Fix: auto-flatten paged /users responses; slim User attributes

[mdorf]

PR description

Summary

• Collection#all detects paged API responses (collection/pageCount/nextPage shape) and walks nextPage links transparently, returning a flat Array. Pre-pagination Array responses pass through unchanged. Internal pagesize: 5_000 to minimize request count.
• Models::User defaults to a slim @include_attrs allow-list (username, email, role, firstName, lastName, created) instead of "all", and overrides .all to inject display_context: false, display_links: false. Drops the heavy User payload (custom ontologies, tokens, hashes, JSON-LD context) for list/select use cases.
• Adds a manual test/benchmark/users.rb harness for reproducing and quantifying the production timeout (not loaded by the test suite — invoked manually with UT_APIKEY=… bundle exec rubytest/benchmark/users.rb).

Why

Production users were unable to create ontologies, with Faraday::TimeoutError from bioportal_web_ui controllers calling LinkedData::Client::Models::User.all. The fix spans four repos:

1. ✅ Fix /users perf with security: idempotent admin?, drop inverse attrs from auth load ontologies_linked_data#286 (merged) — idempotent User#admin?, drop inverse attrs from auth load
2. ncbo/ontologies_api fix/slow-users-endpoint PR — mandatory pagination on GET /users (+ a related /search and /property_search 500 fix)
3. This PR — client-side auto-flatten + slim User attrs
4. ncbo/bioportal_web_ui — bump Gemfile.lock to the new client release (no controller code changes needed)

This client release is what makes the ontologies_api breaking change (mandatory pagination) transparent to existing in-process callers.

Backward / forward compatibility

API response	Old client	New client
Flat Array (current /users, /ontologies, etc.)	returns Array	returns Array (passthrough — paged_collection? false)
Paged Hash (new /users, future paginated endpoints)	returns Hash unchanged → callers iterating it as Array break	walks nextPage, returns flat Array
Caller passes :page explicitly	returns response unchanged	returns response unchanged (passthrough)

Test plan

• UT_APIKEY=<key> bundle exec rake test TEST="./test/models/test_collection.rb" — three new tests pass: test_all_flattens_paged_collections, test_all_returns_page_when_page_requested,
  test_user_all_uses_lightweight_defaults. Existing test_all, test_class_for_type, test_where continue to pass.
• Note: test_find and test_find_by will fail when run against a local API — they hard-code https://data.bioontology.org/... URIs while a local triplestore stores
  http://localhost:9393/.... Pre-existing issue (introduced 2023-07-19, not a regression from this PR). Worth a separate cleanup ticket.
• Manual: UT_APIKEY=<key> bundle exec ruby test/benchmark/users.rb reports per-page and full-walk timings consistent with the table above.
• Smoke test against staging (after API deploys): Models::User.all returns a flat Array; Models::User.all(page: 1) returns a paged response object; Models::Ontology.all continues to return
  a flat Array unchanged.

[codecov-commenter]

Codecov Report

❌ Patch coverage is 96.96970% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 68.34%. Comparing base (8549896) to head (dad23b9).

Files with missing lines	Patch %	Lines
lib/ontologies_api_client/collection.rb	96.55%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master      #55      +/-   ##
==========================================
+ Coverage   66.48%   68.34%   +1.86%     
==========================================
  Files          29       29              
  Lines         919      973      +54     
  Branches      174      188      +14     
==========================================
+ Hits          611      665      +54     
  Misses        308      308              

Flag	Coverage Δ
3.2	68.34% <96.96%> (+1.86%)	⬆️

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