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'sstill around 50 several run links and examples throughout docs:

Links

• Many cross ones in the cmd ref. - ref: replace dvc run examples with dvc stage add + dvc exp run or dvc repro #2997
• Plenty in 3 Use Cases
• Another bunch to review throughout User Guides

Examples

• Some can stay (as stage add) but not all.
• start: Update dvc run references in various GS pages #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 #1637 (comment))

---

ADDITION from #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.