Tools Reference

cks-mcp exposes 63 tools over the Model Context Protocol. Every tool call is a canonical operation: it runs inside a RuntimeSession, and any call that mutates state does so through a Transaction, producing an immutable Version (see Architecture).

This reference is split by function, mirroring how the tools are actually used together rather than their declaration order in the registry:

Group	Tools	What it’s for
Knowledge Lifecycle	validate_knowledge, serialize_knowledge, explain_knowledge, evolve_knowledge	Create, inspect, and change a Knowledge Structure
Version Control	list_versions, revert_version, compare_versions, explain_diff	Time-travel through a session’s history
Branching & Merging	create_branch, merge_branch, merge_knowledge, close_session, fork_sandbox	Isolate experiments and reconcile concurrent edits
Graph Exploration	query_subgraph, search_semantic, visualize_graph	Retrieve and render a neighbourhood of a graph
Verification & Integrity	verify_source, detect_contradictions	Anti-hallucination: provenance and logical consistency
LLM & AI	ai_chat, construct_knowledge, suggest_evolution, ingest_document, request_enrichment, get_llm_status, list_llm_models	AI chat with tool calling, knowledge construction from text/URL, LLM provider status, and available models
Export & Observability	export_knowledge, export_session, get_metrics, export_storage, import_storage, migrate_storage, list_plugins	Get data out, back up, migrate between backends, list installed plugins, and see how the server is performing
Memory & Persistence	register_graph, get_graph, list_graphs, search_graphs, check_graph_freshness, check_component_versions, update_registered_graph, explain_graph, check_graph_health	Save and reuse Knowledge Graphs, check component freshness, update outdated graphs, generate reports, compute health scores
Gossip & Conflict Resolution	list_gossip_conflicts, list_inference_conflicts, arbitrate_inference_conflict, resolve_gossip_conflict, refresh_verification, resolve_temporal_conflict, resolve_contradiction, review_dead_letter, approve_resolution, reject_resolution, claim_conflict_task, complete_conflict_task, fail_conflict_task, dead_letter_conflict_task, list_dead_lettered_conflicts	Drain and resolve conflicts escalated by gossip, inference, provenance, temporal, or contradiction staleness, plus the critic‑agent task lifecycle and human-in-the-loop dead-letter review
Agent Observability	list_agents, agent_status, list_processes, process_status	Monitor background sweepers and standalone agent processes
Agent Control	start_agent, stop_agent, request_process_stop	Start/stop in‑process sweepers and request graceful shutdown of standalone agents
AI Chat	ai_chat	Send a chat turn to an LLM that can call MCP tools AI Chat

Conventions used across every tool

• session_id — nearly every tool accepts or returns one. A session is created by the first call that needs to persist something (validate_knowledge, evolve_knowledge, construct_knowledge, …); pass the returned session_id to every subsequent call that should act on the same structure instead of a fresh one.
• Read vs. write — serialize_knowledge, explain_knowledge, query_subgraph, search_semantic, visualize_graph, detect_contradictions, compare_versions, explain_diff, suggest_evolution (without operations), list_versions, get_metrics, list_gossip_conflicts, list_inference_conflicts, list_dead_lettered_conflicts never create a new version. The critic‑agent tools (claim_conflict_task, complete_conflict_task, fail_conflict_task, dead_letter_conflict_task) modify outbox state but never touch sessions or versions.
• Dry-run before commit — evolve_knowledge, merge_branch, merge_knowledge, and fork_sandbox (when given operations) all validate the prospective result — including a provenance check — before ever opening a transaction. Nothing partially-invalid is ever committed.
• Errors — a failed call returns a plain JSON object with an "error" code and a human-readable "message", never a protocol-level exception. Common codes: missing_parameter, session_not_found, invalid_json, unknown_extension, unsafe_url, validation_failed.
• The json_data fallback path — validate_knowledge, serialize_knowledge, explain_knowledge, evolve_knowledge, and detect_contradictions all accept a raw json_data string as an alternative to session_id, for one-off calls that don’t need a persisted session. Every one of these paths is provenance-gated exactly like the session_id path — see Verification & Integrity.

See also: Extension Model for the opt-in extensions parameter accepted by validate_knowledge.