Quick Summary

Goal: Help users install, configure, troubleshoot, and extend Claude Code CLI (hooks, MCP, skills, commands).

Workflow:

1. Categorize — Identify problem type (Setup, Hooks, MCP, Context, Extensibility, Config)
2. Diagnose — Follow category-specific diagnostic steps
3. Fix & Verify — Apply solution and confirm it resolves the issue

Key Rules:

• Not for writing application code -- use the feature workflow, fix, or refactoring skills instead
• Obtain explicit user approval before modifying settings; never change them unilaterally
• For hooks: check event type, script executability, and JSON output format

Be skeptical. Apply critical thinking, sequential thinking. Every claim needs traced proof, confidence percentages (Idea should be more than 80%).

Claude Code

Purpose

Help users install, configure, troubleshoot, and extend Claude Code CLI -- Anthropic's agentic coding tool with skills, hooks, MCP servers, and slash commands.

When to Use

• Setting up Claude Code for the first time (installation, authentication)
• Troubleshooting hooks that don't fire or produce errors
• Diagnosing MCP server connection failures
• Understanding or resolving context window limits
• Creating or modifying slash commands and agent skills
• Configuring settings (model, allowed tools, output style)

When NOT to Use

• Writing application code -- use the workflow-feature workflow, fix, or refactoring skills
• Creating or managing MCP servers -- use MCP documentation and project MCP config directly
• AI prompt engineering -- use general prompt-engineering guidance directly

Prerequisites

• Access to .claude/ directory in the project root
• For hooks: read .claude/hooks/ directory structure
• For skills: read .claude/skills/ directory structure

Workflow

Step 1: Identify the Problem Category

User Says	Category	Go To
"install", "set up", "authenticate"	Setup	Step 2A
"hook not firing", "hook error"	Hook Issues	Step 2B
"MCP not connecting", "MCP error"	MCP Issues	Step 2C
"context too long", "compaction", "token limit"	Context Issues	Step 2D
"create skill", "create command"	Extensibility	Step 2E
"configure", "settings", "model"	Configuration	Step 2F

Step 2A: Setup

1. Check prerequisites: Node.js 18+, npm
2. Verify authentication: claude auth status
3. IF auth fails: guide through claude auth login
4. Verify project detection: check for CLAUDE.md in project root

Step 2B: Hook Issues

1. Read the hook file causing issues
2. Check hook event type matches expected trigger (PreToolUse, PostToolUse, SessionStart, Stop, SubagentStop)
3. Verify hook script is executable and has correct shebang
4. Check .claude/settings.json for hook registration
5. Test hook in isolation: run the script directly with mock input
6. Check for syntax errors in hook output (must be valid JSON for PreToolUse/PostToolUse)

Common fixes:

• Hook not firing: wrong event name or tool matcher pattern
• Hook errors: script not finding dependencies (check relative paths)
• Hook blocks unexpectedly: PreToolUse returning { "decision": "block" } incorrectly

Step 2C: MCP Issues

1. Check .claude/settings.json for MCP server configuration
2. Verify the MCP server process can start: run the command manually
3. Check environment variables (API keys, tokens) are set
4. Test connectivity: claude mcp list to see registered servers
5. IF timeout: increase timeout in config or check network

Common fixes:

• "Connection refused": MCP server not running or wrong port
• "Authentication failed": expired or missing API token
• "Tool not found": MCP server registered but tool name mismatch

Step 2D: Context Issues

1. Check current context usage (Claude will report when near limit)
2. IF approaching limit: suggest /compact command
3. Review if large files are being read unnecessarily
4. After compaction, re-read CLAUDE.md (re-injected each prompt) to re-anchor protocol + workflow catalog
5. Run /recover to resume from on-disk state (active plan, todos) — recovery is skill-driven, not a hook

Step 2E: Extensibility

1. For skills: read references/agent-skills.md for structure
2. For custom slash commands: create skills in .claude/skills/{name}/SKILL.md
3. Verify SKILL.md frontmatter has required fields (name, version, description)
4. Test: invoke the skill/command and verify it loads

