Inserting externally purchased code into Muse.

I purchased code that I would like to use in my site. How do I use it with Muse? I understand how to place HTML, but right now I have CSS and JQuery files. Is there any way to get it in there?

It's hard to give a useful answer to that question. There's a wide variety of HTML widgets out there with lots of different requirements...
Generally speaking, CSS files usually contain styling info, to control how some HTML elements look.
JS files are scripts that usually attach behavior to certain HTML elements.
Usually you'd also have some HTML to insert so the CSS has something to style and the JS has something to attach behavior to.
Muse has a few features that may help you integrate this fabulous thing into your Muse layout.
1) Insert HTML allows you to insert a bit of HTML which Muse will export along with the rest of your page.
2) The page properties dialog metadata pane allows you to insert HTML code into the <head> of the exported HTML page.
3) The 'Add files for upload' menu item allows you to tell Muse to upload additional files to your website. They'll be uploaded into a folder named 'assets'.
Depending on what you have, you might be able to use some of these features to get your wonderous thing into Muse without editing any of Muse's output.
If these features aren't sufficient for your use case, you may have to edit the exported HTML as suggested by iamDK. Note that if you do this, you'll have to re-edit the exported HTML every time you export/publish/ftp upload from Muse, as Muse does not preserve any edits made to the generated HTML.

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