LifeOS Doctor Tool Capabilities: Checking and Fixing Dependencies Complete Guide

LifeOS Doctor is a self-contained diagnostic utility that probes external tools and services, writes a TTL-based capability manifest, and provides copy-paste fix commands for every detected failure.

The LifeOS Doctor tool, implemented in [Doctor.ts](https://github.com/danielmiessler/LifeOS/blob/main/LifeOS/install/LIFEOS/TOOLS/Doctor.ts), serves as the central health monitor for the LifeOS ecosystem. It performs offline and network-based checks across 13+ capabilities, records results in capabilities.json, and emits actionable remediation commands that users can run immediately. A companion Pulse module at [doctor.ts](https://github.com/danielmiessler/LifeOS/blob/main/LifeOS/install/LIFEOS/PULSE/modules/doctor.ts) exposes this data via API for UI consumption.

Core Diagnostic Actions

LifeOS Doctor executes three primary functions: Probe, Reconcile, and Statusline.

Probe: Capability Detection and Manifest Generation

The Probe action iterates over the CAPS registry and evaluates each capability through a defined lifecycle:

1. Skip if the capability was previously declined
2. Check configuration via the configured() function
3. Execute probeOffline for local validation
4. Optionally execute probeNetwork when --network flag is provided
5. Record results with timestamp, TTL, status, and fixCmd

bun LIFEOS/TOOLS/Doctor.ts

By default, this produces a formatted table showing live, broken, declined, or stale states.

Reconcile: Hook Registration Validation

The Reconcile action compares hooks present on disk against those registered in settings.json. It detects:

• Unwired hooks (registered but missing files)
• Missing hooks (files present but unregistered)
• Interpreter misconfigurations

Statusline: Prompt-Aware Health Signaling

The Pulse module consumes capabilities.json and doctor-heartbeat.json to emit a concise glyph for command-line prompts, signaling only newly-broken capabilities (respecting the ackedBroken list).

The Capability Registry

Each capability is defined in Doctor.ts with these properties:

• id — internal manifest key
• title — human-readable description
• powers — functionality summary
• ttlHours — freshness duration for cached results
• configured() — determines if setup is present
• probeOffline — local validation function
• probeNetwork — optional live service check
• fixCmd — copy-paste remediation command

Complete Capability List and Fix Commands

Capability	What It Checks	Failure Mode	Fix Command
shadow-home	Orphaned memory trees from pre-#1451 installs	Legacy $HOME/.claude/LIFEOS/MEMORY trees exist	bun <configRoot>/LIFEOS/TOOLS/Doctor.ts --reclaim
codex	codex CLI on $PATH and ~/.codex/auth.json	Binary missing or auth file absent	bun install -g @openai/codex && codex login
interceptor	Interceptor skills, Chrome/Brave/Chromium, CLI/daemon, INTERCEPTOR_TEST_CONTEXT_ID	Missing skills, browser, or test context	Run Interceptor skill setup, set INTERCEPTOR_TEST_CONTEXT_ID, then re-run Doctor
cloudflare	CLOUDFLARE_API_TOKEN and wrangler binary; optionally validates via wrangler whoami	Missing token or binary	Add CLOUDFLARE_API_TOKEN to <configRoot>/.env, then: bun LIFEOS/TOOLS/Doctor.ts --network
voice	ELEVENLABS_API_KEY and optionally ELEVENLABS_VOICE_ID; optionally performs TTS request	Missing credentials or API error (e.g., "famous_voice_not_permitted")	Set ELEVENLABS_VOICE_ID to API-permitted voice in <configRoot>/.env
ripgrep	rg binary on $PATH	Binary missing	brew install ripgrep (Linux: sudo apt-get install ripgrep)
imagemagick	magick binary on $PATH	Binary missing	brew install imagemagick (Linux: sudo apt-get install imagemagick)
gh	GitHub CLI gh on $PATH	Binary missing	brew install gh && gh auth login (Linux: see cli.github.com)
ffmpeg	ffmpeg binary on $PATH	Binary missing	brew install ffmpeg (Linux: sudo apt-get install ffmpeg)
ytdlp	yt-dlp binary on $PATH	Binary missing	brew install yt-dlp (Linux: sudo apt-get install yt-dlp)
fabric	fabric binary on $PATH	Binary missing	See fabric project for install instructions
jq	jq binary on $PATH	Binary missing	brew install jq (Linux: sudo apt-get install jq)
hook-interpreters	Executable permissions, valid shebangs, and interpreter availability for registered hooks	Non-executable script, bad shebang, or missing interpreter	bun <configRoot>/LIFEOS/TOOLS/Doctor.ts --hooks

Running Diagnostic Commands

Basic Offline Scan

bun LIFEOS/TOOLS/Doctor.ts

Produces a table with status glyphs: ✅ live, ❌ broken, ⏸ declined, ◌ stale.