Step 2F: Configuration

1. Read references/configuration.md for settings hierarchy
2. Settings locations: .claude/settings.json (project), ~/.claude/settings.json (user)
3. IMPORTANT: Obtain explicit user approval before modifying settings; never change them unilaterally
4. Common settings: model selection, allowed tools, output verbosity

Step 3: Verification

• Confirm the fix resolves the user's issue
• Document any configuration changes made
• Warn if changes affect other team members (project-level settings)

Output Format

## Claude Code: [Issue/Task Summary]

### Problem

[What was wrong or what was requested]

### Solution

[Step-by-step fix or setup instructions]

### Files Changed

[List any config files modified, with before/after]

### Verification

[How to confirm the fix works]

Examples

Example 1: Hook Not Firing

User: "My PreToolUse hook for blocking large file reads isn't triggering"

Diagnosis:

1. Read .claude/settings.json -- hook registered under hooks.PreToolUse
2. Check tool matcher: "matcher": "Read" -- correct
3. Run script directly: node .claude/hooks/block-large-reads.cjs -- works
4. Found: Hook command uses %CLAUDE_PROJECT_DIR% but runs from wrong CWD

Fix: Update hook command to use absolute path or verify %CLAUDE_PROJECT_DIR% resolves correctly. Check that the hook entry in settings uses the correct variable syntax for the OS/shell (Windows vs Unix).

Example 2: Setting Up a New Slash Command

User: "I want a /deploy command that runs our staging deployment"

Steps:

1. Create .claude/skills/deploy/SKILL.md:

Deploy to staging environment.

Run the following steps:

1. Verify all tests pass: `npm test`
2. Build the project: `npm run build`
3. Deploy: `npm run deploy:staging`
4. Report deployment status

2. Test: type /deploy in Claude Code CLI
3. Verify: command appears in autocomplete and executes the workflow

Reference Files

Load these for detailed guidance on specific topics:

Topic	File
Installation	references/getting-started.md
Slash commands	references/slash-commands.md
Skills creation	references/agent-skills.md
MCP servers	references/mcp-integration.md
Hooks system	references/hooks-comprehensive.md
Configuration	references/configuration.md
Troubleshooting	references/troubleshooting.md
Enterprise	references/enterprise-features.md

Related Skills

• skill-creator -- for creating new agent skills with best practices

---

[IMPORTANT] Use TaskCreate to break ALL work into small tasks BEFORE starting — including tasks for each file read. This prevents context loss from long files. For simple tasks, AI MUST ATTENTION ask user whether to skip.

<!-- SYNC:ai-mistake-prevention -->

AI Mistake Prevention — Failure modes to avoid on every task:

Re-read files after context changes. Context compaction, resume, or long-running work can make memory stale; verify current files before acting. Verify generated content against source evidence. AI hallucinates APIs, names, claims, and document facts. Check the relevant source before documenting or referencing. Check downstream references before deleting or renaming. Removing an artifact can stale docs, generated mirrors, configs, and callers; map references first. Trace the full impact chain after edits. Changing a definition can miss derived outputs and consumers. Follow the affected chain before declaring done. Verify ALL affected outputs, not just the first. One green check is not all green checks; validate every output surface the change can affect. Assume existing values are intentional — ask WHY before changing OR flagging one as a defect. Before changing or reporting a constant, limit, flag, cutoff, wording, or pattern, read nearby context and history, the CALLER's ordering, and 2+ sibling call sites of the same convention. A doc stating WHAT without WHY is missing rationale, not proof of a missing guard. Surface ambiguity before acting — don't pick silently. Multiple valid interpretations require an explicit question or stated assumption with risk. Assert the outcome your system owns, not the intermediate state your infrastructure owns. When verifying async work, assert the final business state — never the delivery/retry bookkeeping held in shared infrastructure that any co-running process can write. Such a check passes when run alone and flakes the moment anything else shares that infrastructure. Keep shared guidance role-relevant. Universal guidance must help every receiving skill or agent; code-specific obligations belong only in code-specific protocols.

