docs: the README undercounted the tools and omitted ten of them

It claimed "23 total in the current source". The canonical manifest has
28 local tools, and a live handshake against the published package
advertises 28, so the number was wrong in the direction that undersells
the thing.

Worse than the count, the list left out ten real tools, including
search_codebase, search_docs and index_codebase. Semantic search over
the indexed repository is a differentiating feature and the repository's
front page did not mention it existed.

The list now matches src/shared/tool-manifest.ts exactly: 28 listed,
none missing, no phantoms, verified by diffing the rendered bullets
against localToolNames(). The section now names the manifest as
canonical so the next person knows which one to trust when they drift.

read_context and update_context are separate bullets rather than one
combined line, so that diff stays mechanically checkable.