Update examples and tutorials to not use retrofit agents

[tsmbland]

Description

Please include a summary of the change and which issue is fixed (if any). Please also include relevant motivation and context. List any dependencies that are required for this change.

Fixes #340

Type of change

Please add a line in the relevant section of CHANGELOG.md to document the change (include PR #) - note reverse order of PR #s.

• [ ] New feature (non-breaking change which adds functionality)
• [ ] Optimization (non-breaking, back-end change that speeds up the code)
• [ ] Bug fix (non-breaking change which fixes an issue)
• [ ] Breaking change (whatever its nature)

Key checklist

• [ ] All tests pass: $ python -m pytest
• [ ] The documentation builds and looks OK: $ python -m sphinx -b html docs docs/build

Further checks

• [ ] Code is commented, particularly in hard-to-understand areas
• [ ] Tests added that prove fix is effective or that feature works

[tsmbland]

I've just updated the inputs for some of the models so far (haven't regenerated the results), but does this look reasonable? @dalonsoa

[tsmbland]

Yeah they all run and the results look similar to before, so I think it's all good