docs: add concrete usage examples for all 24 tools

README.md

@@ -76,18 +76,18 @@ The pattern is always the same: vague prompt → Claude guesses → wrong output
 
 ## Quick Start
 
-### Option A: Claude Code CLI (fastest)
+### Option A: npx (fastest — no install)
 
 ```bash
-claude mcp add preflight -- npx tsx /path/to/preflight/src/index.ts
+claude mcp add preflight -- npx -y preflight-dev-serve
 ```
 
 With environment variables:
 
 ```bash
 claude mcp add preflight \
   -e CLAUDE_PROJECT_DIR=/path/to/your/project \
-  -- npx tsx /path/to/preflight/src/index.ts
+  -- npx -y preflight-dev-serve
 ```
 
 ### Option B: Clone & configure manually
@@ -119,9 +119,11 @@ Restart Claude Code. The tools activate automatically.
 
 ```bash
 npm install -g preflight-dev
-claude mcp add preflight -- preflight-dev
+claude mcp add preflight -- preflight-dev-serve
 ```
 
+> **Note:** `preflight-dev` runs the interactive setup wizard. `preflight-dev-serve` starts the MCP server — that's what you want in your Claude Code config.
+
 ---
 
 ## How It Works
@@ -335,6 +337,151 @@ After onboarding, you get:
 
 ---
 
+## Usage Examples
+
+These are real prompts you'd give Claude Code with preflight installed. The tools are called automatically via `preflight_check`, or you can invoke them directly.
+
+### Everyday workflow (just use `preflight_check`)
+
+```
+# Before any task — preflight_check triages and chains the right tools
+preflight_check({ prompt: "refactor the auth middleware to use JWT refresh tokens" })
+
+# Force a full check even if triage says it's simple
+preflight_check({ prompt: "fix the test", force_level: "full" })
+
+# Skip preflight for trivial commands
+preflight_check({ prompt: "git status", force_level: "skip" })
+```
+
+### Planning before coding
+
+```
+# Get a structured execution plan with scope boundaries
+scope_work({ task: "add rate limiting to all public API routes" })
+
+# Scope against a specific branch
+scope_work({ task: "merge feature/payments into main", branch: "feature/payments" })
+```
+
+### Clarifying vague prompts
+
+```
+# "fix the tests" → which tests? what's broken?
+clarify_intent({ user_message: "fix the tests", suspected_area: "tests" })
+
+# "do the same for the others" → which others?
+sharpen_followup({
+  followup_message: "do the same for the others",
+  previous_action: "added input validation to UserForm",
+  previous_files: ["src/components/UserForm.tsx"]
+})
+```
+
+### Sub-agent enrichment
+
+```
+# Before spawning a sub-agent, enrich the task with context
+enrich_agent_task({
+  task_description: "fix the flaky auth tests",
+  target_area: "src/auth/__tests__"
+})
+```
+
+### Searching project history
+
+```
+# First, index your project (one-time setup)
+onboard_project({ project_dir: "/Users/you/my-app" })
+
+# Then search semantically across all sessions
+search_history({ query: "how did we handle the database migration last month?" })
+
+# Search contracts across related services
+search_contracts({ query: "UserProfile", scope: "all", kind: "interface" })
+
+# Chronological view of recent work
+timeline({ since: "3days" })
+```
+
+### Session management
+
+```
+# Save progress before context gets long
+checkpoint({
+  summary: "implemented JWT refresh flow",
+  next_steps: "add tests and update API docs"
+})
+
+# Check if session is getting too long
+check_session_health()
+
+# Generate a handoff brief for the next session
+session_handoff({ direction: "outgoing" })
+
+# Starting a new session? Catch up on what happened
+session_handoff({ direction: "incoming" })
+```
+
+### Analysis and scoring
+
+```
+# Score a single prompt
+prompt_score({ prompt: "fix the bug in auth" })
+# → Grade: C — missing: which bug, which file, what "fixed" looks like
+
+# Generate a weekly trend report
+generate_scorecard({ period: "week", output: "markdown" })
+
+# Estimate token waste
+estimate_cost()
+
+# Detect token waste patterns (repeated reads, bloated context)
+token_audit({ check_mode: "deep" })
+```
+
+### Verification before shipping
+
+```
+# Run type check + tests + git status before declaring done
+verify_completion({ task_description: "add rate limiting to public API routes" })
+
+# Check for stale workspace docs
+audit_workspace()
+```
+
+### Learning from mistakes
+
+```
+# Log a correction so preflight learns the pattern
+log_correction({
+  what_user_said: "no, the auth route is in src/api/auth.ts not src/routes/auth.ts",
+  what_you_did_wrong: "edited the wrong auth file",
+  root_cause: "assumed Rails-style routing structure",
+  category: "wrong_file"
+})
+
+# Check if a new prompt hits known pitfalls
+check_patterns({ prompt: "update the auth route handler" })
+```
+
+### Multi-task sequencing
+
+```
+# Order tasks to minimize context switches
+sequence_tasks({
+  tasks: [
+    "add input validation to UserForm",
+    "write tests for UserForm validation",
+    "add validation to PaymentForm",
+    "update API error responses for validation failures"
+  ],
+  strategy: "locality"
+})
+```
+
+---
+
 ## The 12-Category Scorecard
 
 `generate_scorecard` evaluates your prompt discipline across 12 categories. Each one measures something specific about how you interact with Claude Code:
@@ -500,6 +647,8 @@ Manual contract definitions that supplement auto-extraction:
 
 Environment variables are **fallbacks** — `.preflight/` config takes precedence when present.
 
+> 💡 **Ready-to-use examples:** Copy [`examples/.preflight/`](examples/.preflight/) into your project root for a working starter config with detailed comments.
+
 ---
 
 ## Embedding Providers
@@ -562,6 +711,95 @@ flowchart TB
 
 ---
 
+## Troubleshooting
+
+### "Cannot find module 'vectordb'" or LanceDB import errors
+
+LanceDB uses native binaries. If you see module resolution errors:
+
+```bash
+# Clean install with native deps rebuilt
+rm -rf node_modules package-lock.json
+npm install
+
+# If still failing, check your Node version (20+ required)
+node --version
+```
+
+On Apple Silicon Macs, make sure you're running a native arm64 Node — not Rosetta. Check with `node -e "console.log(process.arch)"` (should print `arm64`).
+
+### First run is slow (~90MB model download)
+
+The local embedding provider ([Xenova/all-MiniLM-L6-v2](https://huggingface.co/Xenova/all-MiniLM-L6-v2)) downloads a ~90MB model on first use. This is a one-time cost — subsequent runs use the cached model. If the download hangs behind a corporate proxy, switch to OpenAI embeddings:
+
+```bash
+export OPENAI_API_KEY=sk-...
+export EMBEDDING_PROVIDER=openai
+```
+
+### "OpenAI API key required for openai embedding provider"
+
+You set `EMBEDDING_PROVIDER=openai` (or `embeddings.provider: openai` in `.preflight/config.yml`) but didn't provide a key. Either:
+
+- Set `OPENAI_API_KEY` in your environment, or
+- Switch back to local: `export EMBEDDING_PROVIDER=local`
+
+### Tools not showing up in Claude Code
+
+1. Make sure the MCP server is registered. Run `claude mcp list` — you should see `preflight`.
+2. If missing, re-add it:
+   ```bash
+   claude mcp add preflight -- npx tsx /path/to/preflight/src/index.ts
+   ```
+3. Restart Claude Code after adding.
+
+### `CLAUDE_PROJECT_DIR` not set
+
+Some tools (onboarding, session search, contracts) need to know your project root. If they return empty results:
+
+```bash
+claude mcp add preflight \
+  -e CLAUDE_PROJECT_DIR=/path/to/your/project \
+  -- npx tsx /path/to/preflight/src/index.ts
+```
+
+Or set it globally: `export CLAUDE_PROJECT_DIR=/path/to/your/project`
+
+### `.preflight/config.yml` parse errors
+
+If you see `warning - failed to parse .preflight/config.yml`, your YAML is malformed. Common issues:
+
+- Tabs instead of spaces (YAML requires spaces)
+- Missing quotes around values with special characters
+- Incorrect indentation under `related_projects`
+
+Validate with: `npx yaml-lint .preflight/config.yml` or paste into [yamllint.com](https://www.yamllint.com/).
+
+### No session data found during onboarding
+
+`onboard_project` looks for JSONL files in `~/.claude/projects/<encoded-path>/`. If nothing is found:
+
+- Make sure you've actually used Claude Code on the project (at least one session)
+- Check that `CLAUDE_PROJECT_DIR` matches the exact path Claude Code was opened in
+- The path encoding is URL-style — `/Users/jack/my-app` becomes `%2FUsers%2Fjack%2Fmy-app`
+
+### Ollama embeddings connection refused
+
+If using Ollama as your embedding provider and getting connection errors:
+
+```bash
+# Make sure Ollama is running
+ollama serve
+
+# Pull the embedding model
+ollama pull all-minilm
+
+# Verify it works
+curl http://localhost:11434/api/embed -d '{"model":"all-minilm","input":"test"}'
+```
+
+---
+
 ## Contributing
 
