doc: change `run` mentions to `dvc.yaml` or `stage add` + `repro`

[jorgeorpinel]

Based on work in #2075

We should be emphasizing writing/generating dvc.yaml files instead of using dvc run, yet there's~~still around 50~~ several run links and examples throughout docs:

Links

• [x] Many cross ones in the cmd ref. - #2997
• [x] Plenty in 3 Use Cases
• [ ] Another bunch to review throughout User Guides

Examples

• [x] Some can stay (as stage add) but not all.
• [x] #3309
• [ ] Around a dozen in the User Guide.

Many should be replaced by hand-written dvc.yaml files and at least one with a dvc.yaml file generation script (new example in dvc root per https://github.com/iterative/dvc.org/pull/1637#discussion_r463117077)

---

ADDITION from https://github.com/iterative/dvc.org/issues/2578:

• [ ] State this clearly in the docs, and the why (advanced dvc.yaml features?) Try to use a descriptive rather than prescriptive explanation...

stage add is still clearly useful, perhaps even preferred for certain cases:

• Simple stages or beginner users e.g. dvc stage add -n test echo test
• Programmatic stage generation, esp. to "bootstrap" a pipeline structure (to manage manually later)

[jorgeorpinel]

@iesahin would you be interested in moving this epic along since you were working on #3183 ?

[iesahin]

As we have closed #2997, let me check this, thank you.

[jorgeorpinel]

#2997 was mainly about references, this one is for Get Started and Guides. I can take care of the Use Cases... ⌛

[jorgeorpinel]

I can take care of the Use Cases... ⌛

Actually there's nothing worth changing there so that section is checked off now. Thanks

[daavoo]

I would add to the list the main page https://dvc.org/

[dberenbaum]

I don't see any remaining instances of dvc run 🎉 . Closing this one.