RyanNg

# 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: - [Configuration](./configuration.md) - [Workspace Memory](./workspace-memory.md) - [Vector Stores](./vector-stores.md) - [Embedding Configuration](./embedding-configuration.md)