TOOLS.md - Available Capabilities

Core OS tools

VFS / Hyperdrive — read/write paths via agent tools (read_file, write_file, list_directory, …) on system and personal drives.
Service and timer ops — use list_services, service_status, and list_timers to inspect initd state and timer drop-ins without ad-hoc shell parsing.
Operational logs and policy — use read_cron_log, read_audit_log, read_boot_policy, and read_kernel_extension_resolution for bounded diagnostics.
Extended ops diagnostics — get_initd_graph, read_unit_journal, inspect_ipc_backpressure, get_network_summary, tail_telemetry_streams, and pkg_index_lookup.
Automation gates — list_verification_scripts, run_maintenance_gate, run_contract_checks, and summarize_build_drift provide safer wrappers for maintenance workflows.
Bridge diagnostics/actions — get_hrpc_bridge_health and get_hrpc_allowlist_status are read-focused; emit_host_notification and request_host_action are policy-gated mutations.
web_fetch — live http(s) fetches only when the operator allows them (ctx.httpFetch, BARE_OS_HTTP_ALLOWLIST / denylist). Same policy as delegated curl / wget.
POSIX-style utilities — via run_command in the guest shell (/bin/*); not full GNU.
Swarm / Protomux — peer discovery and replication are host/booter concerns; you see them through /proc and tools like get_swarm_peers when exposed.
Identity / crypto — only with explicit user approval; never exfiltrate keys or vault material.

Reasoning / process visibility

Runtime process visibility can be configured in ~/.agent/config.json:
- show_reasoning (boolean)
- reasoning_mode (off, summary, trace)
- reasoning_max_chars (bounded output)
- reasoning_include_tools (include tool call/result traces in process output)
Use edit_agent_config to toggle these safely during a session.
For provider xai, keep rest_base_url at https://api.x.ai/v1 and prefer trace mode when reasoning summaries are unavailable.
For provider groq, keep rest_base_url at https://api.groq.com/openai/v1; tool loops use OpenAI-compatible chat/completions with parallel_tool_calls and max_completion_tokens.
For Groq debugging, use trace mode and inspect process logs for provider request shape warnings.

Max-autonomy policy toggles

allow_bridge_mutations: master gate for bridge mutation tools.
allow_host_notifications: required for emit_host_notification.
allow_host_actions: required for request_host_action.
emergency_stop_mutations: immediate kill switch for all mutating bridge tools.

Autonomous coding runner

autonomous_run starts autonomous project execution with a goal, runtime cap, and required checks.
autonomous_run_status reports active state, elapsed/runtime budget, and quality gate configuration.
autonomous_run_stop requests a safe stop at the next loop checkpoint.
Autonomous done criteria require configured checks to pass (for example coreutils-test, parity, man coverage) before completion is accepted.
Guardrails enforce a denylist for dangerous operations and path restrictions even during autonomous runs.

Skills system

The agent has access to modular skills under ~/.agent/workspace/skills/ (and optionally shared skills under ~/.agent/skills/).

A compact list of skill ids + short descriptions is included in the system prompt.
When a task matches a skill, call the read_skill tool to load the full SKILL.md, then follow it exactly.
Prefer using skills over reinventing workflows.

Host-checkout helpers (git workspace on the machine)

When the user is editing the Bare OS repo on the host (not only inside this guest):

verification_hints — suggests npm run … / node scripts/verify-*.mjs from topic keywords or paths; does not run them here.
At the repo root, npm run agent:path-hints takes path arguments; npm run agent:holepunch-index dumps a JSON index of local holepunchto_repos packages.

One-shot diagnostics

runtime_diagnostic_bundle — ctx API version, resource snapshot if available, and all allowlisted /proc/bare_os/* snapshots that exist (bounded).

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