## Summary
Remove gate and integrate SB3 agent natively.
This includes:
- agent saving
- checkpoints
- session output directory
- simulation output (such as syslogs) are now in the session output directory
- agent loading
- training progress bar (with `enlighten`)
## Test process
End to end tests that verify that a session is being created correctly with a network
They also check the outputs exist.
## Checklist
- [y] PR is linked to a **work item**
- [upcoming PR] **acceptance criteria** of linked ticket are met
- [y] performed **self-review** of the code
- [loading not tested but need to move onto Ray now] written **tests** for any new functionality added with this PR
- [n] updated the **documentation** if this PR changes or adds functionality
- [n] written/updated **design docs** if this PR implements new functionality
- [n] updated the **change log**
- [y] ran **pre-commit** checks for code style
- [n] attended to any **TO-DOs** left in the code
Related work items: #1971
## Summary
- Implement the folder/file restore
- Split the FileSystem and its classes into their own files so that it is easier to maintain.
- Reimplement how deleted folders and files are stored in a deleted list, so that it is possible to restore later
## Test process
See https://dev.azure.com/ma-dev-uk/PrimAITE/_git/PrimAITE/pullrequest/206?_a=files&path=/tests/unit_tests/_primaite/_simulator/_file_system
- Unit tests written to make sure methods work as intended
- Integration tests with the apply_request method which tests that the agents can send the request to the simulation to affect it
## Checklist
- [X] PR is linked to a **work item**
- [X] **acceptance criteria** of linked ticket are met
- [X] performed **self-review** of the code
- [X] written **tests** for any new functionality added with this PR
- [ ] updated the **documentation** if this PR changes or adds functionality
- [ ] written/updated **design docs** if this PR implements new functionality
- [ ] updated the **change log**
- [X] ran **pre-commit** checks for code style
- [ ] attended to any **TO-DOs** left in the code
Related work items: #1962
