docs: persistence and config changes become one operator page
The operator parts of the persistence and config-changes pages merge into agents/persistence.md. The sqlite tables, state dirs, mounts and migrations move to 4-implementation/agent-state/persistence.md, and the deploy path, meta flake, deploy markers, startup migrations, root container, system messages and autoupdate move to 4-implementation/agent-state/config-changes.md. Links, code comments and nix comments that named the old sections point at the new pages.
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//! Claude credentials live at `$HOME/.claude` (resolves to
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//! `/home/<agent-name>/.claude` because the harness service runs as a
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//! non-root unix user matching the agent label — see
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//! `docs/2-handbook/agents/persistence.md::First-boot agent-user migration`).
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//! `docs/4-implementation/agent-state/persistence.md::First-boot agent-user migration`).
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//!
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//! All three paths can be overridden via env vars (`HYPERHIVE_STATE_DIR`,
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//! `HYPERHIVE_HARNESS_DIR`, `HYPERHIVE_CLAUDE_DIR`) for dev / test scenarios.
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