| name | reasonix-guide |
| description | Troubleshoot and configure Reasonix capabilities: Skills (project/custom/global/builtin priority, discovery dirs), Commands (override order, /dir:file naming), Hooks (11 events, project trust, matchers, timeouts), MCP (reasonix.toml + .mcp.json + plugin packages, auto_start), plugin packages (native/Codex/Claude manifests), and AGENTS.md / instruction docs. Use when the user asks how to configure, debug missing skills/commands/hooks/MCP/plugins, or diagnose capability loading. |
| runAs | inline |
Reasonix self-diagnostics guide
This skill is inlined. Prefer evidence over guessing.
First action
- Run a static capability report (no network, no MCP subprocesses):
reasonix doctor capabilities --json
- Only if the user explicitly allows starting third-party MCP servers (may network and pass configured env/headers), run live probe:
reasonix doctor capabilities --live --timeout 5s --json
- On desktop, open Settings → Diagnostics for the same report model. The desktop "include current session runtime" toggle only reads the active tab Host (connected/failed/deferred/disabled); it does not start MCP.
Do not invent auto-fixes. Surface stable issue codes, sources, and remediations from the report.
Skills
Config sources and priority
Winner per skill name (highest first):
- project —
<workspace>/{.reasonix,.agents,.agent,.claude}/skills/
- custom —
[skills].paths (and plugin package skill roots)
- global —
<Reasonix home>/skills and home convention dirs
- builtin — shipped skills (including this guide)
Same name: higher scope wins; lower scopes are shadowed. [skills].disabled_skills hides a name from List/Read entirely.
Discovery conventions: .reasonix, .agents, .agent, .claude (see config.ConventionDirs). Layouts: <name>/SKILL.md or flat <name>.md (Claude flat files need skill frontmatter).
Checks
| Entry | How |
|---|
| CLI | reasonix doctor capabilities → Skills section |
| Desktop | Settings → Skills; Settings → Diagnostics |
| Agent | /skill list, /reasonix-guide, run_skill |
Symptom → cause → fix
| Symptom | Likely cause | Fix |
|---|
| Skill missing from index | Disabled, shadowed, missing description, wrong root | Check report codes skill.shadowed, skill.missing_description, disabled list, discovery roots |
| Builtin overridden | Project/global same name | Rename or remove user skill; disable if intentional |
| Flat Claude file ignored | No skill frontmatter under .claude/skills | Add description: / runAs: frontmatter or use SKILL.md folder |
| Body never loads | Expected: bodies are on-demand | Invoke via /name or run_skill |
Ordered triage
reasonix doctor capabilities --json → Skills- Confirm name not in
disabled_skills
- Confirm winner Path/Scope; if shadowed, inspect lower-priority roots
- Missing description: skill may load but index placeholder is weak — add
description:
- Reopen session / Refresh Skills after config changes
Commands (slash templates)
Priority
config.CommandDirsForRoot: home convention commands → Reasonix home commands → project convention commands. Later directory overrides earlier on name clash (command.Load).
Name from path: git/commit.md → /git:commit (slashes → :).
Checks
CLI/Desktop Diagnostics → Commands; invoke /name in chat.
Symptom → cause → fix
| Symptom | Cause | Fix |
|---|
| Wrong body | Shadowed by later dir | Check command.shadowed winners |
| Missing command | Wrong dir / extension | Place *.md under a scanned commands/ root |
| Parse fail | Unreadable file | Fix permissions / encoding (command.read_failed) |
Hooks
Events (11)
PreToolUse, PostToolUse, PermissionRequest, UserPromptSubmit, Stop, PostLLMCall, SessionStart, SessionEnd, SubagentStop, Notification, PreCompact.
Blocking (exit 2 can gate the loop): PreToolUse, UserPromptSubmit. Others warn or contribute context only.
Sources and trust
- Project:
<workspace>/.reasonix/settings.json — only when trusted (trust.json under Reasonix home)
- Plugin packages: installed enabled packages
- Global:
<Reasonix home>/settings.json (always)
Match field is an anchored regex: file does not match read_file; use .*file or *. Timeout is milliseconds (defaults 5s gating / 30s other).
