As mentioned on our Licensing FAQ Atlassian provided source code for commercial, academic, and Starter License holders, allowing for in-house customizations and modifications. However some of Atlassian Add-ons source code are not included since some of it are "Closed-Source".

In order to identify the availability of the bundled plugins source code or any other plugins, you could access the plugin page on Atlassian marketplace. For example, Universal Plugin Manager is an Atlassian Closed Source as mentioned on the page, while you could see the link to the plugin source on Code Block Macro.