KB: Specify sub-folders and files within a project folder to be version controlled in A365 workspace
Solution Details
By default, sub-folder such as "Project Outputs..." of each managed project is excluded from version control, as prescribed by .gitignore file contained inside the git repository folder.
This is to prevent bloating the git repository with unnecessary output files which can be readily re-generated from its source documents which, in turn, are version controlled already.
A line starting with # serves as a comment. Put an escape character backslash ("\") in front of the first hash for the folder path patterns that begin with a hash: https://git-scm.com/docs/gitignore#_pattern_format
While it is conceivable to delete the line to have the sub-folder version-controlled, it is highly discouraged as it is not only redundunt but also the data size can grow exponentially to slow down your daily commit/push/pull process and prone to error "Git Error: request failed with status code...".
If there is a smaller subset of output files that need to be git-version controlled on a daily basis for some reason (not to be confused with the final board design release), you may opt to create another folder with a distinct name to which those files can be saved.
To apply the same behavior across all of your projects, you can create and upload a project template with the configured gitignore file as well as the corresponding outjob specifying output paths. When creating new projects with the project template, it will include the configured gitignore file and the outjob.
As of writing (AD24.1), there is somewhat of a confusing behavior/representation in Save to Server dialog that generated output files such as Gerber are listed with ticks. In reality, as desired, they are not added to the version control as shown in the left Status column, even after the commit/push.
While there is no hard limit on the data storage size, we are monitoring the overuse and may work with you on an individual basis: https://www.altium.com/documentation/altium-365/faqs#!what-is-my-storage-limit-for-a-workspace-on-altium-365