Separate bundle flow seeds from live runtime overlays

[chubes4]

Problem

Agent bundle upgrade previews currently diff one persisted flow artifact that mixes two different ownership domains:

• bundle-owned seed config: source lane defaults, handler/source params, schedule seed, package versioned intent
• live runtime state: prompt/config patch queues, queue mode, consumed queue revision, burn-in throttles, local schedule posture

This makes legitimate site-local burn-in/runtime changes appear as package drift. Even with --rebase-local --policy=burn-in-safe, operators still get noisy PendingActions because the planner is trying to merge seed config and runtime overlays inside one payload.

Current symptom

On intelligence-chubes4, wordpress-com-wiki bundle upgrades correctly apply clean pipeline/package changes, but still stage approval-required flow artifacts for live Flow 2/10/11 because runtime state differs from the packaged seed:

• config_patch_queue
• queue_mode
• _queue_consume_revision
• local max_items: 1 burn-in throttles
• paused/manual scheduling posture

These are not necessarily package drift. They are runtime overlays.

Desired direction

Make runtime overlays first-class so a bundle flow artifact can remain stable while the site carries local runtime state separately.

Conceptually:

bundle flow seed
  package-owned defaults and source-lane intent

runtime overlay
  site-local queue/schedule/throttle/consume state

effective flow
  derived seed + overlay for execution

Acceptance shape

• Bundle upgrade planning can distinguish package drift from runtime overlay drift.
• Runtime queues and consumed revisions do not force bundle artifact approval.
• Burn-in safety throttles can be intentionally preserved without making future upgrades noisy.
• Operators can still preview runtime overlay drift when they ask for it.
• Existing burn-in-safe rebase behavior remains a bridge, but becomes less central once overlays are explicit.

Related context

• Data Machine v0.106.0 added --rebase-local / --policy=burn-in-safe and fixed dual-shape throttle mirroring in fix(bundle): mirror rebased handler throttles #1842.
• This issue is the deeper architecture cleanup after the immediate rebase contract.
• This is separate from pre-1.0 legacy trimming in Trim pre-1.0 legacy baggage #1793.