feat(atlas): execute deterministic Phase 2 panel selection

README.md

@@ -33,7 +33,7 @@ Public progress posts:
 | Mechanism Atlas source catalog | Five resolver-verified grounding sources plus seven mechanically non-grounding leads; public identifiers, licences and hashes are committed |
 | `$TSC2$` `$p.\mathrm{Arg611Gln}$` deterministic pass | Two exact spans passed Gates 1–7; Gate 8 blocked for missing named review; zero accepted claims |
 | Six-variant gate-smoke cohort | 6/6 technical packages passed Gates 1–7 and blocked only at Gate 8; zero accepted claims; explicitly **not** the formal contrast panel |
-| Formal Atlas contrast panel | **Ready, not run** — protocol/registration v1.0.3 now binds enriched universe lock v2; no candidate has been selected |
+| Formal Atlas contrast panel | **`INFEASIBLE_PANEL`** — the reviewed selector exhaustively completed 24 attempts across L0–R7 against universe/map v4 with no budget exhaustion; no panel or candidate was selected |
 
 v3 is a post-hoc semantic correction of the frozen R2 aggregate: it separates
 run integrity, data sufficiency, conditional performance, policy parity and

configs/atlas/panels/tsc2/atlas-phase2-candidate-universe-lock-v3.yaml

@@ -0,0 +1,60 @@
+schema: atlas.candidate_universe_lock.v1
+lock_id: tsc2-phase2-candidate-universe-lock
+lock_version: '3'
+universe_id: tsc2-phase2-contrast-panel-candidate-universe
+universe_version: '3'
+created_at: '2026-08-05T07:48:21Z'
+created_by_role: candidate_universe_custodian
+protocol_version: 1.0.2
+protocol_doc_hash: 685319b54d52183f44e6f98605b0a6d00a1348b8fc055c69b54d334872385efc
+registration_content_hash: 82261ab52ade28f35db35cfe569a6bbcb70b8bac24c46159352d40ce03bbe37e
+universe_content_hash: a500efaff6540bc87442795d9c035a12e95e17a383d84889a7e35840e0b81ab0
+universe_content_hash_algorithm: atlas.candidate_universe_content_hash.v1
+raw_inventory:
+  path: discovery_inventory.raw.yaml
+  content_hash: fee39ffa9c826b6e0ccb85ad583b09c2f81794036b115d91a91eab521365befb
+  content_hash_algorithm: atlas.raw_inventory_hash.v1
+  record_count: 35
+  normalized_byte_length: 6062
+  captured_at: '2026-08-02T19:25:56Z'
+normalization_ledger:
+  hash: 66fc103395f446d553ba9a370bea605ef80ffb5e9dfc8473c99cdc176162571f
+  hash_algorithm: atlas.normalization_ledger_hash.v1
+  row_count: 35
+discovery_set_commitment:
+  hash: 595e311a5c165607e2b8360c83353d1e5f2f11af17e65814480a36cdda890acb
+  hash_algorithm: atlas.discovery_set_commitment.v1
+  count: 35
+  committed_at: '2026-08-05T07:48:21Z'
+pack_binding:
+  pack_id: tsc2
+  pack_version: 1.0.0-phase1
+  pack_content_hash: 1294478c6d112f91e5719ee345d2b5be1925567ec4f4abdff50b0e092ff08927
+identity_map_binding:
+  schema: atlas.raw_identity_map_lock.v2
+  map_id: atlas-raw-identity-map-tsc2
+  map_version: '4'
+  lock_id: atlas-raw-identity-map-lock-tsc2
+  lock_version: '4'
+  map_content_hash: 3adbf3484de28607fa3c133b2bebc4a9d7926b4c2d5b3863b0634507c599cd26
+  lock_content_hash: 85bc2b10e65bd8140a775537204f3c7c7048cd5444d7057fbea9501b7cd4b104
+  response_bundle_hash: fbedf2aae5aa26936807f2d8f26389a18a861fc884b461fdd8ebaf6b7e9f96bc
+  map_record_count: 35
+  pack_binding:
+    pack_id: tsc2
+    pack_version: 1.0.0-phase1
+    pack_content_hash: 1294478c6d112f91e5719ee345d2b5be1925567ec4f4abdff50b0e092ff08927
+storage_location: external_content_root
+completeness_attestation_ref:
+  location: candidate_universe.yaml#completeness_attestation
+  attesting_role: candidate_universe_custodian
+  attested_at: '2026-08-05T07:48:21Z'
+predecessor_lock_ref:
+  lock_version: '2'
+  path: configs/atlas/panels/tsc2/atlas-phase2-candidate-universe-lock-v2.yaml
+  note: 'Superseded, not replaced: lock v2 remains tracked, unchanged and valid for
+    universe_version 2. This lock covers only universe_version 3 (an additive identity
+    correction that supersedes exactly 3 of v2''s own resolved-identity determinations
+    with the official identity-map v4 replay result; all 37 evidence observations
+    are unchanged).'
+lock_content_hash: 64345984bcf45b87d9a89afc113b3cd3266559739abeb754fc331eaa421f4e38

