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.

docs/5-project/process/conventions.md

@@ -414,7 +414,7 @@ into the `Swap` node, then runs `nixos-container update` + stop +
 start across the `StopForUpdate → Swap → RebuildBookkeeping`
 brace and the tail `Reconcile` node. `flake.nix` itself lives in the agent's
 `agent-configs/<name>` repo and rides along with its pinned commit (see
-`docs/2-handbook/agents/config-changes.md::Deploy markers per agent`).
+`docs/4-implementation/agent-state/config-changes.md::Deploy markers per agent`).
 
 Anything that changes per-container state on the host should be
 re-applied here so a manual `↻ R3BU1LD` from the dashboard is
@@ -535,7 +535,7 @@ provisioning time:
 
 (The matrix profile avatar is **not** a oneshot — `hive-matrix-daemon`
 sets it over its live authenticated Client; see
-`docs/2-handbook/agents/persistence.md::matrix avatar`.)
+`docs/4-implementation/agent-state/persistence.md::matrix avatar`.)
 
 Shape contract — every one of these:
 
@@ -556,7 +556,7 @@ Shape contract — every one of these:
 5. **Re-runnable**: a second invocation produces the same final
    state (idempotent uploads, idempotent config rewrites). Used
    by the `.path` watchers that re-fire on token appearance (see
-   `docs/2-handbook/agents/persistence.md::Matrix per-agent daemon`).
+   `docs/4-implementation/agent-state/persistence.md::Matrix per-agent daemon`).
 
 The service stays root-owned so the bootstrap ordering doesn't need a
 user-existence check before each fire.