Story-2140 Walkthrough: Atlas → Mira cutover (matter chat + frame-edit demotion)

Change: RFD-AGT-007 Story G (Epic-2021 final story). Atlas is demoted to the workspace-level Dock agent only; its matter-scoped surfaces (intake wizard, matter chat, span-command, reframe, staleness, explain) are retired to Mira (converse + command) and to Vega (ambient reframe). This PR is the pramaan-agents code cutover. The matter-facing chat + frame-edit traffic flip is a broker/infra action (see §Live evidence).

Scope boundary. Workspace-level Atlas (the Dock: navigate / filter / view / find / server-tool reads) is untouched. Only the matter-scoped routes are removed. Mira already owns converse + command (Stories B–E, merged on main); this story removes Atlas's now-superseded matter code so nothing routes to it.

The core move — Atlas becomes dock-only, matter routes fail closed

The AgentCore entrypoint (agents/atlas/main.py) now serves the single kind="dock_chat" surface. A matter-scoped invoke (the retired intake/chat/reframe/staleness/explain path) is refused before any frame — the ADR-110 "404 the superseded route" demotion, not a compatibility stub:

if payload.get("kind") != "dock_chat":
    raise ValueError(
        "Atlas serves only the workspace Dock (kind='dock_chat'). The matter-scoped "
        "intake/chat/reframe/staleness routes were retired to Mira (Story-2140 / RFD-AGT-007)."
    )

runtime.handle_request is now dock-only; the Bug-1370 boundary watchdog (runtime.stream_invoke) is rewired to emit a Dock terminal (dock_chat._dock_error_turn) instead of the deleted intake turn — the thread-isolated deadline safety is preserved on the surviving path.

What was deleted (no dead routes, no stubs)

Area	Removed (matter-scope)	Kept (workspace Dock)
`agent.py`	the 5 intake sub-agents + `stream_atlas_turn`, `run_reframe/staleness/explain/reflection`, `build_intake_input`, `source_snapshot`, `_error_turn`, intake output-function + completeness gate	`UsageCollector`, `_read_run_usage`/`_capture_usage`/`_run_kwargs`/`_raise_if_truncated`, `_elapsed_ms`/`_log_run_failed` (shared model-call plumbing)
`models.py`	13 intake classes (`AtlasIntakeInput`, `AtlasParty`, `AtlasProposal`, `AtlasFrameOutput`, `AtlasTurn`, `AtlasReflection*`, `AtlasExplain/Reframe/Staleness Output`, `AtlasTrigger`, …)	all Dock models (`DockChatContext`, `AtlasDockTurn`, tool/view/render intents) + `AtlasHistoryMessage`
`runtime.py`	matter dispatch, `_wrap_proposal`/`_turn_event`/`_maybe_reflect`	Dock handlers, `build_dock_context`, watchdog
`prompts/`	`intake/explain/reflect/reframe/staleness.py` + `_render` intake helpers	`dock_chat.py` + fence primitives
`events.py`	`reflection_event`	all v1 event builders
tests / evals	intake tests + the intake grounding/streaming eval harness (`dataset`, `evaluators`, `grounding_*`, `_streaming_probe`, `activity_stream_probe`, `run.py`) + `dev_prompt_test.py`	all Dock/nav/authz/injection-scanner/prompt-leakage/surface-operator gates; `test_latency_invariant` + `test_atlas_stream_watchdog` + `test_prompt_fence` retargeted to the Dock path

Verification — offline (this PR's code rail)

Gate	Result
`ruff check agent_contracts/ tests/ scripts/` + `ruff check agents/`	pass
`scripts/check_brain_egress.py` (ADR-110 §6 brain purity)	clean
`scripts/check_prompt_leakage.py`	clean
governance unit tests (`pytest tests/ -m unit`)	171 passed
atlas suite	507 passed
atlas CI eval gates (authz + surface-operator + injection-scanner + logfire k3 + latency-invariant)	75 passed
other agents (framer 120 / registrar 287 / mira 139 / context_judge 16)	pass
mira adversarial gate (`test_adversarial.py` + `evals.run adversarial`)	40 passed; 13 held / 0 invariant failures

