DDOS-5974: Docs fix prod release

[sg-s]

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[Copilot]

Pull request overview

Updates Drug Discovery documentation and examples for a production release, while aligning SDK behavior/tests with quoting and DTO rehydration semantics.

Changes:

• Simplifies docs navigation and removes legacy/deprecated “not yet released” warnings and legacy pages/assets.
• Updates Docking/ABFE docs and notebooks to use current APIs (e.g., quoting via start(quote=True), ABFE confirmation + watch flow).
• Improves ABFE execution state hydration by using update_from_dto() and adds tests to assert estimate population.

Reviewed changes

Copilot reviewed 22 out of 31 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
zensical.toml	Updates docs nav to remove legacy/future tutorial sections and the removed Complex how-to.
tests/test_abfe.py	Adds coverage for ABFE quote-estimate population and asserts estimate on DTO rehydration.
src/drug_discovery/docking.py	Allows start(quote=True) for single-ligand docking (quote-only path).
src/drug_discovery/abfe.py	Uses update_from_dto() in _start_impl to ensure estimate/cost fields are populated consistently.
docs/stylesheets/extra.css	Removes trailing whitespace/blank line.
docs/notebooks/clean/docking-single-ligand.ipynb	Notebook update (adds an empty trailing code cell).
docs/notebooks/clean/abfe.ipynb	Updates quoting/confirm flow; adds a DTO inspection cell.
docs/images/brd-3d.html	Removes old ligand viewer HTML asset.
docs/images/abfe-running.html	Replaces embedded “running” widget HTML with a newer compact display snippet.
docs/images/abfe-quote.html	Removes old quoted ABFE widget HTML asset.
docs/dd/tutorial/rbfe.md	Removes “in development” admonition; keeps historical/removed status messaging.
docs/dd/tutorial/getting-started.md	Updates prose and fixes Projects API example (projects.create).
docs/dd/tutorial/docking.md	Refreshes tutorial steps, embeds updated iframes, and updates quoting example.
docs/dd/tutorial/abfe.md	Rewrites ABFE tutorial to use SystemPrep + ABFE (jobs-centric flow) and updates parameter guidance.
docs/dd/ref/pocket_finder.md	Removes “not yet released” warning from reference page.
docs/dd/ref/docking.md	Removes “not yet released” warning from reference page.
docs/dd/ref/abfe.md	Removes “not yet released” warning from reference page.
docs/dd/how-to/proteins.md	Removes “coming soon” admonition; minor formatting tweaks.
docs/dd/how-to/ligands.md	Updates iframe asset reference from removed brd-3d.html to brd-ligands.html.
docs/dd/how-to/find-pockets.md	Removes “not yet released” warning from how-to page.
docs/dd/how-to/docking.md	Removes “under development” admonition for constrained docking.
docs/dd/how-to/complex.md	Removes deprecated Complex how-to page.

Comments suppressed due to low confidence (1)

src/drug_discovery/docking.py:258

• start() now allows single-ligand quotes when quote=True, but it still raises for the equivalent explicit call start(approve_amount=0). Since approve_amount=0 is documented as quote-only across executions, consider basing this guard on the resolved approve amount (0 vs non-0) rather than the quote boolean alone, and update the docstring accordingly.

        if len(self.ligands) == 1 and not quote:
            raise ValueError(
                "Cannot start: Docking with a single ligand must use run(), not start()."
            )
        super().start(quote=quote, approve_amount=approve_amount, **kwargs)

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