docs/tests: finish repository structure cleanup

.github/CODEOWNERS

@@ -21,7 +21,7 @@ docs/review/PRE_REGISTERED_PILOT_TEMPLATE.md @Open-Problem-Lab/maintainers
 
 # Benchmarks, calibration, data, and model release need responsible review.
 docs/evidence/BENCHMARK_GOVERNANCE.md @Open-Problem-Lab/maintainers
-docs/CALIBRATION_POLICY.md @Open-Problem-Lab/maintainers
-docs/DATA_GOVERNANCE.md @Open-Problem-Lab/maintainers
-docs/MODEL_CARD_TEMPLATE.md @Open-Problem-Lab/maintainers
+docs/evidence/CALIBRATION_POLICY.md @Open-Problem-Lab/maintainers
+docs/trust/DATA_GOVERNANCE.md @Open-Problem-Lab/maintainers
+docs/trust/MODEL_CARD_TEMPLATE.md @Open-Problem-Lab/maintainers
 configs/recalibration_policy.yaml @Open-Problem-Lab/maintainers

.github/ISSUE_TEMPLATE/claim_review.md

@@ -60,7 +60,7 @@ body:
     attributes:
       label: Checks
       options:
-        - label: `docs/PROOF_LADDER.md` reviewed.
+        - label: `docs/evidence/PROOF_LADDER.md` reviewed.
           required: true
         - label: `docs/evidence/CLAIM_REVIEW_CHECKLIST.md` reviewed.
           required: true

.github/ISSUE_TEMPLATE/data_contribution.md

@@ -7,7 +7,7 @@ body:
   - type: markdown
     attributes:
       value: |
-        Use this template for non-toy data contributions or dataset review. Read `DATA_LICENSE_NOTICE.md` and `docs/DATA_GOVERNANCE.md` first.
+        Use this template for non-toy data contributions or dataset review. Read `DATA_LICENSE_NOTICE.md` and `docs/trust/DATA_GOVERNANCE.md` first.
   - type: textarea
     id: dataset
     attributes:

.github/ISSUE_TEMPLATE/model_release_review.md

@@ -82,8 +82,8 @@ body:
         - MODEL_RELEASE_POLICY.md
         - SAFETY.md
         - RESPONSIBLE_USE.md
-        - docs/MODEL_CARD_TEMPLATE.md
-        - docs/RELEASE_CHECKLIST.md
+        - docs/trust/MODEL_CARD_TEMPLATE.md
+        - docs/trust/RELEASE_CHECKLIST.md
     validations:
       required: true
   - type: checkboxes

.github/ISSUE_TEMPLATE/safety_review.md

@@ -45,7 +45,7 @@ body:
         - SAFETY.md
         - RESPONSIBLE_USE.md
         - MODEL_RELEASE_POLICY.md
-        - docs/PROOF_LADDER.md
+        - docs/evidence/PROOF_LADDER.md
         - docs/review/EXTERNAL_REVIEW_PACKET.md
     validations:
       required: true

.github/PULL_REQUEST_TEMPLATE.md

@@ -37,7 +37,7 @@ See `docs/getting-started/MAINTAINER_GUIDE.md`.
 
 ## Claim discipline
 
-- [ ] Claims are mapped to `docs/PROOF_LADDER.md`
+- [ ] Claims are mapped to `docs/evidence/PROOF_LADDER.md`
 - [ ] Dry-lab outputs are not described as biological proof
 - [ ] No “AI discovered an antibiotic” / “drug candidate” / “safe” / “clinically useful” language unless evidence level supports it
 - [ ] Unsupported claims are explicitly listed or avoided

AGENTS.md

@@ -34,10 +34,10 @@ Before making nontrivial changes, agents should read:
 2. [`SAFETY.md`](SAFETY.md) — safety policy.
 3. [`RESPONSIBLE_USE.md`](RESPONSIBLE_USE.md) — allowed and disallowed uses.
 4. [`docs/getting-started/AGENT_ONBOARDING.md`](docs/getting-started/AGENT_ONBOARDING.md) — task workflow.
-5. [`docs/PROOF_LADDER.md`](docs/PROOF_LADDER.md) — claim levels.
+5. [`docs/evidence/PROOF_LADDER.md`](docs/evidence/PROOF_LADDER.md) — claim levels.
 6. [`docs/operations/HIGH_LEVERAGE_TASKS.md`](docs/operations/HIGH_LEVERAGE_TASKS.md) — task priority map.
 7. [`docs/research/NEXT_100_PR_MAP.md`](docs/research/NEXT_100_PR_MAP.md) — PR-sized backlog.
-8. [`docs/TRUST_CENTER.md`](docs/TRUST_CENTER.md) — trust architecture.
+8. [`docs/trust/TRUST_CENTER.md`](docs/trust/TRUST_CENTER.md) — trust architecture.
 
