Big Bagel

Were you editing your theme’s CSS or options when it occurred? Maybe you just accidentally zoomed out a bit in your browser without realizing it. Pop open your site in a different browser to double check.

If you want to provide a link, I/someone can at least tell you how large your text currently appears to others.

The easiest way is to create a custom menu through “Appearance > Menus”.

Appearance Menus Screen
WordPress Menu User Guide

For consistency and future-proofing it might be best to stick with the normal styling provided by the Settings API. However, if you really want to add meta boxes, I do know that add_meta_box() just adds a meta box to a queue which is then output by the do_meta_boxes() function.

Function Reference/do meta boxes

This reference is a bit old, but may offer a few useful insights/examples:

https://andrewferguson.net/tag/do_meta_boxes/

Whoops! My bad. I blame all my failings on Google. :p

WordPress doesn’t have an in_category() function. Unless it’s a custom function, you’re probably wanting is_category():

Function Reference/is category

remove_action( 'wp_head', 'rsd_link' ); works just fine. Make sure you’re adding it in the proper place and that you aren’t seeing a cached version of your site.

Just to add a couple references for any future visitors:

XML-RPC Support
Weblog Client

Your post headers look like they already have the class header-wrap. You could use that. If you want to add an additional “scroll” class it would look like this:

<h2 class="header-wrap scroll">

If your theme supports it, you can completely customize your nav bar through (Appearance > Menus).

Appearance Menus Screen

Without knowing the theme in question (a link to site would fix that) it’s impossible to give a more definitive answer.

An update to WordPress itself will not touch your theme in any way. If/when the theme you’re using has an update, then you might have a problem. To prevent losing modifications in the event of a theme update, you can look into child themes. As with any core update, making a backup of your files and database beforehand is always a good idea.

Yes, there should be a notice. $atts is whatever parameters the user provides. When this shortcode is used, only $atts['id'] exists:

[media id=81]

The function shotcode_atts() then takes that array and merges it with the defaults you provide, returning the result. If you used:

$merged = shortcode_atts( array( 'id' => '', 'size' => '1/2', 'group' => '', 'showtitle' => true, 'showicon' => true, 'showbody' => true, 'icon' => ''), $atts );

Then $merged would be an array of all the proper values and $atts would still only be an array of whatever the user provided. Your new code in effect merges the given and default parameters then overwrites the $atts array with the new array. Using extract(), like you did before, automatically creates a variable that can be immediately used for each key in the returned array ($id, $size, $group, etc.).

Some good shortcode references:

Shortcode API
https://planetozh.com/blog/2008/03/wordpress-25-shortcodes-api-overview/
https://aaron.jorb.in/blog/2010/02/wordpress-shortcodes-a-how-to-by-example/#.TwyTGG9SQsI
https://wp.smashingmagazine.com/2009/02/02/mastering-wordpress-shortcodes/
https://wp.tutsplus.com/tutorials/getting-started-with-wordpress-shortcodes/

shortcode_atts() combines any user provided parameters ($atts) with the array of defaults you provide and returns the merged array.

Function Reference/shortcode atts

In your example above $atts['size'] doesn’t exist and thus results in an undefined index notice. You want to either store the returned array in a variable or (like you are currently doing) use PHP’s extract function to create individual variables from each element in the array. After using extract(), $size, $id, and $group exist and are already set to the proper values.

Edit:
Just a minor side note, there’s an errant comma in your code. Should be:

'group' => ''

home_url points to the main front-facing page of the installed WordPress blog. The link in question is intended to return any errant visitors to just that page. I fail to see the problem with “Return to Example” linking to example.com.

For example, if I install WordPress into its own directory (example.com/wordpress) but then set it up so that the actual WordPress site is displayed at the root (example.com) then home_url will point to the proper example.com while site_url would point to the publicly non-existent example.com/wordpress.

Use an FTP client or file browser provided by your host to access the problem file.

FTP Clients

Then either completely replace it with a fresh, unaltered copy or fix the syntax error on line 126.

Generally, home_url is where the site exists (the site’s home page), while site_url is where the actual WordPress installation exists. Usually they’re the same. Since this is for a link to the site’s home page, home_url is the proper template tag.

Function Reference/home url
Function Reference/site url

If you’re having problems with the built-in uploader, you can always install a theme manually with an FTP client or a file browser offered by your host. Links that might help to manually install a theme:

https://codex.www.ads-software.com/Using_Themes#Adding_New_Themes
https://www.youtube.com/watch?v=GLYwQN0iI5g

Since you have a premium theme, you should be able to get theme specific support from the developers/sellers.