Generated by
python tools/generate_cli_reference.py. Do not edit the command table manually.
This reference contains all 288 commands registered in the authoritative CommandSpec control plane. A namespace adapter is an explicit compatibility boundary, not a direct typed handler.
| Command | Stage | Coordinator | Risk | Mutates project | Exit policy | Handler | MCP |
|---|---|---|---|---|---|---|---|
accept-revision |
writing | writing_coordinator | human_checkpoint | yes | always_success | manuscript_revision.apply_manuscript_revision |
no |
accept-section-draft |
writing | writing_coordinator | write_project | yes | always_success | manuscript_composer.accept_section_draft |
yes |
acknowledge-checkpoint-notification |
state | state_kernel | write_project | yes | always_success | checkpoint_delivery.acknowledge_checkpoint_notification |
yes |
activate-literature-corpus |
references | reference_coordinator | write_project | yes | always_success | literature_admission.activate_literature_corpus |
yes |
add-custom-reference |
references | reference_coordinator | write_project | yes | always_success | manuscript_revision.add_custom_reference |
yes |
add-literature-source |
references | reference_coordinator | write_project | yes | always_success | literature_sources.register_literature_source |
yes |
adopt-orphan-artifacts |
state | state_kernel | read | no | always_success | workspace_policy.adopt_orphan_artifacts |
yes |
apply-citation-repair |
references | reference_coordinator | write_project | yes | always_success | namespace adapter |
yes |
apply-evidence-rebind |
results | results_coordinator | human_checkpoint | yes | always_success | evidence_binding.apply_evidence_rebind |
no |
apply-literature-sync |
references | reference_coordinator | human_checkpoint | yes | always_success | literature_merge.apply_literature_merge |
no |
apply-managed-change |
state | state_kernel | write_project | yes | always_success | managed_change.apply_managed_change |
yes |
apply-manuscript-completion |
writing | writing_coordinator | human_checkpoint | yes | always_success | manuscript_completion.apply_manuscript_completion |
no |
apply-manuscript-revision |
writing | writing_coordinator | human_checkpoint | yes | always_success | manuscript_revision.apply_manuscript_revision |
no |
apply-orphan-adoption |
state | state_kernel | human_checkpoint | yes | always_success | workspace_policy.apply_orphan_adoption |
no |
apply-result-downgrade |
results | evidence_coordinator | human_checkpoint | yes | always_success | namespace adapter |
no |
apply-revision |
quality_checks | release_coordinator | write_project | yes | always_success | namespace adapter |
yes |
apply-revision-reconciliation |
state | state_kernel | human_checkpoint | yes | always_success | revision_cycle.apply_revision_reconciliation |
no |
apply-section-revision |
writing | writing_coordinator | write_project | yes | always_success | revision_transaction.apply_section_revision |
yes |
assemble-latex |
release | release_coordinator | write_project | yes | always_success | latex_assembly.assemble_latex |
yes |
assess-core-evidence |
results | evidence_coordinator | write_project | yes | decision_pass | gate_handlers.assess_core_evidence_gate |
yes |
assess-core-evidence-readiness |
state | state_kernel | read | no | always_success | core_evidence_readiness.assess_core_evidence_readiness |
yes |
assess-data-feasibility |
data | data_coordinator | write_project | yes | always_success | namespace adapter |
yes |
assess-data-quality |
data | data_coordinator | write_project | yes | quality_pass | gate_handlers.assess_data_quality_gate |
yes |
assess-figure-contracts |
results | evidence_coordinator | write_project | yes | decision_pass | figure_contracts.assess_project_figure_contracts |
yes |
assess-figure-publication-quality |
results | evidence_coordinator | write_project | yes | always_success | namespace adapter |
yes |
assess-functional-quality-release |
release | release_coordinator | write_project | yes | decision_pass | writing_architecture.assess_functional_quality_release |
yes |
assess-manuscript-quality |
writing | writing_coordinator | write_project | yes | always_success | namespace adapter |
yes |
assess-manuscript-quality-release |
quality_checks | release_coordinator | write_project | yes | status_passed | independent_review.assess_manuscript_quality_release |
yes |
assess-method-feasibility |
methods | method_coordinator | write_project | yes | always_success | namespace adapter |
yes |
assess-paper-quality-parity |
release | release_coordinator | write_project | yes | decision_pass | paper_quality_parity.assess_paper_quality_parity |
yes |
assess-plugin-sufficiency |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
assess-pre-execution-support |