 If these docs conflict, safety and claim discipline win.
 
@@ -179,7 +179,7 @@ Agents must follow:
 - [`SAFETY.md`](SAFETY.md)
 - [`RESPONSIBLE_USE.md`](RESPONSIBLE_USE.md)
 - [`MODEL_RELEASE_POLICY.md`](MODEL_RELEASE_POLICY.md)
-- [`docs/SAFETY_DOC_AUDIT.md`](docs/SAFETY_DOC_AUDIT.md)
+- [`docs/trust/SAFETY_DOC_AUDIT.md`](docs/trust/SAFETY_DOC_AUDIT.md)
 
 ## Benchmark rule
 
@@ -207,7 +207,7 @@ Agents must not present proxy models as validated biology.
 
 A virtual-assay module may affect ranking only when the documented gate allows it.
 
-Use [`docs/VIRTUAL_ASSAY_SCOPE.md`](docs/VIRTUAL_ASSAY_SCOPE.md) and [`docs/evidence/SIMULATION_BENCHMARK.md`](docs/evidence/SIMULATION_BENCHMARK.md).
+Use [`docs/evidence/VIRTUAL_ASSAY_SCOPE.md`](docs/evidence/VIRTUAL_ASSAY_SCOPE.md) and [`docs/evidence/SIMULATION_BENCHMARK.md`](docs/evidence/SIMULATION_BENCHMARK.md).
 
 ## Data and model rule
 
@@ -218,9 +218,9 @@ Agents must not commit or release non-toy data, sensitive model artifacts, or ca
 Use:
 
 - [`DATA_LICENSE_NOTICE.md`](DATA_LICENSE_NOTICE.md)
-- [`docs/DATA_GOVERNANCE.md`](docs/DATA_GOVERNANCE.md)
+- [`docs/trust/DATA_GOVERNANCE.md`](docs/trust/DATA_GOVERNANCE.md)
 - [`MODEL_RELEASE_POLICY.md`](MODEL_RELEASE_POLICY.md)
-- [`docs/MODEL_CARD_TEMPLATE.md`](docs/MODEL_CARD_TEMPLATE.md)
+- [`docs/trust/MODEL_CARD_TEMPLATE.md`](docs/trust/MODEL_CARD_TEMPLATE.md)
 - [`docs/engineering/ARTIFACT_VERSIONING.md`](docs/engineering/ARTIFACT_VERSIONING.md)
 
 ## Reproducibility rule

README.md

@@ -12,21 +12,21 @@ The larger mission is more ambitious:
 
 > Build an open **wet-lab compression engine** for AMP discovery: a system that helps qualified scientists decide which small number of experiments are most worth running next, then learns from those outcomes.
 
-The long-term infrastructure ambition is described in [`VISION.md`](VISION.md), [`GOAL.md`](GOAL.md), [`docs/OPEN_BIOTECH_STACK.md`](docs/OPEN_BIOTECH_STACK.md), [`docs/OPEN_INFRASTRUCTURE_MOAT.md`](docs/OPEN_INFRASTRUCTURE_MOAT.md), and [`docs/TRUST_CENTER.md`](docs/TRUST_CENTER.md).
+The long-term infrastructure ambition is described in [`VISION.md`](VISION.md), [`GOAL.md`](GOAL.md), [`docs/research/OPEN_BIOTECH_STACK.md`](docs/research/OPEN_BIOTECH_STACK.md), [`docs/research/OPEN_INFRASTRUCTURE_MOAT.md`](docs/research/OPEN_INFRASTRUCTURE_MOAT.md), and [`docs/trust/TRUST_CENTER.md`](docs/trust/TRUST_CENTER.md).
 
