[update docs] documentation overhaul (#3138)

* quickstarts and userguides

* repositioning docs, edit quickstart guides, user guide, screenshot refreshes, consolidated docs revamp

* adding cancer landing page with some placeholders, userguide updates

* splitting config guide to expose components that are only talked about in that guide, moving to "advanced" to not confuse general users

* consolidating api guide, updating plugin guide

* [update docs] userguide updates, devguide updates, faq, api, tutorials, WIP plugin tutorial, SS updates

* [update docs] fixing broken links and faq

* [update docs] final touches on dev tutorial 1

* no build plugin tutorial

* plugin usage guides

* revert changes to file structure to preserve historical links

* build

* Fix build complaints

* Underscore in user_guide

* Misc

* lint and minor sidebar arrangement

* moving const

* hiding cancer portal until we have a refreshed video to display

Co-authored-by: Colin <colin.diesh@gmail.com>

products/jbrowse-web/src/Loader.tsx

@@ -53,14 +53,6 @@ function NoConfigMessage() {
         Configuration not found. You may have arrived here if you requested a
         config that does not exist or you have not set up your JBrowse yet.
       </h4>
-
-      <p>
-        If you want to complete your setup, visit our{' '}
-        <a href="https://jbrowse.org/jb2/docs/quickstart_web">
-          Quick start guide
-        </a>
-      </p>
-
       {inDevelopment ? (
         <>
           <div>Sample JBrowse configs:</div>
@@ -192,9 +184,10 @@ const ErrMessage = ({ err }: { err: unknown }) => {
         >
           No config.json found. If you want to learn how to complete your setup,
           visit our{' '}
-          <a href="https://jbrowse.org/jb2/docs/quickstart_web">
-            Quick start guide
+          <a href="https://jbrowse.org/jb2/docs/quickstarts/quickstart_web/">
+            quick start guide
           </a>
+          .
         </div>
       ) : (
         <Suspense fallback={<div>Loading...</div>}>

website/docs/Makefile

@@ -25,7 +25,7 @@ cli.md: ../../products/jbrowse-cli/README.md
 	cp $^ $@
 
 combined.md: $(SRC_FILES)
-	(echo '---\ntitle: JBrowse 2 combined guide\nid: combined\n---\n\nThis document is a collection of all our documentation. It includes our quick start guide, user guide, configuration guide, CLI guide, developer guide, and FAQ. You can browse the other documents individually, but this page is to help simple ctrl+f searching and easy browsing. You can also download a pdf version of these same docs located at https://jbrowse.org/jb2/jbrowse2.pdf\n\nimport Figure from "./figure"' && for f in $^; do cat $$f | node md_parser.js; done) > $@
+	(echo '---\ntitle: Consolidated docs\nid: combined\n---\n\nThis document is a collection of all our documentation. It includes our quick start guides, user guides, configuration guides, CLI guides, developer guides, and FAQ.\n:::info Note\nYou can browse the other documents individually using the sidebar on the left. **This page is to help simplify `ctrl+f` searching and easy browsing.**\n:::\nYou can also download a pdf version of these same docs located at https://jbrowse.org/jb2/jbrowse2.pdf.\n\nimport Figure from "./figure"\nimport config from "../docusaurus.config.json"' && for f in $^; do cat $$f | node md_parser.js; done) > $@
 
 clean:
 	git clean -fdx .

website/docs/api_guide.md

@@ -1,13 +1,13 @@
 ---
 id: api_guide
-title: API guide
+title: API
 toplevel: true
 ---
 
 import Figure from './figure'
 
-In this guide, will cover API level documentation e.g. methods that can be
-called on different objects and data model formats
+This guide will cover the API level documentation for methods and tools
+useful to developers looking to enhance JBrowse or write plugins.
 
 ## MenuItems objects
 
@@ -108,7 +108,7 @@ As an example, the here is an array of MenuItems and the resulting menu:
 Users can customize the top-level menu items using these functions that are
 available on the rootModel:
 
-#### appendMenu
+#### `appendMenu`
 
 Add a top-level menu
 
@@ -122,7 +122,7 @@ Add a top-level menu
 
 The new length of the top-level menus array
 
-#### insertMenu
+#### `insertMenu`
 
 Insert a top-level menu
 
@@ -137,7 +137,7 @@ Insert a top-level menu
 
 The new length of the top-level menus array
 
-#### appendToMenu
+#### `appendToMenu`
 
 Add a menu item to a top-level menu
 
@@ -152,7 +152,7 @@ Add a menu item to a top-level menu
 
 The new length of the menu
 
-#### insertInMenu
+#### `insertInMenu`
 
 Insert a menu item into a top-level menu
 
@@ -168,7 +168,7 @@ Insert a menu item into a top-level menu
 
 The new length of the menu
 
-#### appendToSubMenu
+#### `appendToSubMenu`
 
 Add a menu item to a sub-menu
 
@@ -183,7 +183,7 @@ Add a menu item to a sub-menu
 
 The new length of the sub-menu
 
-#### insertInSubMenu
+#### `insertInSubMenu`
 
 Insert a menu item into a sub-menu
 
@@ -202,30 +202,28 @@ The new length of the sub-menu
 ## Extension points
 
 In the core codebase, we have the concept of extension points that users can
-call or add to
+call or add to.
 
 The API is
 
 ```js
 pluginManager.evaluateExtensionPoint(extensionPointName, args)
 ```
 
-There is also an async version
+There is also an async method:
 
 ```js
 pluginManager.evaluateAsyncExtensionPoint(extensionPointName, args)
 ```
 
-Users can additionall add to extension points, so that when they are evaluated,
-it runs a chain of callbacks that are registered to that extension point
-
-This looks like
+Users can additionally add to extension points, so that when they are evaluated,
+it runs a chain of callbacks that are registered to that extension point:
 
 ```js
 pluginManager.addToExtensionPoint(extensionPointName, callback => newArgs)
 ```
 
-Here are the extension points in the core codebase
+Here are the extension points in the core codebase:
 
 ### Core-extendPluggableElement
 
@@ -268,4 +266,4 @@ hierarchical track menu when tracks are added to the selection
 
 Users that want to add further extension points can do so. The naming system,
 "Core-" just refers to the fact that these extension points are from our core
-codebase. Plugin developers may choose their own prefix to avoid collisions
+codebase. Plugin developers may choose their own prefix to avoid collisions.