configs/atlas/panels/tsc2/atlas-phase2-candidate-universe-lock-v4.yaml

@@ -0,0 +1,59 @@
+schema: atlas.candidate_universe_lock.v1
+lock_id: tsc2-phase2-candidate-universe-lock
+lock_version: '4'
+universe_id: tsc2-phase2-contrast-panel-candidate-universe
+universe_version: '4'
+created_at: '2026-08-05T11:13:11Z'
+created_by_role: candidate_universe_custodian
+protocol_version: 1.0.3
+protocol_doc_hash: df9b9a33a4343968c20993feaab6622d129118152cd0c90452936c4b5f81cfc0
+registration_content_hash: d79486b3b74f81d87a3d25c10bd1f0eea31ada562a940d632f4a29ef8574b7b2
+universe_content_hash: 98edd3bf3cef36b7a1231bc389a37be6efdae7deb2210c869c317dfb6e8bef30
+universe_content_hash_algorithm: atlas.candidate_universe_content_hash.v1
+raw_inventory:
+  path: discovery_inventory.raw.yaml
+  captured_at: '2026-08-02T19:25:56Z'
+  record_count: 35
+  content_hash_algorithm: atlas.raw_inventory_hash.v1
+  content_hash: fee39ffa9c826b6e0ccb85ad583b09c2f81794036b115d91a91eab521365befb
+  normalized_byte_length: 6062
+  format: yaml
+normalization_ledger:
+  hash: 66fc103395f446d553ba9a370bea605ef80ffb5e9dfc8473c99cdc176162571f
+  hash_algorithm: atlas.normalization_ledger_hash.v1
+  row_count: 35
+discovery_set_commitment:
+  hash: 595e311a5c165607e2b8360c83353d1e5f2f11af17e65814480a36cdda890acb
+  hash_algorithm: atlas.discovery_set_commitment.v1
+  count: 35
+  committed_at: '2026-08-05T11:13:11Z'
+pack_binding:
+  pack_id: tsc2
+  pack_version: 1.0.0-phase1
+  pack_content_hash: 1294478c6d112f91e5719ee345d2b5be1925567ec4f4abdff50b0e092ff08927
+identity_map_binding:
+  schema: atlas.raw_identity_map_lock.v2
+  map_id: atlas-raw-identity-map-tsc2
+  map_version: '4'
+  lock_id: atlas-raw-identity-map-lock-tsc2
+  lock_version: '4'
+  map_content_hash: 3adbf3484de28607fa3c133b2bebc4a9d7926b4c2d5b3863b0634507c599cd26
+  lock_content_hash: 85bc2b10e65bd8140a775537204f3c7c7048cd5444d7057fbea9501b7cd4b104
+  response_bundle_hash: fbedf2aae5aa26936807f2d8f26389a18a861fc884b461fdd8ebaf6b7e9f96bc
+  map_record_count: 35
+  pack_binding:
+    pack_id: tsc2
+    pack_version: 1.0.0-phase1
+    pack_content_hash: 1294478c6d112f91e5719ee345d2b5be1925567ec4f4abdff50b0e092ff08927
+  map_created_at: '2026-08-05T05:56:56Z'
+storage_location: external_content_root
+completeness_attestation_ref:
+  location: candidate_universe.yaml#completeness_attestation
+  attesting_role: candidate_universe_custodian
+  attested_at: '2026-08-05T11:13:11Z'
+predecessor_lock_ref:
+  lock_version: '3'
+  path: configs/atlas/panels/tsc2/atlas-phase2-candidate-universe-lock-v3.yaml
+  note: Lock v3 is retained but inactive because it recorded stale v1.0.2 bindings
+    after protocol v1.0.3 was already in force.
+lock_content_hash: f94ce81b8633bac777fd667e26c7b8d3a726b7e4d7eed9f8ed2128f9ed32b50e