capabilities | capability_coordinator | write_project | yes | always_success | pre_execution_support.assess_pre_execution_support |
yes |
assess-publication-readiness |
quality_checks | release_coordinator | write_project | yes | always_success | namespace adapter |
yes |
assess-research-plan-feasibility |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
assess-result-support |
results | evidence_coordinator | write_project | yes | always_success | namespace adapter |
yes |
assess-result-validity |
results | evidence_coordinator | write_project | yes | decision_pass | gate_handlers.assess_result_validity_gate |
yes |
assess-review-rule-coverage |
capabilities | capability_coordinator | write_project | yes | always_success | statistical_validation.assess_review_rule_coverage |
yes |
assess-review-rules |
quality_checks | release_coordinator | write_project | yes | always_success | namespace adapter |
yes |
audit-checkpoint-v5-migration |
state | state_kernel | read | no | always_success | checkpoint_migration.audit_checkpoint_v5_migration |
yes |
audit-citations |
citation_audit | release_coordinator | write_project | yes | status_passed | citation_audit.audit_citations |
yes |
audit-evidence-governance |
quality_checks | state_kernel | read | no | always_success | governance_contract.evaluate_governance |
yes |
audit-evidence-identity |
state | state_kernel | read | no | status_passed | evidence_audit.audit_evidence_identity |
yes |
audit-human-checkpoint-policy |
state | state_kernel | read | no | always_success | protected_action_policy.audit_registered_human_checkpoint_policy |
yes |
audit-literature-integrity |
references | reference_coordinator | write_project | yes | status_passed | literature_integrity.audit_literature_integrity |
yes |
audit-longitudinal-consistency |
quality_checks | state_kernel | write_project | yes | always_success | longitudinal_consistency.audit_longitudinal_consistency |
yes |
audit-project-capabilities |
capabilities | capability_coordinator | write_project | yes | always_success | project_capability_audit.audit_project_capabilities |
yes |
audit-research-plan-migration |
capabilities | capability_coordinator | read | no | always_success | research_plan_confirmation.audit_research_plan_migration |
yes |
audit-workflow-runtime |
state | state_kernel | read | no | always_success | workflow_trace.audit_workflow_runtime |
yes |
begin-managed-change |
state | state_kernel | write_project | yes | always_success | managed_change.begin_managed_change |
yes |
begin-revision-cycle |
state | state_kernel | human_checkpoint | yes | always_success | revision_cycle.begin_revision_cycle |
no |
benchmark-document-parsers |
quality_checks | release_coordinator | write_project | yes | always_success | literature_benchmark.run_document_parser_benchmark |
yes |
benchmark-literature-quality |
quality_checks | release_coordinator | write_project | yes | always_success | literature_benchmark.run_literature_quality_benchmark |
yes |
bootstrap-discipline-foundation |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
build-argument-matrices |
state | state_kernel | write_project | yes | always_success | namespace adapter |
yes |
build-code-provenance |
methods | method_coordinator | write_project | yes | always_success | namespace adapter |
yes |
build-data-context |
data | data_coordinator | write_project | yes | always_success | namespace adapter |
yes |
build-manuscript-source-map |
writing | writing_coordinator | write_project | yes | always_success | manuscript_revision.build_manuscript_source_map |
yes |
build-method-context |
methods | method_coordinator | write_project | yes | always_success | namespace adapter |
yes |
build-panel-contracts |
state | state_kernel | write_project | yes | always_success | namespace adapter |
yes |
build-paper-narrative |
state | state_kernel | write_project | yes | always_success | namespace adapter |
yes |
build-reference-registry |
references | reference_coordinator | write_project | yes | always_success | bibliography.build_reference_registry |
yes |
build-results-synthesis |
results | evidence_coordinator | write_project | yes | always_success | namespace adapter |
yes |
build-section-lifecycles |
writing | writing_coordinator | write_project | yes | always_success | namespace adapter |
yes |
build-statistical-validation-contract |
capabilities | capability_coordinator | write_project | yes | always_success | statistical_validation.build_statistical_validation_contract |
yes |
capture-discipline-learning |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
checkpoint |
state | state_kernel | write_project | yes | always_success | namespace adapter |
no |
classify-code-ownership |
methods | method_coordinator | write_project | yes | always_success | namespace adapter |
yes |
classify-data-access |
data | data_coordinator | write_project | yes | always_success | namespace adapter |
yes |
classify-plugin-reusability |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
classify-skill-source |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
collect-literature |
references | reference_coordinator | write_project | yes | always_success | literature_sources.collect_literature_sources |
yes |
collect-method-plan |
methods | method_coordinator | write_project | yes | always_success | namespace adapter |
yes |
commit-revision-candidate |
release | state_kernel | human_checkpoint | yes | always_success | revision_cycle.commit_revision_candidate |
no |
compare-checkpoint-decision |
state | state_kernel | read | no | always_success | checkpoint_summary.compare_checkpoint_decision |
yes |
compare-research-plan-decision |
capabilities | capability_coordinator | read | no | always_success | research_plan_confirmation.compare_research_plan_decision |
yes |
compile-latex-pdf |
release | release_coordinator | execute_science | yes | always_success | namespace adapter |
yes |
compile-skill-source |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
configure-review-policy |
state | state_kernel | human_checkpoint | yes | always_success | review_policy.configure_review_policy |
no |
confirm-final-manuscript |
release | release_coordinator | human_checkpoint | yes | always_success | final_manuscript_confirmation.confirm_final_manuscript |
no |
confirm-literature-corpus |
references | literature_coordinator | human_checkpoint | yes | always_success | literature_confirmation.confirm_literature_corpus |
no |
confirm-research-plan |
capabilities | capability_coordinator | human_checkpoint | yes | always_success | research_plan_confirmation.confirm_research_plan |
no |
continue |
state | state_kernel | write_project | yes | always_success | workflow_macros.continue_workflow |
yes |
create-project |
state | state_kernel | write_project | yes | always_success | namespace adapter |
yes |
create-project-version |
state | state_kernel | write_project | yes | always_success | project_versioning.create_project_version_from_plan |
yes |
detect-artifact-drift |
state | state_kernel | read | no | always_success | namespace adapter |
yes |
diagnose-figure-execution |
results | evidence_coordinator | write_project | yes | always_success | namespace adapter |
yes |
diagnose-gate-failures |
quality_checks | release_coordinator | write_project | yes | always_success | namespace adapter |
yes |
discover-research-code |
capabilities | capability_coordinator | write_project | yes | always_success | literature_code_enrichment.discover_research_code |
yes |
discover-research-repos |
capabilities | capability_coordinator | network_external | yes | always_success | namespace adapter |
yes |
discover-review-workflow-gaps |
quality_checks | release_coordinator | write_project | yes | always_success | namespace adapter |
yes |
doctor |
state | state_kernel | read | no | always_success | doctor.doctor_project |
yes |
doctor-project-layout |
state | state_kernel | read | no | always_success | workspace_policy.doctor_project_layout |
yes |
enrich-literature-code-leads |
references | reference_coordinator | write_project | yes | always_success | literature_code_enrichment.enrich_literature_code_leads |
yes |
eval |
quality_checks | release_coordinator | write_project | yes | always_success | eval_runtime.run_eval_command |
yes |
evaluate-capability-routing |
capabilities | capability_coordinator | read | no | always_success | namespace adapter |
yes |
evaluate-checkpoint-authority |
state | state_kernel | read | no | always_success | review_policy.evaluate_checkpoint_authority |
yes |
execute-data-plugins |
capabilities | capability_coordinator | execute_science | yes | always_success | namespace adapter |
yes |
execute-method-plugins |
capabilities | capability_coordinator | execute_science | yes | always_success | namespace adapter |
yes |
explain-reconfirmation |
state | state_kernel | read | no | always_success | checkpoint_summary.explain_reconfirmation |
yes |
explain-research-plan-reconfirmation |
capabilities | capability_coordinator | read | no | always_success | research_plan_confirmation.explain_research_plan_reconfirmation |
yes |
extension-doctor |
state | state_kernel | read | no | always_success | extensions.status_projection.extension_status |
yes |
extract-method-formulas |
methods | method_coordinator | write_project | yes | always_success | namespace adapter |
yes |
extract-plugin-candidates |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
extract-review-rule-signals |
quality_checks | release_coordinator | write_project | yes | always_success | namespace adapter |
yes |
extract-skill-capabilities |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
fetch-research-code-archive |
capabilities | capability_coordinator | human_checkpoint | yes | always_success | literature_code_enrichment.fetch_research_code_archive |
no |
finalize-core-evidence-batch |
state | state_kernel | write_project | yes | always_success | core_evidence_readiness.finalize_core_evidence_batch |
yes |
generalize-plugin-candidate |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
generate-analysis-code |
methods | method_coordinator | execute_science | yes | always_success | namespace adapter |
yes |
generate-citation-repair-plan |
references | reference_coordinator | write_project | yes | always_success | namespace adapter |
yes |
generate-plan |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
generate-revision-plan |
quality_checks | release_coordinator | write_project | yes | always_success | namespace adapter |
yes |
grant-agent-review |
state | state_kernel | human_checkpoint | yes | always_success | review_policy.grant_agent_review |
no |
import-review-findings |
writing | writing_coordinator | write_project | yes | always_success | manuscript_revision.import_review_findings |
yes |
import-version-assets |
state | state_kernel | write_project | yes | always_success | project_versioning.import_version_assets |
yes |
index-skill-source |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
inspect-evidence-bindings |
results | results_coordinator | read | no | always_success | evidence_binding.inspect_evidence_bindings |
yes |
inspect-project-migration |
state | state_kernel | read | no | always_success | project_state.inspect_project_migration |
yes |
inspect-reference-duplicates |
references | reference_coordinator | write_project | yes | always_success | bibliography.inspect_reference_duplicates |
yes |
inspect-research-code-source |
capabilities | capability_coordinator | write_project | yes | always_success | literature_code_enrichment.inspect_research_code_source |
yes |
inspect-research-repo |
capabilities | capability_coordinator | read | no | always_success | namespace adapter |
yes |
inspect-review-evidence |
state | state_kernel | read | no | always_success | review_evidence.inspect_review_evidence |
yes |
inspect-skill-source |
capabilities | capability_coordinator | read | no | always_success | namespace adapter |
yes |
inspect-system-of-record |
state | state_kernel | read | no | always_success | project_system_of_record.inspect_project_system_of_record |
yes |
install-skill |
state | state_kernel | write_project | no | always_success | skill_sync.install_skill |
no |
inventory-data |
data | data_coordinator | write_project | yes | always_success | namespace adapter |
yes |
inventory-data-sources |
data | data_coordinator | write_project | yes | always_success | namespace adapter |
yes |
inventory-results |
results | evidence_coordinator | write_project | yes | always_success | namespace adapter |
yes |
job-cancel |
state | state_kernel | human_checkpoint | yes | always_success | jobs.job_cancel |
no |
job-notifications |
state | state_kernel | read | no | always_success | jobs.job_notifications |
yes |
job-status |
state | state_kernel | read | no | always_success | jobs.job_status |
yes |
learn-writing-style-from-draft |
writing | writing_coordinator | write_project | yes | always_success | namespace adapter |
yes |
list-capability-packs |
capabilities | capability_coordinator | read | no | always_success | namespace adapter |
yes |
list-literature-sources |
references | reference_coordinator | read | no | always_success | literature_sources.list_literature_sources |
yes |
list-revision-tasks |
writing | writing_coordinator | read | no | always_success | manuscript_revision.list_revision_tasks |
yes |
list-zotero-collections |
references | reference_coordinator | read | no | always_success | namespace adapter |
yes |
load-project |
state | state_kernel | read | no | always_success | namespace adapter |
yes |
manuscript-completion-status |
writing | writing_coordinator | read | no | always_success | manuscript_completion.manuscript_completion_status |
yes |
map-repository-workflow |
state | state_kernel | write_project | yes | always_success | namespace adapter |
yes |
map-skill-capabilities |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
mark-stage-stale |
state | state_kernel | write_project | yes | always_success | namespace adapter |
yes |
mcp-doctor |
state | state_kernel | read | no | always_success | mcp_install.mcp_doctor |
yes |
mcp-install |
state | state_kernel | write_project | no | always_success | mcp_install.mcp_install |
no |
migrate-core-evidence-batch |
state | state_kernel | write_project | yes | always_success | core_evidence_batch.migrate_legacy_core_evidence_batch |
yes |
migrate-literature-index |
references | reference_coordinator | write_project | yes | always_success | literature_migration.migrate_literature_index |
yes |
migrate-project |
state | state_kernel | write_project | yes | always_success | project_state.migrate_project |
yes |
package-plugin-contribution |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
parse-literature-document |
references | reference_coordinator | write_project | yes | always_success | mineru_adapter.parse_literature_document |
yes |
parse-literature-source-documents |
references | reference_coordinator | write_project | yes | always_success | literature_sources.parse_registered_literature_documents |
yes |
path-budget-check |
state | state_kernel | read | no | status_passed | workspace_policy.assess_path_budget |
yes |
pending-checkpoint-notification |
state | state_kernel | read | no | always_success | checkpoint_delivery.pending_checkpoint_notification |
yes |
plan-figures |
results | evidence_coordinator | write_project | yes | always_success | namespace adapter |
yes |
plan-project-version |
state | state_kernel | read | no | always_success | project_versioning.plan_project_version |
yes |
preflight-plugin-contribution |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
preflight-research-feasibility |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
prepare-analysis-revision |
quality_checks | release_coordinator | write_project | yes | always_success | namespace adapter |
yes |
prepare-core-evidence-batch |
state | state_kernel | write_project | yes | always_success | core_evidence_batch.prepare_core_evidence_batch |
yes |
prepare-data-acquisition |
data | data_coordinator | write_project | yes | always_success | namespace adapter |
yes |
prepare-discussion-comparison |
writing | writing_coordinator | write_project | yes | always_success | namespace adapter |
yes |
prepare-evidence-rebind |
results | results_coordinator | write_project | yes | always_success | evidence_binding.prepare_evidence_rebind |
yes |
prepare-independent-manuscript-review |
quality_checks | release_coordinator | write_project | yes | always_success | independent_review.prepare_independent_manuscript_review |
yes |
prepare-literature-admission |
references | reference_coordinator | write_project | yes | always_success | literature_admission.build_literature_admission_packet |
yes |
prepare-manuscript-completion |
writing | writing_coordinator | write_project | yes | always_success | manuscript_completion.prepare_manuscript_completion |
yes |
prepare-method-blueprint |
methods | method_coordinator | write_project | yes | always_success | namespace adapter |
yes |
prepare-panel-repair |
state | state_kernel | write_project | yes | always_success | namespace adapter |
yes |
prepare-plugin-rescue |
capabilities | capability_coordinator | network_external | yes | always_success | plugin_rescue.prepare_plugin_rescue |
yes |
prepare-pre-execution-rescue |
capabilities | capability_coordinator | write_project | yes | always_success | pre_execution_support.prepare_pre_execution_rescue |
yes |
prepare-project-method-implementation |
methods | capability_coordinator | write_project | yes | always_success | project_method_implementation.prepare_project_method_implementation |
yes |
prepare-result-rescue |
results | evidence_coordinator | human_checkpoint | yes | always_success | namespace adapter |
no |
prepare-results-semantic-repair |
results | evidence_coordinator | write_project | yes | always_success | namespace adapter |
yes |
prepare-revision |
writing | writing_coordinator | write_project | yes | always_success | manuscript_revision.prepare_revision_from_task |
yes |
prepare-revision-reconciliation |
state | state_kernel | write_project | yes | always_success | revision_cycle.prepare_revision_reconciliation |
yes |
prepare-scientific-editor |
writing | writing_coordinator | write_project | yes | always_success | writing_architecture.prepare_scientific_editor |
yes |
prepare-section-outline |
writing | writing_coordinator | write_project | yes | always_success | namespace adapter |
yes |
prepare-section-writing |
writing | writing_coordinator | write_project | yes | always_success | manuscript_composer.build_section_evidence_packet |
yes |
preview-checkpoint-summary |
state | state_kernel | read | no | always_success | checkpoint_summary.preview_checkpoint_summary |
yes |
preview-manuscript-completion |
writing | writing_coordinator | write_project | yes | always_success | manuscript_completion.preview_manuscript_completion |
yes |
preview-manuscript-revision |
writing | writing_coordinator | write_project | yes | always_success | manuscript_revision.preview_manuscript_revision |
yes |
preview-revision |
writing | writing_coordinator | read | no | always_success | manuscript_revision.inspect_revision_preview |
yes |
promote-plugin-candidate |
capabilities | capability_coordinator | human_checkpoint | yes | always_success | namespace adapter |
no |
propose-review-engineering-plan |
quality_checks | release_coordinator | write_project | yes | always_success | namespace adapter |
yes |
quality-check |
release | release_coordinator | write_project | yes | status_passed | quality_gate.run_quality_check |
yes |
quarantine-orphan-literature |
references | reference_coordinator | human_checkpoint | yes | always_success | literature_integrity.manage_orphan_literature_quarantine |
no |
re-audit-citations |
references | reference_coordinator | write_project | yes | always_success | namespace adapter |
yes |
re-review |
quality_checks | release_coordinator | write_project | yes | always_success | namespace adapter |
yes |
rebase-project-passport |
state | state_kernel | human_checkpoint | yes | always_success | workflow_macros.rebase_project_passport |
no |
rebuild-checkpoint-presentation |
state | state_kernel | write_project | yes | always_success | checkpoint_summary.rebuild_checkpoint_presentation |
yes |
rebuild-derived |
state | state_kernel | read | no | always_success | doctor.rebuild_derived |
yes |
rebuild-literature-index |
references | reference_coordinator | write_project | yes | always_success | literature_merge.rebuild_literature_index |
yes |
recommend-statistical-revision |
quality_checks | release_coordinator | write_project | yes | always_success | namespace adapter |
yes |
reconcile-literature |
references | reference_coordinator | write_project | yes | always_success | literature_sources.reconcile_literature_sources |
yes |
reconcile-project-drift |
state | state_kernel | human_checkpoint | yes | always_success | stale_sync.reconcile_project_drift |
no |
record-independent-manuscript-review |
quality_checks | release_coordinator | write_project | yes | always_success | independent_review.record_independent_manuscript_review |
yes |
record-observation |
state | state_kernel | write_project | yes | always_success | namespace adapter |
yes |
record-plugin-rescue-outcome |
capabilities | capability_coordinator | network_external | yes | always_success | plugin_rescue.record_plugin_rescue_outcome |
yes |
record-remote-parser-consent |
references | reference_coordinator | write_project | yes | always_success | remote_parser_consent.record_consent |
yes |
record-scientific-editor-revision |
quality_checks | release_coordinator | write_project | yes | always_success | namespace adapter |
yes |
record-stage-receipt |
state | state_kernel | write_project | yes | always_success | stage_receipts.record_stage_receipt |
yes |
recover |
state | state_kernel | read | no | always_success | workflow_macros.recover_workflow |
yes |
recover-jobs |
state | state_kernel | write_project | yes | always_success | jobs.recover_jobs |
yes |
render-checkpoint-audit |
state | state_kernel | write_project | yes | always_success | checkpoint_summary.render_checkpoint_audit |
yes |
render-reference-proof |
quality_checks | reference_coordinator | write_project | yes | always_success | bibliography.render_reference_proof |
yes |
render-third-party-notices |
state | state_kernel | write_project | yes | always_success | namespace adapter |
yes |
reopen-core-evidence |
results | evidence_coordinator | human_checkpoint | yes | always_success | namespace adapter |
no |
reopen-research-plan |
capabilities | capability_coordinator | human_checkpoint | yes | always_success | research_plan_confirmation.reopen_research_plan |
no |
repair-figure-data |
results | evidence_coordinator | execute_science | yes | always_success | namespace adapter |
yes |
repair-figure-method |
results | evidence_coordinator | execute_science | yes | always_success | namespace adapter |
yes |
repair-literature-identities |
references | reference_coordinator | write_project | yes | always_success | literature_merge.repair_literature_identities |
yes |
resolve-figure-evidence |
results | evidence_coordinator | write_project | yes | always_success | evidence_resolver.resolve_figure_evidence |
yes |
resolve-journal-template |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
resolve-paragraph-evidence |
writing | evidence_coordinator | write_project | yes | always_success | evidence_resolver.resolve_paragraph_evidence |
yes |
resolve-reference-version |
references | reference_coordinator | write_project | yes | always_success | bibliography.resolve_reference_version |
yes |
resolve-research-capabilities |
capabilities | capability_coordinator | write_project | yes | always_success | research_capabilities.resolve_research_capabilities |
yes |
resolve-result-evidence |
results | evidence_coordinator | write_project | yes | always_success | namespace adapter |
yes |
resolve-venue-writing-style |
writing | writing_coordinator | write_project | yes | always_success | namespace adapter |
yes |
resume |
state | state_kernel | write_project | yes | always_success | namespace adapter |
no |
review |
quality_checks | release_coordinator | read | no | always_success | workflow_macros.review_workflow |
yes |
review-authority-shadow |
state | state_kernel | write_project | yes | always_success | review_policy.build_review_authority_shadow |
yes |
review-checkpoint |
state | state_kernel | write_project | yes | always_success | review_policy.review_checkpoint |
yes |
review-draft |
quality_checks | release_coordinator | write_project | yes | always_success | namespace adapter |
yes |
review-final-manuscript |
release | release_coordinator | write_project | yes | always_success | final_manuscript_confirmation.review_final_manuscript |
yes |
review-literature-coverage |
references | reference_coordinator | write_project | yes | always_success | literature_coverage.review_literature_coverage |
yes |
review-plugin-contribution |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
review-policy-status |
state | state_kernel | read | no | always_success | review_policy.review_policy_status |
yes |
review-research-plan |
capabilities | capability_coordinator | write_project | yes | always_success | research_plan_confirmation.review_research_plan |
yes |
review-results-with-discipline-rules |
results | evidence_coordinator | write_project | yes | always_success | namespace adapter |
yes |
revise |
writing | writing_coordinator | write_project | yes | always_success | manuscript_revision.preview_manuscript_revision |
yes |
revise-research-objective |
state | capability_coordinator | write_project | yes | always_success | research_objective.revise_research_objective |
yes |
revise-research-plan |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
revoke-agent-review |
state | state_kernel | human_checkpoint | yes | always_success | review_policy.revoke_agent_review |
no |
rollback-literature-migration |
references | reference_coordinator | human_checkpoint | yes | always_success | literature_migration.rollback_literature_migration |
no |
rollback-manuscript-completion |
writing | writing_coordinator | human_checkpoint | yes | always_success | manuscript_completion.rollback_manuscript_completion |
no |
rollback-manuscript-revision |
writing | writing_coordinator | human_checkpoint | yes | always_success | manuscript_revision.rollback_manuscript_revision |
no |
rollback-orphan-literature |
references | reference_coordinator | human_checkpoint | yes | always_success | literature_integrity.rollback_orphan_literature_quarantine |
no |
route-stage-code |
methods | method_coordinator | write_project | yes | always_success | namespace adapter |
yes |
run-citation-repair-loop |
references | reference_coordinator | write_project | yes | always_success | namespace adapter |
yes |
run-integrity-gate |
quality_checks | release_coordinator | write_project | yes | decision_pass | gate_handlers.run_integrity_gate |
yes |
run-pipeline |
state | state_kernel | read | no | always_success | namespace adapter |
yes |
score-research-repos |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
search-literature |
references | reference_coordinator | network_external | yes | always_success | namespace adapter |
yes |
session-preflight |
state | state_kernel | write_project | yes | always_success | runtime_handshake.session_preflight |
yes |
set-manuscript-metadata |
writing | writing_coordinator | write_project | yes | always_success | manuscript_revision.set_manuscript_metadata |
yes |
set-revision-mode |
state | state_kernel | human_checkpoint | yes | always_success | revision_cycle.set_revision_mode |
no |
shadow-checkpoint-v5 |
state | state_kernel | read | no | always_success | checkpoint_shadow.shadow_checkpoint_v5 |
yes |
shadow-checkpoint-v6 |
state | state_kernel | read | no | always_success | checkpoint_shadow.shadow_checkpoint_v6 |
yes |
shadow-core-evidence-batch-migration |
state | state_kernel | read | no | always_success | core_evidence_batch.shadow_core_evidence_batch_migration |
yes |
show-checkpoint-audit |
state | state_kernel | read | no | always_success | checkpoint_summary.show_checkpoint_audit |
yes |
show-checkpoint-summary |
state | state_kernel | read | no | always_success | checkpoint_summary.show_checkpoint_summary |
yes |
show-confirmation-continuity |
state | state_kernel | read | no | always_success | checkpoint_summary.show_confirmation_continuity |
yes |
show-human-review-packet |
capabilities | capability_coordinator | read | no | always_success | research_plan_confirmation.show_research_plan_review_packet |
yes |
show-scientific-baseline |
state | state_kernel | read | no | always_success | scientific_baseline.show_scientific_baseline |
yes |
show-stage-activity |
state | state_kernel | read | no | always_success | stage_activity.show_stage_activity |
yes |
skill-doctor |
state | state_kernel | read | no | always_success | skill_sync.skill_doctor |
yes |
snapshot-plugin-catalog |
capabilities | capability_coordinator | write_project | yes | always_success | plugin_catalog.write_plugin_catalog_snapshot |
yes |
snapshot-skill-source |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
start |
state | state_kernel | write_project | yes | always_success | workflow_macros.start_workflow |
yes |
status |
state | state_kernel | read | no | always_success | namespace adapter |
yes |
submit-figure-semantic-annotations |
results | evidence_coordinator | write_project | yes | always_success | namespace adapter |
yes |
submit-job |
state | state_kernel | execute_science | yes | always_success | jobs.submit_job |
yes |
submit-section-draft |
writing | writing_coordinator | write_project | yes | always_success | manuscript_composer.submit_section_draft |
yes |
summarize-plugin-candidates |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
sync-artifact-stale |
state | state_kernel | write_project | yes | always_success | namespace adapter |
yes |
sync-literature-sources |
references | reference_coordinator | write_project | yes | always_success | literature_merge.sync_literature_sources |
yes |
token-report |
state | state_kernel | read | no | always_success | token_report.build_token_cost_report |
yes |
trace-figures-to-code |
results | evidence_coordinator | write_project | yes | always_success | namespace adapter |
yes |
update-stage-status |
state | state_kernel | write_project | yes | always_success | namespace adapter |
yes |
validate-bibliography |
quality_checks | reference_coordinator | write_project | yes | status_passed | bibliography.validate_bibliography |
yes |
validate-checkpoint-readability |
state | state_kernel | read | no | always_success | checkpoint_summary.validate_checkpoint_readability |
yes |
validate-command-contracts |
state | state_kernel | read | no | always_success | command_contracts.validate_command_contracts |
yes |
validate-confirmed-figure-alignment |
results | evidence_coordinator | write_project | yes | decision_pass | figure_contracts_v026.validate_confirmed_figure_alignment |
yes |
validate-figure-captions |
results | evidence_coordinator | write_project | yes | decision_pass | figure_contracts_v026.validate_figure_captions |
yes |
validate-figure-plugin-trace |
results | evidence_coordinator | write_project | yes | always_success | namespace adapter |
yes |
validate-plugin-candidate |
capabilities | capability_coordinator | write_project | yes | always_success | namespace adapter |
yes |
validate-plugin-contract-diff |
capabilities | capability_coordinator | read | no | status_passed | plugin_catalog.validate_plugin_contract_diff |
yes |
validate-project |
state | state_kernel | read | no | always_success | namespace adapter |
yes |
validate-project-version |
state | state_kernel | read | no | status_passed | project_versioning.validate_project_version |
yes |
validate-research-plan-review |
capabilities | capability_coordinator | read | no | always_success | research_plan_confirmation.validate_research_plan_review |
yes |
validate-template-registry |
state | state_kernel | read | no | always_success | namespace adapter |
yes |
validate-third-party-provenance |
state | state_kernel | read | no | always_success | namespace adapter |
yes |
verify-environment |
environment | state_kernel | execute_science | no | status_passed | environment_verification.verify_environment |
no |
verify-methods |
methods | method_coordinator | execute_science | yes | status_success | gate_handlers.verify_methods_gate |
yes |
verify-next-action |
state | state_kernel | read | no | status_passed | doctor.verify_next_action |
yes |
write-data |
data | data_coordinator | write_project | yes | always_success | namespace adapter |
yes |
write-discussion |
writing | writing_coordinator | write_project | yes | always_success | namespace adapter |
yes |
write-github-contribution-guide |
state | state_kernel | write_project | yes | always_success | namespace adapter |
yes |
write-introduction |
writing | writing_coordinator | write_project | yes | always_success | namespace adapter |
yes |
write-methods |
methods | method_coordinator | write_project | yes | always_success | namespace adapter |
yes |
write-results |
results | evidence_coordinator | write_project | yes | always_success | namespace adapter |
yes |
human_checkpointcommands require explicit user confirmation and are not exposed as unattended MCP actions.execute_sciencecommands may run project-local scientific code within the declared execution and write-set policy.- A non-passing hard gate returns a nonzero process status according to its exit policy.
- Allowed read/write globs, input/output schemas, timeout, resource class and confirmation policy remain available from the machine-readable command-contract report.
Run draftpaper validate-command-contracts to verify parser, registry, handler and release-manifest consistency.