Checks
/hooks, Settings → Hooks, Diagnostics → Hooks.
Symptom → cause → fix
| Symptom | Cause | Fix |
|---|
| Project hooks silent | Untrusted project | Trust project (hook.untrusted_project) |
| Matcher never fires | Non-anchored assumption / bad regex | Fix match (hook.invalid_matcher) |
| Command missing | Empty command / missing context file | Fix settings entry |
| Malformed JSON | Invalid settings.json | Repair JSON (file yields no hooks, no crash) |
MCP servers
Merge order
config.LoadForRoot merges:
- User/project TOML
[[plugins]] (higher name wins vs later sources when already defined)
- Project
.mcp.json servers not already in TOML
- Enabled plugin packages MCP (skipped if name already defined)
Transports: stdio (default), http / streamable-http, sse. auto_start=false skips startup; nil/true = automatic. Tier eager blocks boot handshake; empty/background connects without blocking chat.
Env/header values may contain secrets — diagnostics list keys only.
Checks
| Mode | Behavior |
|---|
| Static doctor | Config validity, command path / URL shape, start intent — no subprocess |
CLI --live | Isolated Host via boot.PluginSpecsForRoot + plugin.Start; auto-start only; concurrency 4; always Close |
| Desktop runtime | Read active tab Host only |
Symptom → cause → fix
| Symptom | Cause | Fix |
|---|
| Not connected | auto_start=false or failed start | Enable / fix command/URL (mcp.command_not_found, mcp.start_failed) |
| No tools | Connected but empty tools/list | Server config or permissions (mcp.no_tools) |
| Wrong source | Shadowed by TOML vs .mcp.json vs package | Inspect report Source / package owner |
| Invalid transport | Bad type | Use stdio/http/sse (mcp.invalid_transport) |
Plugin packages
Manifests
- Native:
reasonix-plugin.json
- Codex:
.codex-plugin/plugin.json
- Claude:
.claude-plugin/plugin.json (+ limited Claude compatibility paths)
State: <Reasonix home>/plugin-packages.json. Disabled packages do not contribute skills/hooks/MCP.
Unmapped Claude-only features may appear as compatibility warnings — Reasonix does not invent support.
Checks
reasonix plugin doctor <name>, Settings → Plugins, Diagnostics → Plugins.
Symptom → cause → fix
| Symptom | Cause | Fix |
|---|
| Package missing | Bad root path | Reinstall / fix root (plugin.missing_root) |
| Invalid manifest | Parse failure | Fix JSON/manifest (plugin.invalid_manifest) |
| Skills missing | Disabled package | Enable package |
Instructions (AGENTS.md / REASONIX.md)
Load order (ascending specificity)
User global docs → ancestor chain → project docs → project-local (*.local.md).
Recognized names: REASONIX.md, AGENTS.md, CLAUDE.md (and *.local.md variants). Multiple files in one directory can load; symlink identity is deduped.
Not the same as Hooks trust. Instructions fold into the system prompt at session boot (cache-stable prefix).
Checks
Diagnostics → Instructions; memory Settings; read files on disk.
Symptom → cause → fix
| Symptom | Cause | Fix |
|---|
| Guidance ignored | Wrong filename / empty file | Use recognized names under correct dir |
| Wrong scope won | Local override | Check load order in report |
Desktop Diagnostics page
- Static report on open; Refresh re-runs static collect
- Copy redacted JSON
- Optional session runtime merge (read-only Host)
- Jump to Settings for MCP / Skills / Plugins / Hooks when issue
settings_tab is set
- Never auto-edit config, auto-trust, or auto-reconnect from this page
Safety
- Prefer static diagnostics
- Live MCP may run third-party code and network
- Do not print tokens, header values, env values, URL query strings, usernames, or machine-absolute external paths
- Report paths as
<workspace>/…, ~/…, or <external>/…