 ## Start here
 
 | You are | Read first | Then read |
 |---|---|---|
 | New human contributor | [`docs/README.md`](docs/README.md) | [`docs/getting-started/FIRST_RUN_WALKTHROUGH.md`](docs/getting-started/FIRST_RUN_WALKTHROUGH.md), [`CONTRIBUTING.md`](CONTRIBUTING.md) |
 | AI agent | [`AGENTS.md`](AGENTS.md) | [`docs/getting-started/AGENT_ONBOARDING.md`](docs/getting-started/AGENT_ONBOARDING.md), [`docs/operations/HUMAN_AGENT_COLLABORATION.md`](docs/operations/HUMAN_AGENT_COLLABORATION.md) |
-| Reviewer | [`docs/getting-started/REVIEWER_ONBOARDING.md`](docs/getting-started/REVIEWER_ONBOARDING.md) | [`docs/evidence/CLAIM_REVIEW_CHECKLIST.md`](docs/evidence/CLAIM_REVIEW_CHECKLIST.md), [`docs/RISK_REGISTER.md`](docs/RISK_REGISTER.md) |
+| Reviewer | [`docs/getting-started/REVIEWER_ONBOARDING.md`](docs/getting-started/REVIEWER_ONBOARDING.md) | [`docs/evidence/CLAIM_REVIEW_CHECKLIST.md`](docs/evidence/CLAIM_REVIEW_CHECKLIST.md), [`docs/trust/RISK_REGISTER.md`](docs/trust/RISK_REGISTER.md) |
 | Computational scientist | [`docs/evidence/README.md`](docs/evidence/README.md) | [`docs/evidence/METRICS_CURRENT.md`](docs/evidence/METRICS_CURRENT.md), [`docs/evidence/BENCHMARKING.md`](docs/evidence/BENCHMARKING.md) |
-| Data/schema/model contributor | [`docs/engineering/SCHEMA_REGISTRY.md`](docs/engineering/SCHEMA_REGISTRY.md) | [`docs/DATA_GOVERNANCE.md`](docs/DATA_GOVERNANCE.md), [`docs/engineering/ADAPTER_AUTHOR_GUIDE.md`](docs/engineering/ADAPTER_AUTHOR_GUIDE.md) |
+| Data/schema/model contributor | [`docs/engineering/SCHEMA_REGISTRY.md`](docs/engineering/SCHEMA_REGISTRY.md) | [`docs/trust/DATA_GOVERNANCE.md`](docs/trust/DATA_GOVERNANCE.md), [`docs/engineering/ADAPTER_AUTHOR_GUIDE.md`](docs/engineering/ADAPTER_AUTHOR_GUIDE.md) |
 | Wet-lab/domain expert | [`docs/review/WET_LAB_HANDOFF.md`](docs/review/WET_LAB_HANDOFF.md) | [`docs/review/EXTERNAL_REVIEW_PACKET.md`](docs/review/EXTERNAL_REVIEW_PACKET.md), [`docs/review/PRE_REGISTERED_PILOT_TEMPLATE.md`](docs/review/PRE_REGISTERED_PILOT_TEMPLATE.md) |
-| Safety reviewer | [`docs/TRUST_CENTER.md`](docs/TRUST_CENTER.md) | [`SAFETY.md`](SAFETY.md), [`SECURITY.md`](SECURITY.md) |
-| Funder/institution | [`docs/OPEN_INFRASTRUCTURE_MOAT.md`](docs/OPEN_INFRASTRUCTURE_MOAT.md) | [`docs/ADOPTION_METRICS.md`](docs/ADOPTION_METRICS.md), [`GOVERNANCE.md`](GOVERNANCE.md) |
-| Maintainer | [`GOVERNANCE.md`](GOVERNANCE.md) | [`docs/operations/SUSTAINABILITY_AND_BUS_FACTOR.md`](docs/operations/SUSTAINABILITY_AND_BUS_FACTOR.md), [`docs/RELEASE_CHECKLIST.md`](docs/RELEASE_CHECKLIST.md) |
+| Safety reviewer | [`docs/trust/TRUST_CENTER.md`](docs/trust/TRUST_CENTER.md) | [`SAFETY.md`](SAFETY.md), [`SECURITY.md`](SECURITY.md) |
+| Funder/institution | [`docs/research/OPEN_INFRASTRUCTURE_MOAT.md`](docs/research/OPEN_INFRASTRUCTURE_MOAT.md) | [`docs/research/ADOPTION_METRICS.md`](docs/research/ADOPTION_METRICS.md), [`GOVERNANCE.md`](GOVERNANCE.md) |
+| Maintainer | [`GOVERNANCE.md`](GOVERNANCE.md) | [`docs/operations/SUSTAINABILITY_AND_BUS_FACTOR.md`](docs/operations/SUSTAINABILITY_AND_BUS_FACTOR.md), [`docs/trust/RELEASE_CHECKLIST.md`](docs/trust/RELEASE_CHECKLIST.md) |
 
