Gate rebuilds on native GPU proof

[TheGreenCedar]

Context

Agent sidecar repair could begin a long semantic rebuild after detecting an accelerator and reaching the embedding endpoint without proving that the exact selected runtime performed meaningful accelerator work. A failed retry could also leave an older verified broker proof visible.

Closes #1025
Refs #884

What Changed

• added a five-second embedding smoke before ready-repair and direct Agent-profile retrieval indexing
• bound proof to the persisted namespace, endpoint, requested provider/device, and unchanged runtime identity
• require current positive GPU offload logs plus measured smoke latency
• validate native launch identity before and after the smoke
• persist and validate running Docker container ID/start identity before and after the smoke
• overwrite stale verified broker proof with gpu_unverified on gate failure
• keep CPU-allowed policy degraded and explicitly classify external accelerator endpoints as unverified
• documented the operator contract and updated the changelog

CI Failure and Root Fix

The first workspace run failed four retrieval_bootstrap_contracts because Docker identity persistence inspected a container even for --skip-compose bootstrap. The initial correction exposed a second lifecycle edge: identity captured before a possible force-recreate could immediately become stale.

The final path leaves skip-compose bootstrap observational, performs any Compose refresh first, then captures the final running container ID/start tuple and atomically writes it into sidecar state. The Agent rebuild gate still fails closed when no bound identity exists.

How To Review

1. Follow ensure_embedding_accelerator_smoke_for_runtime through native, Docker, external, and CPU-allowed branches.
2. Confirm both run_ready_repair_with_native_embedding_lease and Agent retrieval index invoke the gate before run_indexing_blocking.
3. Check broker failure persistence and exact request/runtime identity regression tests.
4. Confirm final Docker identity publication occurs after the optional refresh path and is skipped for --skip-compose.

Verification

• cargo test -p codestory-cli --test retrieval_bootstrap_contracts --locked -- --nocapture — 6 passed
• cargo test -p codestory-retrieval sidecar_state_replacement_is_complete_and_leaves_no_temp_file --locked -- --nocapture — passed; covers atomic recreated-identity replacement
• cargo test -p codestory-retrieval --locked — 337 passed, 2 ignored; integration suites passed
• cargo test -p codestory-retrieval accelerator_smoke -- --nocapture — 4 passed
• cargo test -p codestory-retrieval container_identity_requires_running_state -- --nocapture — passed
• cargo test -p codestory-cli failed_smoke_replaces_verified_proof_for_current_runtime -- --nocapture — passed
• cargo test -p codestory-cli ready_repair_ --locked -- --nocapture — 35 unit tests and ready-command integration passed
• cargo clippy -p codestory-retrieval -p codestory-cli --all-targets --all-features --locked -- -D warnings
• node .github/scripts/check-doc-links.mjs
• git diff --check

Risk

The gate intentionally fails closed for accelerator-required external endpoints because CodeStory cannot bind provider-owned process/log identity. Live physical-GPU proof remains a post-merge environment check; deterministic tests cover the decision logic without requiring GPU hardware. No screenshot-visible UI changed.