Nucleus Sovereign Agent OS

Enforce file integrity, security posture, and automated verification loops for the Nucleus Agent OS. Use this tool when you need to lock files against modification, switch security modes, or run auto-fix cycles. Do NOT use for task management (use nucleus_tasks), session state (use nucleus_sessions), or memory storage (use nucleus_engrams). Actions: 'lock' sets an immutable flag on a file preventing modification. 'unlock' removes that flag (destructive: re-enables writes). 'set_mode' switches between 'red' (restricted, blocks dangerous ops) and 'blue' (permissive) security modes. 'auto_fix_loop' runs a verify-diagnose-fix-retry cycle: it executes your verification_command, and if it fails, attempts to fix the file, then retries until the command passes or max retries exceeded. 'delete_file' permanently removes a file (destructive, irreversible). 'watch' monitors a file path and returns changes detected within the duration window. 'curl' proxies HTTP requests through Nucleus egress controls. 'pip_install' installs Python packages with governance audit logging. 'status' returns current security mode and lock state. 'list_directory' returns directory contents. Side effects: lock/unlock modify filesystem extended attributes. delete_file removes data permanently. Prerequisites: .brain directory must exist. Returns JSON with {success: boolean, data: object}. Example: {action: 'auto_fix_loop', params: {file_path: 'src/app.py', verification_command: 'python -m py_compile src/app.py'}} returns {success: true, data: {iterations: 2, fixed: true}}.

Store, query, and search persistent memory (engrams) that survives across AI sessions, plus health monitoring and context graph visualization. Use this tool when you need to remember something for future sessions, recall past decisions, search the knowledge base, or check system health. Do NOT use for task tracking (use nucleus_tasks), session lifecycle (use nucleus_sessions), or agent coordination (use nucleus_agents). Engrams are the fundamental memory unit — each has content, optional tags for categorization, source attribution, and arbitrary metadata. Actions: 'write_engram' persists new knowledge to .brain/engrams/ (side effect: creates a JSONL entry). 'query_engrams' retrieves engrams filtered by tag, context, or intensity. 'search_engrams' performs full-text search across all stored knowledge. 'health' checks brain directory integrity and returns file counts and sizes. 'version' returns Nucleus version, Python version, and platform info. 'audit_log' shows the decision audit trail with timestamps. 'morning_brief' generates a daily status report with task summaries, session history, and recommendations. 'governance_status' shows current security mode and lock state. 'context_graph' builds a relationship map between related engrams. 'engram_neighbors' traverses the graph from a specific engram. 'pulse_and_polish' analyzes engram quality and suggests improvements. 'fusion_reactor' cross-references multiple engrams to generate insights. 'billing_summary' shows resource usage. All read operations are non-destructive. Prerequisites: .brain directory must exist. Returns JSON with {success: boolean, data: object}. Example: {action: 'write_engram', params: {content: 'Auth uses JWT with 24h expiry', tags: ['architecture', 'auth']}} returns {success: true, data: {key: 'engram_a1b2c3', stored: true}}.

Manage a priority task queue with escalation, human-in-the-loop (HITL) gates, and cognitive depth tracking to prevent context-switch overhead and rabbit-holing. Use this tool when you need to create, assign, update, or track work items. Do NOT use for persistent knowledge storage (use nucleus_engrams), session management (use nucleus_sessions), or multi-agent coordination (use nucleus_agents). Actions: 'add' creates a new task with a priority level (critical/high/medium/low) and optional tags. 'list' shows tasks filtered by status — returns an array of task objects. 'get_next' returns the highest-priority unclaimed task. 'claim' assigns a task to the current agent (side effect: sets status to in_progress). 'update' changes task status (pending/in_progress/done/blocked) with optional notes. 'escalate' flags a task for human review with a reason. 'import_jsonl' bulk-imports tasks from a JSONL file. 'depth_push' increments cognitive nesting depth (tracks how deep into subtasks you've gone). 'depth_pop' decrements it. 'depth_show' returns current depth and max. 'depth_reset' clears depth to zero. 'depth_set_max' sets the maximum allowed depth — system warns when exceeded. 'depth_map' visualizes the full depth tree. 'context_switch' saves current task state and loads another task's context. All mutations write to .brain/tasks/. Prerequisites: .brain directory. Returns JSON with {success: boolean, data: object}. Example: {action: 'add', params: {title: 'Fix auth bug', priority: 'high', tags: ['backend']}} returns {success: true, data: {task_id: 'task_x1y2', created: true}}.

Manage session lifecycles with save/resume, structured event logging, key-value state persistence, and named checkpoints for rollback. Use this tool to maintain continuity across AI conversations, track what happened during a work session, and hand off context between sessions or agents. Do NOT use for persistent knowledge (use nucleus_engrams), task tracking (use nucleus_tasks), or multi-agent sync (use nucleus_sync). Actions: 'start' begins a new session with a stated goal and optional tags. 'save' persists current session state to .brain/sessions/. 'resume' restores a previous session with full context including events, state, and active tasks. 'end' closes the active session and records duration. 'emit_event' appends a structured event to the session log (side effect: writes to events.jsonl). 'read_events' retrieves event history with optional filters. 'get_state' reads the session's key-value state. 'update_state' sets a key-value pair. 'checkpoint' creates a named snapshot of current state for later rollback. 'resume_checkpoint' restores state from a checkpoint. 'handoff_summary' generates context for transitioning to a new session or agent. 'archive_resolved' removes completed sessions (destructive: deletes session files). 'garbage_collect' removes stale sessions older than threshold (destructive). Prerequisites: .brain directory. Returns JSON with {success: boolean, data: object}. Example: {action: 'start', params: {goal: 'Fix authentication bug', tags: ['backend', 'auth']}} returns {success: true, data: {session_id: 'sess_abc123', started: true}}.

Coordinate state across multiple AI agents, store and retrieve named artifacts, manage trigger-based automation, and orchestrate deployments. Use this tool when multiple agents need to share data, when you need to persist artifacts for cross-session use, or when managing deployment workflows. Do NOT use for persistent memory (use nucleus_engrams), session state (use nucleus_sessions), or task assignment (use nucleus_tasks). Actions: 'identify_agent' registers the current agent's identity in the brain. 'sync_status' shows sync state. 'sync_now' forces immediate state replication between brains (may overwrite remote data). 'write_artifact' stores a named data blob in .brain/artifacts/ for cross-session sharing (side effect: creates file). 'read_artifact' retrieves a stored artifact. 'list_artifacts' shows all stored artifacts. 'trigger_agent' dispatches an event to another registered agent. 'get_triggers'/'evaluate_triggers' manage automated trigger rules. 'start_deploy_poll' begins monitoring a deployment service for readiness. 'check_deploy' queries deployment status. 'complete_deploy' marks deployment as finished. 'smoke_test' validates a deployed service endpoint by hitting its URL. 'shared_read'/'shared_write'/'shared_list' manage a shared key-value store visible to all agents. Prerequisites: .brain directory. Sync operations require at least two configured brains. Deploy actions require network access. Returns JSON with {success: boolean, data: object}. Example: {action: 'write_artifact', params: {name: 'api_schema', content: '{...}', mime_type: 'application/json'}} returns {success: true, data: {stored: true, path: '.brain/artifacts/api_schema'}}.

Activate Synthesizer agent to orchestrate the current sprint.

Initialize a new sprint with the given goal.

Get instant context when starting a new session. Call this first.

Live state.json content — current session, active tasks, config

Recent events from the event ledger with timestamps

Automation trigger rules and their evaluation state

Current cognitive depth state — shows nesting level in task tree

Full context for new sessions — read this first in any new conversation