 This project is young and there's plenty to do. Check the [issues](https://github.com/TerminalGravity/preflight/issues) — several are tagged `good first issue`.

bin/serve.js

@@ -0,0 +1,10 @@
+#!/usr/bin/env node
+// Starts the preflight MCP server (as opposed to the init wizard).
+// Used by .mcp.json configs generated by `preflight-dev init`.
+import { fileURLToPath } from 'url';
+import { dirname, join } from 'path';
+
+const __filename = fileURLToPath(import.meta.url);
+const __dirname = dirname(__filename);
+
+await import(join(__dirname, '../dist/index.js'));

examples/.preflight/config.yml

@@ -0,0 +1,35 @@
+# .preflight/config.yml — Drop this in your project root
+#
+# This is an example config for a typical Next.js + microservices setup.
+# Every field is optional — preflight works with sensible defaults out of the box.
+# Commit this to your repo so the whole team gets the same preflight behavior.
+
+# Profile controls how much detail preflight returns.
+#   "minimal"  — only flags ambiguous+ prompts, skips clarification detail
+#   "standard" — balanced (default)
+#   "full"     — maximum detail on every non-trivial prompt
+profile: standard
+
+# Related projects for cross-service awareness.
+# Preflight will search these for shared types, routes, and contracts
+# so it can warn you when a change might break a consumer.
+related_projects:
+  - path: /Users/you/code/auth-service
+    alias: auth
+  - path: /Users/you/code/billing-api
+    alias: billing
+  - path: /Users/you/code/shared-types
+    alias: types
+
+# Behavioral thresholds — tune these to your workflow
+thresholds:
+  session_stale_minutes: 30                # Warn if no activity for this long
+  max_tool_calls_before_checkpoint: 100    # Suggest a checkpoint after N tool calls
+  correction_pattern_threshold: 3          # Min corrections before flagging a pattern
+
+# Embedding provider for semantic search over session history.
+# "local" uses Xenova transformers (no API key needed, runs on CPU).
+# "openai" uses text-embedding-3-small (faster, needs OPENAI_API_KEY).
+embeddings:
+  provider: local
+  # openai_api_key: sk-...               # Uncomment if using openai provider

examples/.preflight/contracts/api.yml

@@ -0,0 +1,58 @@
+# .preflight/contracts/api.yml — Manual contract definitions
+#
+# Define shared types and interfaces that preflight should know about.
+# These supplement auto-extracted contracts from your codebase.
+# Manual definitions win on name conflicts with auto-extracted ones.
+#
+# Why manual contracts?
+#   - Document cross-service interfaces that live in docs, not code
+#   - Define contracts for external APIs your services consume
+#   - Pin down types that are implicit (e.g., event payloads)
+
+- name: User
+  kind: interface
+  description: Core user model shared across all services
+  fields:
+    - name: id
+      type: string
+      required: true
+    - name: email
+      type: string
+      required: true
+    - name: tier
+      type: "'free' | 'pro' | 'enterprise'"
+      required: true
+    - name: createdAt
+      type: Date
+      required: true
+
+- name: AuthToken
+  kind: interface
+  description: JWT payload structure from auth-service
+  fields:
+    - name: userId
+      type: string
+      required: true
+    - name: permissions
+      type: string[]
+      required: true
+    - name: expiresAt
+      type: number
+      required: true
+
+- name: WebhookPayload
+  kind: interface
+  description: Standard webhook envelope for inter-service events
+  fields:
+    - name: event
+      type: string
+      required: true
+    - name: timestamp
+      type: string
+      required: true
+    - name: data
+      type: Record<string, unknown>
+      required: true
+    - name: source
+      type: string
+      required: true