setup and use the following data to build the recipe:

Input feed: https://hypothes.is/stream.atom?user=username (change username to your user name)
Optional title: {{EntryTitle}}
Body: {{EntryContent}} from {{EntryUrl}}
{{EntryPublished}}

Categories: Highlight (use whatever categories you prefer, but be aware they’ll apply to all your future posts from this feed)
Tags: hypothes.is
Post status (optional): I set mine to “Draft” so I have the option to keep it privately or to publish it publicly at a later date.

Posting this solely to compare my Hypothes.is highlights and annotations on my website with Will’s version.

I’m still tinkering with mine and should have a Micropub based version using IFTTT and Webhooks done soon.

Annotated Journal of the First Voyage to America, 1492-1493 (Excerpt) by Christopher Columbus ( The Open Anthology of Earlier American Literature)
IN THE NAME OF OUR LORD JESUS CHRIST

I thought this was important all on its own. Did they put this before everything? Was he just really religious?–Tmoon95 annotation on September 9, 2015

This statement also has a lot to do with the culture of the time: The Tribunal of the Holy Office of the Inquisition (Spanish: Tribunal del Santo Oficio de la Inquisición), commonly known as the Spanish Inquisition (Inquisición española), was established in 1478 by Catholic Monarchs Ferdinand II of Aragon and Isabella I of Castile. It was intended to maintain Catholic orthodoxy in their kingdoms and to replace the Medieval Inquisition, which was under Papal control.

Recall that Ferdinand and Isabella were the reigning monarchs who funded Columbus’ voyages.