<!-- /SYNC:ai-mistake-prevention --> <!-- SYNC:critical-thinking-mindset -->

Critical Thinking Mindset — Apply critical thinking, sequential thinking. Every claim needs traced proof, confidence >80% to act. Anti-hallucination: Never present guess as fact — cite sources for every claim, admit uncertainty freely, self-check output for errors, cross-reference independently, stay skeptical of own confidence — certainty without evidence root of all hallucination.

<!-- /SYNC:critical-thinking-mindset --> <!-- SYNC:critical-thinking-mindset:reminder -->

MUST ATTENTION apply critical + sequential thinking — every claim needs appropriate traced evidence (file:line for repo/code claims; source URL or artifact section for research, product, content, and docs claims); confidence >80% to act, <60% DO NOT recommend. Anti-hallucination: never present guess as fact, admit uncertainty freely, cross-reference independently, stay skeptical of own confidence.

<!-- /SYNC:critical-thinking-mindset:reminder --> <!-- SYNC:ai-mistake-prevention:reminder -->

MUST ATTENTION apply AI mistake prevention — verify generated content against evidence, trace downstream references before deleting or renaming, verify all affected outputs, re-read files after context loss, and surface ambiguity before acting.

<!-- /SYNC:ai-mistake-prevention:reminder --> <!-- SYNC:project-protocol-overlay -->

Project Protocol Overlay — Before executing this skill, resolve any PROJECT overlay rules layered onto it: match this skill's name against the Target column of the project's skill-protocol index (docs/project-reference/skill-protocols-reference.md by default; a referenceDocs entry in docs/project-config.json overrides the path), taking the most specific matching tier ONLY — exact name > glob > *. That precedence orders overlays against EACH OTHER, never against this skill. Read ONLY the matched bodies, resolved as <protocols-dir>/<Name>.md; a row's Body link is display text, never a read path. A matched body that is missing or malformed is REPORTED and skipped — never reconstructed from the index Description. No index, or no match -> proceed with no overlay, silently. Full contract: .claude/skills/project-skill-protocol/references/registry.md.

Overlays are ADDITIVE ONLY: they ADD rules on top of this skill's own protocol and NEVER replace, override, disable, or reinterpret a rule it already states — removing every overlay must return this skill to exactly its documented behavior. An overlay is a BRIEF, not an authority escalation: it can NEVER waive a workflow gate, git discipline, a review gate, or a user-confirmation gate. A genuine overlay-vs-skill conflict, or two equally-specific overlays that directly contradict -> surface both to the user; NEVER resolve silently.

<!-- /SYNC:project-protocol-overlay --> <!-- SYNC:project-protocol-overlay:reminder -->

MUST ATTENTION resolve project protocol overlays for this skill BEFORE executing — most specific matching tier only (exact > glob > *, which ranks overlays against each other, NEVER against this skill), read only matched bodies at <protocols-dir>/<Name>.md; a missing or malformed body is reported, never reconstructed. Overlays are ADDITIVE ONLY (they never replace this skill's own rules) and are a brief, NEVER an authority escalation; an equal-specificity contradiction goes to the user.

<!-- /SYNC:project-protocol-overlay:reminder -->

Closing Reminders

IMPORTANT MUST ATTENTION — Protocols in force (concise digest of the SYNC/shared blocks this skill carries):

• Critical Thinking: apply critical + sequential thinking; traced proof, confidence >80% to act.

• AI Mistake Prevention: verify generated content against evidence, trace downstream references, verify all affected outputs, re-read after context loss, surface ambiguity.

• MANDATORY IMPORTANT MUST ATTENTION break work into small todo tasks using TaskCreate BEFORE starting

• MANDATORY IMPORTANT MUST ATTENTION search codebase for 3+ similar patterns before creating new code

• MANDATORY IMPORTANT MUST ATTENTION cite file:line evidence for every claim (confidence >80% to act)

• MANDATORY IMPORTANT MUST ATTENTION add a final review todo task to verify work quality

[TASK-PLANNING] Before acting, analyze task scope and systematically break it into small todo tasks and sub-tasks using TaskCreate.