Sphinx docs: `hyp.manip` missing from `docs/api.rst`; two orphaned `hypertools.tools.*` pages not in any toctree

[jeremymanning]

Imported from jeremymanning#31

Original request: "need to check over sphinx documentation and make sure everything recompiles and is updated to reflect toolbox changes"

Current status (verified 2026-07-07 against the 1.0 branch):

A full sphinx -b html build completes successfully (exit 0), with only cosmetic warnings (docutils title-underline length, one unrelated 404 fetching a scipy.org static asset, and a sphinx-gallery config cache-pickling warning). docs/sg_execution_times.rst shows a full gallery build was run as recently as 2026-07-06.

Two concrete "not updated to reflect toolbox changes" gaps found:

1. docs/api.rst has no section for hyp.manip (the toolbox's newest public function/dispatcher) — every other public function (load, analyze, plot, normalize, reduce, align, cluster, predict, impute, apply_model, describe) has an autosummary entry, but manip does not.
2. docs/hypertools.tools.align.rst and docs/hypertools.tools.normalize.rst are pre-1.0-layout pages still present in the repo but not included in any toctree (confirmed via the build's own toc.not_included warnings), i.e. dead documentation left over from the module reorganization.

Suggested next step: add a hyp.manip autosummary entry to docs/api.rst (once #28's docstring gap for manip is filled) and remove or properly retire the two orphaned hypertools.tools.* rst pages.