configs/atlas/panels/tsc2/atlas-phase2-raw-identity-map-lock-v4.yaml

@@ -0,0 +1,93 @@
+schema: atlas.raw_identity_map_lock.v2
+lock_id: atlas-raw-identity-map-lock-tsc2
+lock_version: '4'
+created_at: '2026-08-05T05:56:56Z'
+map_id: atlas-raw-identity-map-tsc2
+map_version: '4'
+map_content_hash: 3adbf3484de28607fa3c133b2bebc4a9d7926b4c2d5b3863b0634507c599cd26
+map_record_count: 35
+raw_inventory_content_hash: fee39ffa9c826b6e0ccb85ad583b09c2f81794036b115d91a91eab521365befb
+raw_inventory_record_count: 35
+response_bundle_hash: fbedf2aae5aa26936807f2d8f26389a18a861fc884b461fdd8ebaf6b7e9f96bc
+response_file_count: 88
+response_byte_count: 904564
+pack_binding:
+  pack_id: tsc2
+  pack_version: 1.0.0-phase1
+  pack_content_hash: 1294478c6d112f91e5719ee345d2b5be1925567ec4f4abdff50b0e092ff08927
+reference_binding:
+  provider: NCBI/NLM
+  database: clinvar+clinicaltables
+  transcript: NM_000548.5
+  protein: NP_000539.2
+  assembly: GRCh38
+  protein_reference_total_count: 6428
+  protein_reference_page_size: 500
+  protein_reference_response_pins:
+  - offset: 0
+    count: 500
+    relative_path: reference/protein-00000.json
+    sha256: b7fb356cdbb3342e18ddf3935a2b1bf7870b576708e055e6c1fada2bddf3caba
+    byte_length: 58623
+  - offset: 500
+    count: 500
+    relative_path: reference/protein-00500.json
+    sha256: 6cd8cbd69f7da7064edce87284418a1d521009bc63a8bfe6c792e427c52a4a7d
+    byte_length: 58808
+  - offset: 1000
+    count: 500
+    relative_path: reference/protein-01000.json
+    sha256: be9c567a1ac11ca036031003595984542ce15a1becc96afc90b9520ed9e6959f
+    byte_length: 58336
+  - offset: 1500
+    count: 500
+    relative_path: reference/protein-01500.json
+    sha256: bdcf9d1352e82c6fd24b258f94cf87a93ab30f9d2af33c77da2e66339595bc5b
+    byte_length: 58646
+  - offset: 2000
+    count: 500
+    relative_path: reference/protein-02000.json
+    sha256: 66c8b999b3f7f9c9351bd245a23031999e758184d7591da2f4f5db63738e49b8
+    byte_length: 57612
+  - offset: 2500
+    count: 500
+    relative_path: reference/protein-02500.json
+    sha256: 40bd7b14c5211b70160d64c5dbd5dbb8cc7f17f6fc65298fab613eb6f32925db
+    byte_length: 58301
+  - offset: 3000
+    count: 500
+    relative_path: reference/protein-03000.json
+    sha256: ccafd17c38561575111ee87d12f885f01ab9b2b431fd2936f210bbe0e6d385ef
+    byte_length: 57621
+  - offset: 3500
+    count: 500
+    relative_path: reference/protein-03500.json
+    sha256: 8c1a4634ae2308968d5ebda1a8bb5a80af0e035ebe4cbb7c44aa9cd226c2a7f5
+    byte_length: 55655
+  - offset: 4000
+    count: 500
+    relative_path: reference/protein-04000.json
+    sha256: 8d7333d2ea2cd7fdc8906850667116ec43f54c61a8096e50b80596c423839cbb
+    byte_length: 59489
+  - offset: 4500
+    count: 500
+    relative_path: reference/protein-04500.json
+    sha256: 0906dd8ffca9c7e21fe5ac057d0b26f762bdace135305a29ca5f3a88afefc08d
+    byte_length: 59520
+  - offset: 5000
+    count: 500
+    relative_path: reference/protein-05000.json
+    sha256: 50dbcf47a17dfbe0dd72ecba3ad8f6e2dc12dd19664382dcf4d110f7ca314455
+    byte_length: 58824
+  - offset: 5500
+    count: 500
+    relative_path: reference/protein-05500.json
+    sha256: 57ab68cdf462bed31889b704989b4152f40e0dbd1cb876fd2bb31a8e98b5925f
+    byte_length: 58640
+  - offset: 6000
+    count: 500
+    relative_path: reference/protein-06000.json
+    sha256: b84965a97649e0b987ee27b6a85b9fc857e2c97cb657ceabefc1497d8f04e308
+    byte_length: 49135
+acquisition_tool_sha256: 7c0593954f249e136a8690cd580f8bcdc40ebec1108a23f03626451bfd67251e
+lock_content_hash: 85bc2b10e65bd8140a775537204f3c7c7048cd5444d7057fbea9501b7cd4b104