Live evidence — ADR-110 rail-by-rail (HONEST STATUS)

A green unit test is NOT cutover proof (AGENTS.md / ADR-110). The matter-chat traffic is served by Mira on staging only once Mira's AgentCore runtime is deployed and the broker matter-surface default is flipped. As of this PR, AgentCore staging (ap-south-1) has runtimes pramaanAgents_{atlas,framer,registrar} — no mira runtime, and the deployed atlas artifact still carries the pre-demotion code. Deploys run via Terraform in pramaan-infra (the agentcore CLI is retired, ADR-109). This PR therefore must merge AFTER the infra deploy lands; live ADR-110 evidence is attached then (by a follow-up), not fabricated now.

Rail (ADR-110)	Status	How it is proven
AgentCore response contract (Atlas demotion)	code-proven	Offline: `test_atlas_entrypoint` asserts a non-dock invoke fails closed; watchdog + dock stream pinned. Live: post-deploy, `aws bedrock-agentcore invoke-agent-runtime` against `pramaanAgents_atlas` with a matter envelope returns the fail-closed error.
Broker reachability (matter → Mira)	gated on deploy	Broker already speaks Mira (Stories B–E). Post-deploy: broker log shows the matter-surface invoke targeting the Mira runtime; the default-flip lands broker-side.
AgentCore response contract (Mira converse/command)	gated on deploy	Post-deploy smoke: `invoke-agent-runtime` on `pramaanAgents_mira` — `intent=converse` streams `turn.delta`…`turn.completed`; `intent=command` runs Vega's panel → proposed `FrameOutput`. Logfire `service_name='pramaan-agents-mira'` shows the `invoke_agent` spans.
App-side render	gated on deploy	Post-deploy: matter conversation panel + CCB (Story-F) render Mira's stream / proposed frame diff on the existing ratify rail.
Durable run truth	gated on deploy	Post-deploy: a Mira command proposal persists as a frame version (Story-E rail); Confirm promotes to canonical, Reject discards; stale-base race handled via generation CAS.

Terraform surface the pramaan-infra story needs

This PR adds the mira entry to agentcore/agentcore.json (local-dev manifest parity with framer/registrar; not a deploy authority). The infra story must:

Create the Mira runtime: name pramaanAgents_mira, CodeZip, entrypoint main.py, codeLocation agents/mira/, PYTHON_3_12, ap-south-1. Artifact = the CodeZip closure from uv export --package mira --no-dev --no-emit-workspace.
Env / secrets Mira reads (brain is os.getenv-only; secrets bootstrapped from ARNs at cold start, ADR-121 D3):
- OPENROUTER_SECRET_ARN → OPENROUTER_API_KEY (inference, ADR-116)
- LOGFIRE_SECRET_ARN → LOGFIRE_TOKEN (observability, ADR-118; optional — absent = no-op)
- IAM: secretsmanager:GetSecretValue scoped to Mira's own two ARNs only
- Optional config env (defaults in llm.yaml/code, no baked model ids): MIRA_<ROLE>_MODEL, MIRA_CACHE_<SEAT>, MIRA_CALL_TIMEOUT_S (150), MIRA_CONVERSE_ATTEMPT_TIMEOUT_S (20), MIRA_INVOKE_BUDGET_S (780), MIRA_REGION/AWS_REGION
Redeploy the Atlas artifact too: the demoted agents/atlas/ code in this PR must ship — the currently-deployed Atlas still serves matter routes, so the cutover is incomplete until the new Atlas CodeZip replaces it.
Broker default flip: confirm/flip the matter-surface default to the Mira runtime (pramaan-functions).

One-line recall: this PR makes the pramaan-agents code the cutover — Atlas is workspace-Dock-only, Mira owns the matter surface — verified offline; the live traffic flip lands with the pramaan-infra deploy + broker default, and the ADR-110 rail evidence is attached then.