I've seen when updating and messing around in the configs, that there are configs for both a project environment, and a shotgun_project environment.
Are both necessary? Are they really two different environments? Also seen them for shot and sequence.
Great question! The shotgun_*.yml environment files are primarily configs for the Toolkit-related menu items in the Shotgun UI for a specific entity type. So shotgun_task.yml controls what instances of the Launcher app are enabled for Tasks in Shotgun. This ultimately allows you to add a "Launch Nuke" menu item to Tasks in the Shotgun UI. The environment files that don't start with shotgun_ are the more general Toolkit environment config files that are used for all of the Toolkit apps and engines once you've launched Toolkit.
To answer your specific question... the project.yml is the general Toolkit environment config file that is used in any Toolkit applications when you're in the Project environment. This controls what engines and apps are enabled and their settings when working on the project level. For example, when you launch Nuke from SG Desktop, it puts you in the project environment by default (since it doesn't know what specific Shot, Asset, or Task you're working on... yet).
The shotgun_project.yml file controls the Toolkit menu items that are available in Shotgun at the Project level. If you launch Nuke from the Toolkit menu in Shotgun on a Project page, Nuke will open up and Toolkit will then initialize using the project.yml environment.