 ## Why this repo exists
 
@@ -157,37 +157,37 @@ openamp-foundry/
   models/README.md                       # model directory rules
   docs/README.md                         # task-based documentation front door
   docs/PROJECT_INDEX.md                  # exhaustive document catalog
-  docs/TRUST_CENTER.md                   # safety/evidence/governance trust front door
-  docs/OPEN_INFRASTRUCTURE_MOAT.md       # durable infrastructure thesis
-  docs/NUMBER_ONE_REPO_STANDARD.md       # category-leader standard
+  docs/trust/TRUST_CENTER.md                   # safety/evidence/governance trust front door
+  docs/research/OPEN_INFRASTRUCTURE_MOAT.md       # durable infrastructure thesis
+  docs/research/NUMBER_ONE_REPO_STANDARD.md       # category-leader standard
   docs/getting-started/FIRST_RUN_WALKTHROUGH.md          # first-run path
   docs/getting-started/COMMAND_SURFACE.md                # command workflows and claim boundaries
   docs/engineering/SCHEMA_REGISTRY.md                # schema and artifact registry
   docs/engineering/RUN_MANIFEST_STANDARD.md          # provenance standard
   docs/engineering/ADAPTER_AUTHOR_GUIDE.md           # safe adapter authoring
-  docs/RISK_REGISTER.md                  # major risks and mitigations
+  docs/trust/RISK_REGISTER.md                  # major risks and mitigations
   docs/operations/SUSTAINABILITY_AND_BUS_FACTOR.md  # sustainability and bus-factor plan
-  docs/PUBLICATION_POLICY.md             # public claims policy
+  docs/trust/PUBLICATION_POLICY.md             # public claims policy
   docs/research/NEXT_100_PR_MAP.md                # PR-sized roadmap
   docs/engineering/CI_AND_QUALITY_GATES.md           # CI and quality gates
   docs/operations/HUMAN_AGENT_COLLABORATION.md      # human-agent collaboration model
   docs/getting-started/REVIEWER_ONBOARDING.md            # reviewer guide
-  docs/ADOPTION_METRICS.md               # adoption metrics focused on trust
+  docs/research/ADOPTION_METRICS.md               # adoption metrics focused on trust
   docs/operations/DECISION_RECORD_TEMPLATE.md       # decision record template
   docs/getting-started/HUMAN_ONBOARDING.md               # human contributor onboarding
   docs/getting-started/AGENT_ONBOARDING.md               # agent task protocol
-  docs/PROOF_LADDER.md                   # evidence levels and claim ladder
+  docs/evidence/PROOF_LADDER.md                   # evidence levels and claim ladder
   docs/evidence/CLAIM_REVIEW_CHECKLIST.md         # claim review checklist
-  docs/DATA_GOVERNANCE.md                # data governance standard
-  docs/MODEL_CARD_TEMPLATE.md            # model/adapter card template
+  docs/trust/DATA_GOVERNANCE.md                # data governance standard
+  docs/trust/MODEL_CARD_TEMPLATE.md            # model/adapter card template
   docs/engineering/ARTIFACT_VERSIONING.md            # artifact compatibility policy
-  docs/RELEASE_CHECKLIST.md              # release checklist
+  docs/trust/RELEASE_CHECKLIST.md              # release checklist
   docs/evidence/BENCHMARKING.md                   # benchmark suite
   docs/evidence/BENCHMARK_GOVERNANCE.md           # benchmark lifecycle and governance
   docs/evidence/METRICS_CURRENT.md                # current benchmark summary
-  docs/CALIBRATION_POLICY.md             # recalibration gate policy
+  docs/evidence/CALIBRATION_POLICY.md             # recalibration gate policy
   docs/evidence/EVIDENCE_CERTIFICATE.md           # candidate certificate spec
-  docs/VIRTUAL_ASSAY_SCOPE.md            # virtual-assay scope and gates
+  docs/evidence/VIRTUAL_ASSAY_SCOPE.md            # virtual-assay scope and gates
   docs/review/WET_LAB_HANDOFF.md                # safe expert-review handoff guide
   examples/                              # toy datasets only
   outputs/.gitkeep                       # generated files ignored by git