Hi Josh,
The online SDK clone CLI command will only clone module library modules and SDK modules and not external added ones such as the Adventure Works theme.
However, now that the Adventure Works theme is our primary reference theme (it used to be Fabrikam), we are working on adding this theme directly in the online SDK in our github repo, however until then it's rather simple to manually do the steps to create a copy of the theme for your own use using the below steps after you've added the reference.
1. Install the AW theme : Install the Adventure Works theme - Commerce | Dynamics 365 | Microsoft Docs
2. Create a "theme" directory under "\src" if one doesn't exist already and another directory for the name of your theme example for a theme named "contoso" : "\src\themes\contoso"
3. Copy the "...\Msdyn365.Commerce.Online\node_modules\@msdyn365-commerce-theme\adventureworks-theme-kit\src\modules\adventureworks" directory to your "\src\themes\contoso" directory and rename it to the new name of your theme example "...\Msdyn365.Commerce.Online\src\themes\contoso" (if you are naming the theme contoso
4. If you followed the steps when installing the AW theme in step 1 above, you already have a copy of the "resources" and "public" folder so you can remove those two folders from the new theme files. Also there is a "__test__" file you won't need unless you are adding your own unit tests for the theme.
5. Next step is rename a few files in the theme to match your new theme name. There are some files at the root "adventureworks.definition.json", "adventureworks.theme.settings.json" and "adventureworks.tsx" rename each to the name of your theme example : "contoso.definition.json", "contoso.theme.settings.json" and "contoso.tsx"
6. Edit the contoso.definition.json file and proivde a new "name" (ex: "contoso") and friendly name/description
7.Rename styles files. Under the "styles" directory you'll find "adventureworks.definition.scss.json", "adventureworks.scss" , rename with your new theme name, example "contoso.definition.scss.json", "contoso.scss"
8. Edit contoso.defintion.scss.json and change the name of the style preset to the name of your new theme "contoso" (also change the description).
Now if you run "yarn start" you should be able to test your new theme out using the ?theme=contoso query string parameter (change contoso to the name of your theme that is inside the definition file set in step 6. An example test is to preview one of the module library modules such as the "promo banner" module using: localhost:4000/modules
Hope that helps,
Sam