Fix cross-references and index title

Co-authored-by: eeholmes <2545978+eeholmes@users.noreply.github.com>

Author: Copilot

book/content/setup.md

@@ -48,9 +48,9 @@ Once your server starts, you'll see the JupyterLab interface with a Launcher sho
 
 Now that you're up and running:
 
-1. **Learn JupyterLab basics**: See [Intro to JupyterLab](02-intro-to-lab.md)
-2. **Learn RStudio basics**: See [RStudio](02-rstudio.md)
-3. **Set up Git**: See [Git in JupyterLab](02-git-jupyter.md)
+1. **Learn JupyterLab basics**: See [Intro to JupyterLab](../topics-skills/02-intro-to-lab.md)
+2. **Learn RStudio basics**: See [RStudio](../topics-skills/02-rstudio.md)
+3. **Set up Git**: See [Git in JupyterLab](../topics-skills/02-git-jupyter.md)
 4. **Explore tutorials**: Browse the skills sections in the navigation
 
 ## Important Notes
@@ -64,7 +64,7 @@ Now that you're up and running:
 
 If you run into issues:
 
-- Check the [FAQ](../topics-skills/01-intro-to-jupyterhub.md#faq)
+- Check the [FAQ](../topics-skills/01-intro-to-jupyterhub.md)
 - Post in [Discussions](https://github.com/nmfs-opensci/NOAAHackDays/discussions)
 - Report bugs in [Issues](https://github.com/nmfs-opensci/NOAAHackDays/issues)
 

book/topics-skills/01-intro-to-jupyterhub.md

@@ -45,15 +45,15 @@ When you are in the JupyterLab tab (note the Jupyter Logo), you will see a Launc
 ![Jupyterhub Launcher](./img/jhub-launcher.png)
 Clicking on the "Python 3", Terminal, Text File and Markdown File buttons will open a new tab in JupyterLab. You can also use the File dropdown menu for these.
 
-To get an overview of JupyterLab, go here: [Intro to JupyterLab](./content/02-intro-to-lab.html) 
+To get an overview of JupyterLab, go here: [Intro to JupyterLab](./02-intro-to-lab.md) 
 
 ## RStudio
 
 If you click the RStudio button in Launcher, RStudio will open in a new browser tab. 
 
 ![RStudio](./img/rstudio.png)
 
-To get an overview of RStudio, go here: [Intro to RStudio](./content/02-rstudio.html) 
+To get an overview of RStudio, go here: [Intro to RStudio](./02-rstudio.md) 
 
 ## End your session
 

book/topics-skills/02-git-jupyter.md

@@ -2,20 +2,16 @@
 title: Basic Git/GitHub Skills in JupyterLab git GUI
 ---
 
-::: {.callout-note icon=false}
-
-## Learning Objectives
-
-- Learn how to use the Git GUI in JupyterLab
-- Practice 4 basic Git/GitHub skills: cloning, committing, push/pull
-
-## Prerequisites
-
-- Read [Intro to Git](topics-skills/02-git.html)
-- Have a [GitHub](https://github.com/) account
-- [Git Authentication](topics-skills/02-git-authentication.html)
-
-:::
+> **Learning Objectives**
+>
+> - Learn how to use the Git GUI in JupyterLab
+> - Practice 4 basic Git/GitHub skills: cloning, committing, push/pull
+>
+> **Prerequisites**
+>
+> - Read [Intro to Git](02-git.md)
+> - Have a [GitHub](https://github.com/) account
+> - [Git Authentication](02-git-authentication.md)
 
 ## Create a GitHub account
 
@@ -26,7 +22,7 @@ information for how to create your user account and you will find lots of inform
 
 ## Setting up Git Authentication
 
-Before we can work with Git in the JupyterHub, your need to authenticate. Do the steps here: [Git Authentication](topics-skills/02-git-authentication.html)
+Before we can work with Git in the JupyterHub, your need to authenticate. Do the steps here: [Git Authentication](02-git-authentication.md)
 
 ## Git extension in JupyterLab
 

book/topics-skills/02-git-rstudio.md

@@ -11,9 +11,9 @@ title: Basic Git/GitHub Skills in RStudio
 
 ## Prerequisites
 
-- Read [Intro to Git](topics-skills/02-git.html)
+- Read [Intro to Git](02-git.md)
 - Have a [GitHub](https://github.com/) account
-- [Git Authentication](topics-skills/02-git-authentication.html)
+- [Git Authentication](02-git-authentication.md)
 
 :::
 
@@ -26,7 +26,7 @@ information for how to create your user account and you will find lots of inform
 
 ## Setting up Git Authentication
 
-Before we can work with Git in the JupyterHub, your need to do some set up. Do the steps here: [Git Authentication](topics-skills/02-git-authentication.html)
+Before we can work with Git in the JupyterHub, your need to do some set up. Do the steps here: [Git Authentication](02-git-authentication.md)
 
 ## Git tab in RStudio
 

book/topics-skills/02-git-terminal.md

@@ -11,9 +11,9 @@ title: Basic Git/GitHub Skills in the Terminal
 
 ## Prerequisites
 
-- Read [Intro to Git](topics-skills/02-git.html)
+- Read [Intro to Git](02-git.md)
 - Have a [GitHub](https://github.com/) account
-- [Git Authentication](topics-skills/02-git-authentication.html)
+- [Git Authentication](02-git-authentication.md)
 
 :::
 
@@ -26,7 +26,7 @@ information for how to create your user account and you will find lots of inform
 
 ## Setting up Git Authentication
 
-Before we can work with Git in the JupyterHub, your need to do some set up. Do the steps here: [Git Authentication](topics-skills/02-git-authentication.html)
+Before we can work with Git in the JupyterHub, your need to do some set up. Do the steps here: [Git Authentication](02-git-authentication.md)
 
 ## Git in the terminal
 

book/topics-skills/index.md

@@ -1,5 +1,7 @@
 ---
-title: "JupyterHub"
+title: "JupyterHub Skills"
 ---
 
+# JupyterHub Skills
+
 Explore the topics in the left navigation bar to learn how to use JupyterLab, RStudio and Git in the JupyterHub plus the other resources available.