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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//! `agent-permissions` bucket when the swarm UI creates her.
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//!
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//! Kill-switch: `HIVE_SKIP_META_MIGRATION=1`. Full sequence and phase
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//! details: `docs/2-handbook/agents/config-changes.md::Startup migrations (older hosts)`.
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//! details: `docs/4-implementation/agent-state/config-changes.md::Startup migrations (older hosts)`.
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use std::path::Path;
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use std::time::Duration;
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