Add instantiators parameters

[mauvilsa]

What does this PR do?

• New instantiators parameter of ArgumentParser.instantiate, auto_cli and FromConfigMixin.from_config, to use custom instantiators only within that call, including nested classes and partials for callables that return a class. This is recommended over the global add_instantiator, which affects other libraries that use jsonargparse.
• The deprecation message of ArgumentParser.add_instantiator and the v5 migration guide now point to the new parameter.
• Fixed custom instantiators with an applied_instantiation_links parameter missing links for classes nested in the init_args of another class, and for the partials that instantiate gives for callables that return a class.

These changes are also applied to the v4 branch via #994

Before submitting

• Did you read the contributing guideline?
• If you used a coding agent, did you fully understand and validate all generated code and ensure it follows the contributing guidelines?
• Did you update the documentation? (readme and public docstrings)
• Did you write unit tests such that there is 100% coverage on related code? (required for bug fixes and new features)
• Did you verify that new and existing tests pass locally?
• If this is a bug fix, did you verify that the tests fail without the code fix?
• Did you make sure that all changes preserve backward compatibility?
• Did you update the CHANGELOG including a pull request link? (not for typos, docs, test updates, or minor internal changes/refactors)

[greptile-apps]

Confidence Score: 3/5

[Medium risk] Adds optional instantiators parameter to class instantiation.

The PR is not ready to merge because auto_cli bypasses scoped instantiators for class components and fails with an existing-signature custom parser override.

Findings

1.  Class instantiators are bypassed ▶
2.  Custom parser overrides reject instantiators ▶

Summary

The PR adds call-scoped class instantiators to parser instantiation, auto_cli, and from_config, and carries instantiator and applied-link information into nested and deferred instantiation.

• Adds validation and scoped-context propagation while retaining global instantiators as fallback.
• Adds coverage and documentation for nested classes, links, subcommands, and deferred callables.
• The auto_cli class-component and custom-parser paths need attention before the new option works consistently.

Diagram

%%{init: {'theme': 'neutral'}}%%
flowchart TD
  A["auto_cli(..., instantiators=...)"] --> B["parser.instantiate(cfg)"]
  B --> C["Instantiate nested arguments"]
  C --> D["_run_component"]
  D --> E["Direct class construction"]
  D --> F["Function invocation"]
  E -. "Bypasses scoped instantiator" .-> G["Class component"]

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 100.00%. Comparing base (a6236e8) to head (f35a8cd).
✅ All tests successful. No failed tests found.

Additional details and impacted files

@@            Coverage Diff            @@
##              main      #995   +/-   ##
=========================================
  Coverage   100.00%   100.00%           
=========================================
  Files           27        27           
  Lines         9617      9647   +30     
=========================================
+ Hits          9617      9647   +30     

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[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
100.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud