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Draftpaper-loop CLI Reference

Generated by python tools/generate_cli_reference.py. Do not edit the command table manually.

This reference contains all 211 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
add-custom-reference references reference_coordinator write_project yes always_success manuscript_revision.add_custom_reference 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-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-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 namespace adapter yes
assess-core-evidence results evidence_coordinator write_project yes decision_pass gate_handlers.assess_core_evidence_gate 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-citations citation_audit release_coordinator write_project yes status_passed citation_audit.audit_citations yes
audit-project-capabilities capabilities capability_coordinator write_project yes always_success project_capability_audit.audit_project_capabilities yes
audit-workflow-runtime state state_kernel read no always_success workflow_trace.audit_workflow_runtime 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 human_checkpoint 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-method-plan methods method_coordinator write_project yes always_success namespace adapter 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
confirm-final-manuscript release release_coordinator human_checkpoint yes always_success final_manuscript_confirmation.confirm_final_manuscript no
confirm-research-plan capabilities capability_coordinator human_checkpoint yes always_success research_plan_confirmation.confirm_research_plan no
continue state state_kernel read no 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-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
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
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
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
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
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-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-repo capabilities capability_coordinator read no always_success namespace adapter 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-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-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
path-budget-check state state_kernel read no status_passed workspace_policy.assess_path_budget 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-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-independent-manuscript-review quality_checks release_coordinator write_project yes always_success independent_review.prepare_independent_manuscript_review 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 namespace adapter 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-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-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
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-derived state state_kernel read no always_success doctor.rebuild_derived yes
recommend-statistical-revision quality_checks release_coordinator write_project yes always_success namespace adapter yes
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 namespace adapter 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-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
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 human_checkpoint yes always_success namespace adapter no
review quality_checks release_coordinator read no always_success workflow_macros.review_workflow 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-plugin-contribution capabilities capability_coordinator write_project yes always_success namespace adapter 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
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
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
set-manuscript-metadata writing writing_coordinator write_project yes always_success manuscript_revision.set_manuscript_metadata 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
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-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-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-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

Interpretation

  • human_checkpoint commands require explicit user confirmation and are not exposed as unattended MCP actions.
  • execute_science commands 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.