data/atlas/runs/2026-08-05/candidate_universe_v3_summary.json

@@ -0,0 +1,32 @@
+{
+  "schema": "raptor.atlas_public_candidate_universe_summary.v1",
+  "universe_id": "tsc2-phase2-contrast-panel-candidate-universe",
+  "universe_version": "3",
+  "generated_at": "2026-08-05T07:48:21Z",
+  "universe_content_hash": "a500efaff6540bc87442795d9c035a12e95e17a383d84889a7e35840e0b81ab0",
+  "lock_content_hash": "64345984bcf45b87d9a89afc113b3cd3266559739abeb754fc331eaa421f4e38",
+  "normalization_ledger_hash": "66fc103395f446d553ba9a370bea605ef80ffb5e9dfc8473c99cdc176162571f",
+  "discovery_set_hash": "595e311a5c165607e2b8360c83353d1e5f2f11af17e65814480a36cdda890acb",
+  "identity_map_lock_hash": "85bc2b10e65bd8140a775537204f3c7c7048cd5444d7057fbea9501b7cd4b104",
+  "counts": {
+    "raw_rows": 35,
+    "ledger_rows": 35,
+    "records": 35,
+    "resolved_identities": 25,
+    "unresolved_identities": 10,
+    "missense_hints": 31,
+    "non_missense_hints": 4,
+    "evidence_bearing_records": 32,
+    "evidence_absent_records": 3,
+    "observations": 37,
+    "resolved_to_unresolved_corrections": 3,
+    "official_replay_mismatches": 0
+  },
+  "reported_outcome_buckets": {
+    "near_reference": 15,
+    "intermediate_deviation": 3,
+    "substantial_deviation": 19
+  },
+  "no_selection_performed": true,
+  "next_gate": "registration_amendment_required_before_formal_selection"
+}

data/atlas/runs/2026-08-05/candidate_universe_v4_summary.json

@@ -0,0 +1,18 @@
+{
+  "schema": "raptor.atlas_public_candidate_universe_summary.v1",
+  "universe_version": "4",
+  "generated_at": "2026-08-05T11:13:11Z",
+  "universe_content_hash": "98edd3bf3cef36b7a1231bc389a37be6efdae7deb2210c869c317dfb6e8bef30",
+  "lock_content_hash": "f94ce81b8633bac777fd667e26c7b8d3a726b7e4d7eed9f8ed2128f9ed32b50e",
+  "predecessor_universe_version": "3",
+  "predecessor_universe_content_hash": "a500efaff6540bc87442795d9c035a12e95e17a383d84889a7e35840e0b81ab0",
+  "protocol_version_at_lock": "1.0.3",
+  "protocol_doc_hash_at_lock": "df9b9a33a4343968c20993feaab6622d129118152cd0c90452936c4b5f81cfc0",
+  "registration_content_hash_at_lock": "d79486b3b74f81d87a3d25c10bd1f0eea31ada562a940d632f4a29ef8574b7b2",
+  "identity_map_lock_hash": "85bc2b10e65bd8140a775537204f3c7c7048cd5444d7057fbea9501b7cd4b104",
+  "records": 35,
+  "observations": 37,
+  "identity_or_observation_changes_from_v3": 0,
+  "no_selection_performed": true,
+  "reason": "Administrative re-lock under the protocol and registration actually in force at lock creation."
+}

