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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@ -330,7 +330,7 @@ KEYS
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The file lives in the agent's bind-mounted **harness** dir, not `state/`
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— `harness/` survives container rebuilds exactly like `state/` does, but
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(unlike `state/`) is never bind-mounted into a parent agent's container
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(see `docs/2-handbook/agents/persistence.md`'s "Parent access to child state"), so an API
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(see `docs/4-implementation/agent-state/persistence.md`'s "Parent access to child state"), so an API
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key placed here is reachable by nothing but this agent and the host. The
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file doesn't stay root-owned, though: the container's activation chowns the
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whole harness dir to the agent, so after the next boot the file is agent-owned
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