Each assistant's workspace has a real folder of files. What the assistant creates there stays put: between one task and the next, and after the workspace goes to sleep and wakes again. You do not need to ask it to save anything.
When you connect a source-control tool such as GitHub, the Coder clones your repository into its own workspace, before its first task. It never clones onto your computer and never works in a folder on your machine.
That has a few practical effects:
Your own copy of the repository is never touched while the Coder works.
Each Coder has its own copy, so several Coders never trip over each other's files.
Your login for the repository is passed to a single command at a time. It is never written into the repository settings or shown in the Files view.
If the clone fails, the job stops as Blocked before any coding, with a plain sentence saying what to fix, such as the token not being able to read that repository.
What happens to the work afterwards depends on your house rules. The Coder can open a pull request for review, and merge when your house rules allow it. Pushing waits for your Approve unless your house rules allow it. See approvals and house rules.