Fix doc references

[AVHopp]

This PR fixes incorrect doc references and makes some general changes to how we check our internal links.

The core issue that is fixed here is that we previously ignored all links that do not contain or start with baybe. As a consequence, internal relative links were being skipped, and if those links were broken, we simply didn't know. This was now removed. As a consequence, we however now need to manually add a lot of additional regexes that we need to ignore now. I still need to investigate if all of these are actually necessary, so this list it self might still change.

Note that this PR does not yet solve the issue related to the warnings being emitted after the first PR, so it is expected that this still fails.

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[Copilot]

Pull request overview

This PR updates Sphinx/doc cross-references and refines documentation build/link-check behavior so that internal (relative) references are no longer implicitly ignored, while adding targeted suppressions for external/unresolvable references. It also moves recursive autosummary stub generation off the documentation landing page.

Changes:

• Restructure API reference generation by moving the recursive autosummary directive from docs/index.md into a dedicated docs/api_reference.md page.
• Expand and reorganize nitpick_ignore_regex and suppress_warnings in docs/conf.py to handle more external/inherited/unresolvable references now that non-baybe links are no longer blanket-ignored.
• Fix/adjust several doc references and directive options in both docs and docstrings.

Reviewed changes

Copilot reviewed 8 out of 8 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
docs/templates/custom-module-template.rst	Adjust autosummary module listing to skip kmedoids.
docs/index.md	Remove recursive autosummary directive from the landing page; keep API reference pointing to generated autosummary tree.
docs/conf.py	Replace blanket nitpick ignore with categorized ignore regexes; expand suppressed warning categories.
docs/components/transformations.md	Fix MyST admonition option syntax (:class: note).
docs/api_reference.md	New page to trigger recursive autosummary stub generation without rendering the module summary table on index.md.
baybe/transformations/base.py	Fix/fully qualify docstring cross-references to Transformation.
baybe/surrogates/gaussian_process/core.py	Fix cross-reference role for MeanFactoryProtocol to match its nature (object/type alias).
baybe/recommenders/meta/base.py	Fully qualify a method cross-reference in docstring.

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