Lost `run.md` documentation details

[hsteptoe]

Commit e73ef70 seems to have deleted a lot of helpful documentation from docs/source/run.md, for example e73ef70#diff-2998450a26e5b37fa39847fe6f0ecbcfa7f206569c35485243a9c048ffe8f026L61-L77

@nhsavage Was this intentional/temporary?

[nhsavage]

The way the code is run is changed and this is why this was updated but there is probably stuff that needs to be added back in.

[hsteptoe]

OK, but you've lost details that explain the parameters... such as e73ef70#diff-2998450a26e5b37fa39847fe6f0ecbcfa7f206569c35485243a9c048ffe8f026L61-L77, plus the new parameters you've added.