Include Network Validation

bun LIFEOS/TOOLS/Doctor.ts --network

Enables live API calls for cloudflare (wrangler whoami) and voice (ElevenLabs TTS probe).

JSON Export for Automation

bun LIFEOS/TOOLS/Doctor.ts --json > doctor-report.json

Outputs the full Manifest structure including version, updatedAt, capabilities array, and integrity hash.

Opt-Out of Specific Capabilities

bun LIFEOS/TOOLS/Doctor.ts decline voice

Permanently silences voice warnings. The entry is marked declined in capabilities.json.

Re-Enable Declared Capabilities

bun LIFEOS/TOOLS/Doctor.ts enable voice

Removes the declined flag; subsequent runs will probe the capability again.

Acknowledge Current Failures

bun LIFEOS/TOOLS/Doctor.ts ack

Adds all currently broken capabilities to ackedBroken, suppressing the statusline glyph until a new regression appears.

Diagnose Hook Interpreters

bun LIFEOS/TOOLS/Doctor.ts --hooks

Reports per-hook issues such as:

• myhook.hook.ts: not executable (chmod +x)
• somehook.hook.sh: shebang interpreter sh not on PATH

Reclaim Legacy Memory Trees

bun LIFEOS/TOOLS/Doctor.ts --reclaim

Detects pre-#1451 shadow $HOME/.claude/LIFEOS/MEMORY trees, merges JSONL logs, copies missing artifacts, and moves old data to timestamped backups.

Key Files and Their Roles

File	Purpose	Location
Doctor.ts	Core implementation, capability definitions, CLI, manifest I/O	LIFEOS/install/LIFEOS/TOOLS/Doctor.ts
doctor.ts (Pulse)	Read-only API serving manifest, heartbeat, and hook reconciliation	LIFEOS/install/LIFEOS/PULSE/modules/doctor.ts
settings.json	User hook registrations; inspected by hook-interpreters check	~/.claude/settings.json (user-specific)
capabilities.json	TTL-based advisory cache with SHA-256 integrity hash	~/.claude/LIFEOS/MEMORY/STATE/ (runtime)
doctor-heartbeat.json	Run timestamp and network flag record	~/.claude/LIFEOS/MEMORY/STATE/ (runtime)
.capabilities-salt	32-byte random salt for manifest hashing	~/.claude/LIFEOS/MEMORY/STATE/ (runtime)

The manifest is write-locked to the Doctor tool itself; the UI and Pulse module consume it read-only, ensuring single-source-of-truth integrity.

Summary

• LifeOS Doctor probes 13+ capabilities ranging from CLI binaries (rg, jq, ffmpeg) to authenticated services (codex, cloudflare, voice)
• Three action modes: Probe (manifest generation), Reconcile (hook validation), and Statusline (prompt health glyph)
• TTL-based caching prevents redundant checks while keeping results fresh per-capability
• Copy-paste fix commands eliminate guesswork for every detected failure
• Network probing (--network) validates live service authentication without making it mandatory
• Declarative lifecycle management via decline, enable, and ack subcommands lets users curate their dependency surface

Frequently Asked Questions

How does LifeOS Doctor determine if a capability is broken?

LifeOS Doctor calls the configured() function for each capability to check whether required setup exists (binaries on $PATH, environment variables, auth files). If configured() returns false, the capability is marked broken immediately with its fixCmd. Otherwise, probeOffline runs to validate functionality. Network probes only execute with the --network flag.

What is the difference between declined and ackedBroken states?

Declined (bun Doctor.ts decline <cap>) permanently removes a capability from consideration—the user explicitly opts out. AckedBroken (bun Doctor.ts ack) suppresses the statusline glyph for currently broken capabilities while keeping them in the manifest; new failures will still trigger alerts.

Can I use LifeOS Doctor output in CI/CD pipelines?

Yes. Run bun LIFEOS/TOOLS/Doctor.ts --json to emit machine-readable output. The JSON contains the full Manifest type with version, timestamp, per-capability status, and fix commands. Parse the capabilities array to gate workflows on specific dependency availability.

{
  "mcpServers": {
    "instagit": {
      "command": "npx",
      "args": ["-y", "instagit@latest"]
    }
  }
}