`Agent.from_spec` raised `TypeError` on `RAGCapability` and `AnalysisCapability`,
whose constructors take a state class, packaged instruction text and a tool-name
set, and silently omitted both from the generated spec schema. The two
zero-configuration capabilities constructed but with `id=None`, so pydantic-ai's
duplicate-id rejection no longer held and a spec could register two citation
policies, defeating the single-decision-maker invariant.
Override `from_spec` on all four, delegating to `create_capability()` so ids and
instructions come from one place. The spec surface is `db_path`, `config`,
`defer_loading`, `request_limit` and `vision`; a live `HaikuRAG` client stays out
of it, and a `config` mapping is validated through `AppConfig`.
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