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Built-in Tools in Cipher

This page summarizes the built-in tools that ship with Cipher, grouped by category. It shows each tool’s purpose at a glance and how it’s typically used. Some tools are internal-only; others are agent-accessible.

Notes

  • Some tools depend on embeddings. If embeddings are disabled or unavailable, those tools are skipped automatically.
  • Workspace Memory tools require USE_WORKSPACE_MEMORY=true.
  • Knowledge Graph tools require KNOWLEDGE_GRAPH_ENABLED=true.

Memory Tools

  • cipher_extract_and_operate_memory:
    • Extracts knowledge from interactions and immediately applies ADD/UPDATE/DELETE/NONE as one atomic operation. Embedding-dependent.
  • cipher_memory_search:
    • Semantic search over stored knowledge to retrieve relevant facts/code patterns. Embedding-dependent.
  • cipher_store_reasoning_memory:
    • Stores high-quality reasoning traces for future analysis (append-only reflection memory). Embedding-dependent.

Reasoning (Reflection) Tools

  • cipher_extract_reasoning_steps (internal):
    • Extracts structured reasoning steps from user input (explicit and implicit patterns).
  • cipher_evaluate_reasoning (internal):
    • Evaluates a reasoning trace for quality and generates improvement suggestions.
  • cipher_search_reasoning_patterns (agent-accessible):
    • Searches reflection memory for relevant reasoning patterns; supports optional query refinement.

Workspace Memory Tools (team context)

  • cipher_workspace_search:
    • Searches team/project workspace memory for progress, bugs, PR summaries, and collaboration context. Embedding-dependent.
  • cipher_workspace_store:
    • Background tool capturing team and project signals into workspace memory. Embedding-dependent.

Knowledge Graph Tools

  • cipher_add_node, cipher_update_node, cipher_delete_node:
    • Manage entities (nodes) in the knowledge graph.
  • cipher_add_edge:
    • Create relationships between entities.
  • cipher_search_graph, cipher_enhanced_search:
    • Search the graph with basic and enhanced strategies.
  • cipher_get_neighbors:
    • Retrieve related entities around a node.
  • cipher_extract_entities:
    • Extract entities for graph insertion from text.
  • cipher_query_graph:
    • Run graph queries and retrieve structured results.
  • cipher_relationship_manager:
    • Higher-level relationship operations and maintenance.

System Tools

  • cipher_bash (agent-accessible):
    • Execute bash commands. Supports one-off or persistent sessions with working dir and timeout controls.

Operational Notes

  • Embedding-dependent tools are automatically excluded in chat-only mode or when embeddings are disabled.
  • Workspace tools are included only when USE_WORKSPACE_MEMORY=true (and can disable default memory with DISABLE_DEFAULT_MEMORY=true).
  • Knowledge Graph tools are included only when KNOWLEDGE_GRAPH_ENABLED=true.

For setup and environment flags, see: