feat(overlay_sssom): replay mappings on linkml schemas

[noelmcloughlin]

This PR has two purposes:

1. Supply two demo SSSOM TSV mapping files.
2. Supply script to replay mappings onto the LinkML Schema, with unit test, idempotent.

See #176

[noelmcloughlin]

Charlie Hodt suggested using sssom instead so moving back to draft

[matentzn]

@noelmcloughlin two meta observations from my side:

1. can you add a spec of what you are doing here to the issue? Without asking my agent, its incredibly difficult to understand what is happening (no mental model of the term "replay"; a loooot of code etc).
2. Not sure if everyone that uses copier w/o an option would want to see SSSOM demo files - my guess is that most folks will just continue to manually curate the mappings in the schema files themselves
3. Anything you can do to reduce the number of lines in the code would be much appreciated
4. sssom is a pretty heavy dependency (for no good reason) so again we should see that somehow its inclusion is kept optional

Thanks for working on this!

[noelmcloughlin]

Hi Nico,
Apologies for my sloppiness but I was not intending to contribute this feature until I realized there was demand (Inge is interested also) so i got Claude's to consolidate my fragmented variants of this script into single version. I was thinking about reusing sssom but we agreed to keep out of scope.

Done:

• I updated commit with smaller script (happy path)
• Added src/slug/mappings/README.md.jinja which is closest thing to a specificiaton

Is this forced design?

• No - people in a hurry (no example schema) get no example sssom files - everyone else selecting "yes" to "example schema" is sending a strong signal they should receive example sssom files (learners, new adopters, not in hurry, non-production phase).

• Maybe - The files scripts/overlay_sssom.py and src/{{project_slug}}/mappings/README.md are always supplied because it offers adoption path.

We should be clear about benefit- nobody should be editing LinkML to manage mappings - mappings are independent artifacts with different audience, lifecycle, and semantics - I see no conflict forcing adoption path into LinkML project copier - projects that edit LinkML mappings directly should consider moving to sssom.

[matentzn]

1. Can we make use of sssom explicitly OPT-IN at copier.yaml level?
2. Not so sure TSVs should be SOTA for all cases. Most LinkML users will want to continue the exact_mappings route in the model - are we offering any "exports" for ths case?