chore: promote experimental APIs to main API surface

[SkyeAv]

Promotes the former TCT.experimental developer-friendly finder wrappers into the main API surface, exported through the existing __all__ + star-import pattern.

What changed

• Finder entry points live in their submodules: pathfinder in TCT/TCT_pathfinder.py and neighborhood_finder in TCT/TCT_neighborhood_finder.py, re-exported from TCT/TCT.py (repo convention: finder logic in its submodule, public names imported back into TCT).
• Single neighborhood_finder: the legacy low-level neighborhood_finder / neighborhood_finder_multiple_inputs wrappers are removed; the developer-friendly neighborhood_finder (handles single + multiple inputs via a list, returns a FinderResult) is now the only implementation, defined directly under its public name — no _neighborhood_finder alias.
• Shared infrastructure stays in TCT/TCT.py: the result/resource dataclasses (FinderResult, ResolvedNode, TranslatorResources), get_translator_resources / clear_translator_resource_cache, and the node/category/resource helpers. The legacy Path_finder and Neighborhood_finder entry points are removed.
• Internal caller migrated: TCT_network_annotator.network_annotator now uses the new neighborhood_finder API (one query+parse per gene via FinderResult.raw), replacing the old call-then-parse_results_for_neighborhood_finder pair and dropping the unused ranked tuple.
• TCT/experimental.py: deleted.
• Tests: tests/test_experimental.py → tests/test_finder_api.py (11 tests), with the finder-test monkeypatches retargeted at the submodules; helper tests unchanged.
• Notebooks: quick-start sections for the promoted APIs added to Path_finder, Neighborhood_finder, and Neighborhood_finder_multiple_nodes; the detailed neighborhood-workflow cells in Neighborhood_extender, Neighborhood_finder, Connecting_userAPI, and Neighborhood_finder_multiple_nodes migrated to the new neighborhood_finder API (legacy call + re-parse collapsed into finder_result.raw); all four re-executed end-to-end against Translator endpoints so the migrated cells carry live outputs. Experimental_API_tutorial.ipynb deleted.
• Docs/README: experimental wording removed; promoted wrappers mentioned in README and docs intro.
• CI: reverted the ci: harden sphinx and codespell workflows commit so this PR does not bundle unrelated CI hardening.
• pyproject.toml intentionally untouched (no version bump).

Verification

• uv run pytest: finder API tests pass (11/11); the only failures are the pre-existing tests/test_main.py cases that require the optional fastmcp (MCP) extra, unrelated to this change.
• ruff check: no new findings vs main baseline (remaining findings are pre-existing in untouched code).
• Neighborhood notebooks (Neighborhood_finder, Neighborhood_finder_multiple_nodes, Neighborhood_extender, Connecting_userAPI) re-executed successfully; migrated neighborhood_finder cells carry live outputs.
• Live smoke: get_translator_resources, pathfinder('asthma','albuterol',['Gene','Protein']), single + multi-input neighborhood_finder, refresh=True, and clear_translator_resource_cache all ran successfully against Translator endpoints.
• CODE_REVIEWER pass completed; findings fixed in an earlier commit.

Known limitation

Connecting_userAPI.ipynb is executed with errors allowed: its cell hitting the external user-API endpoint (amlkg.systemsbiology.org:9990) fails with an SSL error (endpoint currently unreachable), which is unrelated to this change. All other cells, including the migrated neighborhood_finder cell, execute successfully.

[SkyeAv]

Update: restructured so the finder entry points are not all dumped in TCT.py, and reverted the CI hardening so it isn't bundled with this PR.

Two new commits:

1. Revert "ci: harden sphinx and codespell workflows" — drops the unrelated CI changes (codespell/sphinx workflow hardening). CI may now flag codespell/sphinx; that's intentional for this PR.
2. refactor: relocate finder entry points into their submodules — moves the code out of TCT.py using the repo's existing conventions:
   • pathfinder → TCT/TCT_pathfinder.py
   • neighborhood_finder → TCT/TCT_neighborhood_finder.py (as _neighborhood_finder, re-exported under its public name to avoid colliding with the existing low-level neighborhood_finder used by the network annotator + notebooks — no legacy caller changes)
   • Stays in TCT.py: get_translator_resources, clear_translator_resource_cache, and the result/resource dataclasses + shared helpers (_resolve_node, _get_resources, _build_finder_result, etc.)
   • Submodule re-exports sit at the end of TCT.py (after the helpers are defined) to avoid a circular import; finder-test monkeypatches retargeted at the submodules, helper tests unchanged.

Verified: uv run pytest tests/test_finder_api.py → 11/11 pass; full suite green except the pre-existing tests/test_main.py failures (missing optional fastmcp extra). ruff check introduces no new findings vs main.

[SkyeAv]

Update: collapsed to a single neighborhood_finder (no more _neighborhood_finder alias) and migrated TCT's internal caller to the new API. New commit c9042c6.

• TCT_neighborhood_finder: removed the legacy low-level neighborhood_finder and neighborhood_finder_multiple_inputs wrappers; the promoted neighborhood_finder (single + multiple inputs via a list, returns FinderResult) is now the only implementation, under its public name. TCT.py re-exports it directly (from .TCT_neighborhood_finder import neighborhood_finder).
• TCT_network_annotator.network_annotator (the internal caller): now uses the new API — one query+parse per gene via FinderResult.raw, replacing the old call-then-parse_results_for_neighborhood_finder pair (and dropping the ranked tuple it never consumed). Net −252 lines across the PR.
• Notebooks: migrated the detailed neighborhood-workflow cells in Neighborhood_extender, Neighborhood_finder, Connecting_userAPI, and Neighborhood_finder_multiple_nodes to the new API (finder_result.raw). Outputs of the rewritten cells are cleared pending re-execution.

Verified: pytest finder tests 11/11 pass (only pre-existing fastmcp failures remain); ruff introduces no new findings; migrated cells parse cleanly; no stray references to the removed functions anywhere.

Notebook re-execution (to refresh outputs) is left as a follow-up — flag if you'd like me to re-run them against the Translator endpoints.

[SkyeAv]

Re-executed the four neighborhood notebooks against the Translator endpoints (commit 9b7ff15) — the migrated neighborhood_finder cells now carry live outputs.

• Neighborhood_finder, Neighborhood_finder_multiple_nodes, Neighborhood_extender: executed cleanly end-to-end.
• Connecting_userAPI: executed with errors allowed. The only failure is the pre-existing SSL error on the external user-API endpoint (amlkg.systemsbiology.org:9990), unrelated to the migration; the migrated neighborhood_finder cell ran successfully.

Updated the PR description accordingly (removed the "pending re-execution" note).