data/atlas/runs/2026-08-05/identity_map_v4_summary.json

@@ -0,0 +1,28 @@
+{
+  "schema": "raptor.atlas_public_identity_map_summary.v1",
+  "map_schema": "atlas.raw_identity_map.v2",
+  "map_id": "atlas-raw-identity-map-tsc2",
+  "map_version": "4",
+  "map_content_hash": "3adbf3484de28607fa3c133b2bebc4a9d7926b4c2d5b3863b0634507c599cd26",
+  "lock_schema": "atlas.raw_identity_map_lock.v2",
+  "lock_version": "4",
+  "lock_content_hash": "85bc2b10e65bd8140a775537204f3c7c7048cd5444d7057fbea9501b7cd4b104",
+  "response_bundle_hash": "fbedf2aae5aa26936807f2d8f26389a18a861fc884b461fdd8ebaf6b7e9f96bc",
+  "response_file_count": 88,
+  "response_byte_count": 904564,
+  "raw_inventory_content_hash": "fee39ffa9c826b6e0ccb85ad583b09c2f81794036b115d91a91eab521365befb",
+  "record_count": 35,
+  "resolved_count": 25,
+  "unresolved_count": 10,
+  "reference_binding": {
+    "provider": "NCBI/NLM",
+    "database": "clinvar+clinicaltables",
+    "transcript": "NM_000548.5",
+    "protein": "NP_000539.2",
+    "assembly": "GRCh38",
+    "protein_reference_total_count": 6428,
+    "protein_reference_page_count": 13
+  },
+  "candidate_bearing_map_location": "external_content_root",
+  "selection_performed": false
+}

data/atlas/runs/2026-08-06/atlas_phase2_panel_selection_precondition_attempt_1.json

@@ -0,0 +1,61 @@
+{
+  "schema": "atlas.panel_selection_precondition_attempt.v1",
+  "recorded_at": "2026-08-06T09:15:36.4184949Z",
+  "attempted_at": null,
+  "attempted_at_note": "The CLI did not emit an attempt timestamp because it failed before producing a run record.",
+  "git_head": "45d5222",
+  "command": [
+    "python",
+    "scripts/run_panel_selection.py",
+    "--repo-root",
+    "D:\\AIProjects\\raptor-worktrees\\atlas-panel-selection",
+    "--protocol",
+    "D:\\AIProjects\\raptor-worktrees\\atlas-panel-selection\\docs\\project\\atlas\\ATLAS_PHASE2_PANEL_SELECTION_PROTOCOL.md",
+    "--registration",
+    "D:\\AIProjects\\raptor-worktrees\\atlas-panel-selection\\docs\\project\\atlas\\atlas-phase2-panel-selection-registration-v1.yaml",
+    "--pack",
+    "D:\\AIProjects\\raptor-worktrees\\atlas-panel-selection\\configs\\atlas\\packs\\tsc2\\pack.yaml",
+    "--universe",
+    "D:\\AIProjects\\raptor-data\\atlas\\tsc2-phase2-panel-v4\\candidate_universe.yaml",
+    "--raw-inventory",
+    "D:\\AIProjects\\raptor-data\\atlas\\tsc2-phase2-panel-v4\\discovery_inventory.raw.yaml",
+    "--content-root",
+    "D:\\AIProjects\\raptor-data\\atlas",
+    "--identity-map",
+    "D:\\AIProjects\\raptor-data\\atlas\\tsc2-phase2-identity-map-v4\\raw_identity_map.yaml",
+    "--identity-map-response-root",
+    "D:\\AIProjects\\raptor-data\\atlas\\tsc2-phase2-identity-map-v4\\official_responses",
+    "--anchor-spdi",
+    "NC_000016.10:2070570:G:A",
+    "--anchor-residue",
+    "611",
+    "--executor-identity",
+    "sdrona_microsoft",
+    "--out",
+    "D:\\AIProjects\\raptor-worktrees\\atlas-panel-selection\\data\\atlas\\tsc2_phase2_panel_selection_run_2026-08-06.json"
+  ],
+  "node_budget_override_supplied": false,
+  "exit_code": 3,
+  "error": {
+    "code": "INPUT_FAULT",
+    "check_id": null,
+    "message": "registration has schema 'atlas.panel_selection_registration.v1', expected 'atlas.phase2_panel_selection_registration.v1'"
+  },
+  "registration": {
+    "path": "docs/project/atlas/atlas-phase2-panel-selection-registration-v1.yaml",
+    "observed_registration_content_hash": "5b8980024bd88f9f3c7269badf7fc3e709fef4ba135b3575a7513e5d17ad1653"
+  },
+  "output": {
+    "path": "data/atlas/tsc2_phase2_panel_selection_run_2026-08-06.json",
+    "written": false
+  },
+  "selection_result_emitted": false,
+  "panel_emitted": false,
+  "promotion_invoked": false,
+  "classification": "BLOCKED_PRECONDITION_ATTEMPT_NOT_A_SELECTION_RESULT",
+  "repair": {
+    "test_contract_commit": "212fa72",
+    "implementation_commit": "cb17117",
+    "frozen_registration_modified": false
+  }
+}