Update links to example research code where that code is old and unmaintained

[StevenMaude]

In #1572, it was noted that there is at least one link to research code that doesn't do things exactly as might be the OpenSAFELY best practice today (it uses run: jupyter:latest and not run: python:v2).

Links to code repositories are currently in:

• docs/data-sources/apc.md
• docs/data-sources/ecds.md
• docs/data-sources/systmone.md
• docs/data-sources/cpns.md
• docs/federation.md
• docs/protocol.md
• docs/reports/intro.md
• docs/study-def-flowcharts.md
• docs/study-def-tricks.md

If these are outdated, we should replace them with more current examples.

[lucyb]

I've spoken to Brian and someone in the research team will be able to update this code.

[wjchulme]

no action needed

• The links from the data source pages are fine.
• The study-def-flowcharts.md and study-def-tricks.md are now under legacy so can stay as is.

non-urgent action needed

• The walkthrough in docs/federation.md should be replaced with an example in ehrQL, when such an example exists. The text currently acknowledges that the example is outdated as it uses study definitions, so think that enough until we can fully replace.
• The docs/protocol.md page links to protocols in repos, not code, so this is fine. Though we may want to update to more recent examples at some stage.
• The report/intro.md page includes one link to code that is out-of-date

[alschaffer]

Don't know if this fits here, but some references to modifying study def variables in cohortextractor here:
"Making changes to the study definition variables"
https://docs.opensafely.org/updating-the-docs/

I'm not even sure what that paragraph is about so unsure if it needs updating, or deleting (I suspect the latter though).

[StevenMaude]

I'm not even sure what that paragraph is about so unsure if it needs updating, or deleting (I suspect the latter though).

It's not really helpful now as it doesn't apply to ehrQL, so I deleted it in #1642.

[rebkwok]

@StevenMaude While updating docs (#1639) on the new project.yaml version (which deprecated cohort-extractor), @alarthast noticed that there is also the case control studies example in docs/case-control-studies.md which is still using cohort-extractor code. Can we add this one to your list, please?

[alschaffer]

@rebkwok There is already an issue for the case control page (#1492) - it is awaiting a decision on whether to delete or rewrite.