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+# Configuration Reference
+
+Detailed configuration options for Repomix.
+
+## Configuration File
+
+Create `repomix.config.json` in project root:
+
+```json
+{
+  "output": {
+    "filePath": "repomix-output.xml",
+    "style": "xml",
+    "removeComments": false,
+    "showLineNumbers": true,
+    "copyToClipboard": false
+  },
+  "include": ["**/*"],
+  "ignore": {
+    "useGitignore": true,
+    "useDefaultPatterns": true,
+    "customPatterns": ["additional-folder", "**/*.log", "**/tmp/**"]
+  },
+  "security": {
+    "enableSecurityCheck": true
+  }
+}
+```
+
+### Output Options
+
+- `filePath`: Output file path (default: `repomix-output.xml`)
+- `style`: Format - `xml`, `markdown`, `json`, `plain` (default: `xml`)
+- `removeComments`: Strip comments (default: `false`). Supports HTML, CSS, JS/TS, Vue, Svelte, Python, PHP, Ruby, C, C#, Java, Go, Rust, Swift, Kotlin, Dart, Shell, YAML
+- `showLineNumbers`: Include line numbers (default: `true`)
+- `copyToClipboard`: Auto-copy output (default: `false`)
+
+### Include/Ignore
+
+- `include`: Glob patterns for files to include (default: `["**/*"]`)
+- `useGitignore`: Respect .gitignore (default: `true`)
+- `useDefaultPatterns`: Use default ignore patterns (default: `true`)
+- `customPatterns`: Additional ignore patterns (same format as .gitignore)
+
+### Security
+
+- `enableSecurityCheck`: Scan for sensitive data with Secretlint (default: `true`)
+- Detects: API keys, passwords, credentials, private keys, AWS secrets, DB connections
+
+## Glob Patterns
+
+**Wildcards:**
+- `*` - Any chars except `/`
+- `**` - Any chars including `/`
+- `?` - Single char
+- `[abc]` - Char from set
+- `{js,ts}` - Either extension
+
+**Examples:**
+- `**/*.ts` - All TypeScript
+- `src/**` - Specific dir
+- `**/*.{js,jsx,ts,tsx}` - Multiple extensions
+- `!**/*.test.ts` - Exclude tests
+
+### CLI Options
+
+```bash
+# Include patterns
+repomix --include "src/**/*.ts,*.md"
+
+# Ignore patterns
+repomix -i "tests/**,*.test.js"
+
+# Disable .gitignore
+repomix --no-gitignore
+
+# Disable defaults
+repomix --no-default-patterns
+```
+
+### .repomixignore File
+
+Create `.repomixignore` for Repomix-specific patterns (same format as .gitignore):
+
+```
+# Build artifacts
+dist/
+build/
+*.min.js
+out/
+
+# Test files
+**/*.test.ts
+**/*.spec.ts
+coverage/
+__tests__/
+
+# Dependencies
+node_modules/
+vendor/
+packages/*/node_modules/
+
+# Large files
+*.mp4
+*.zip
+*.tar.gz
+*.iso
+
+# Sensitive files
+.env*
+secrets/
+*.key
+*.pem
+
+# IDE files
+.vscode/
+.idea/
+*.swp
+
+# Logs
+logs/
+**/*.log
+```
+
+### Pattern Precedence
+
+Order (highest to lowest priority):
+1. CLI ignore patterns (`-i`)
+2. `.repomixignore` file
+3. Custom patterns in config
+4. `.gitignore` (if enabled)
+5. Default patterns (if enabled)
+
+### Pattern Examples
+
+**TypeScript:**
+```json
+{"include": ["**/*.ts", "**/*.tsx"], "ignore": {"customPatterns": ["**/*.test.ts", "dist/"]}}
+```
+
+**React:**
+```json
+{"include": ["src/**/*.{js,jsx,ts,tsx}", "*.md"], "ignore": {"customPatterns": ["build/"]}}
+```
+
+**Monorepo:**
+```json
+{"include": ["packages/*/src/**"], "ignore": {"customPatterns": ["packages/*/dist/"]}}
+```
+
+## Output Formats
+
+### XML (Default)
+```bash
+repomix --style xml
+```
+Structured AI consumption. Features: tags, hierarchy, metadata, AI-optimized separators.
+Use for: LLMs, structured analysis, programmatic parsing.
+
+### Markdown
+```bash
+repomix --style markdown
+```
+Human-readable with syntax highlighting. Features: syntax highlighting, headers, TOC.
+Use for: documentation, code review, sharing.
+
+### JSON
+```bash
+repomix --style json
+```
+Programmatic processing. Features: structured data, easy parsing, metadata.
+Use for: API integration, custom tooling, data analysis.
+
+### Plain Text
+```bash
+repomix --style plain
+```
+Simple concatenation. Features: no formatting, minimal overhead.
+Use for: simple analysis, minimal processing.
+
+## Advanced Options
+
+```bash
+# Verbose - show processing details
+repomix --verbose
+
+# Custom config file
+repomix -c /path/to/custom-config.json
+
+# Initialize config
+repomix --init
+
+# Disable line numbers - smaller output
+repomix --no-line-numbers
+```
+
+### Performance
+
+**Worker Threads:** Parallel processing handles large codebases efficiently (e.g., facebook/react: 29x faster, 123s → 4s)
+
+**Optimization:**
+```bash
+# Exclude unnecessary files
+repomix -i "node_modules/**,dist/**,*.min.js"
+
+# Specific directories only
+repomix --include "src/**/*.ts"
+
+# Remove comments, disable line numbers
+repomix --remove-comments --no-line-numbers
+```
--- a/skills/repomix/references/usage-patterns.md
+++ b/skills/repomix/references/usage-patterns.md
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+# Usage Patterns
+
+Practical workflows and patterns for using Repomix in different scenarios.
+
+## AI Analysis Workflows
+
+### Full Repository
+```bash
+repomix --remove-comments --style markdown -o full-repo.md
+```
+**Use:** New codebase, architecture review, complete LLM context, planning
+**Tips:** Remove comments, use markdown, check token limits, review before sharing
+
+### Focused Module
+```bash
+repomix --include "src/auth/**,src/api/**" -o modules.xml
+```
+**Use:** Feature analysis, debugging specific areas, targeted refactoring
+**Tips:** Include related files only, stay within token limits, use XML for AI
+
+### Incremental Analysis
+```bash
+git checkout feature-branch && repomix --include "src/**" -o feature.xml
+git checkout main && repomix --include "src/**" -o main.xml
+```
+**Use:** Feature branch review, change impact, before/after comparison, migration planning
+
+### Cross-Repository
+```bash
+npx repomix --remote org/repo1 -o repo1.xml
+npx repomix --remote org/repo2 -o repo2.xml
+```
+**Use:** Microservices, library comparisons, consistency checks, integration analysis
+
+## Security Audit
+
+### Third-Party Library
+```bash
+npx repomix --remote vendor/library --style xml -o audit.xml
+```
+**Workflow:** Package library → enable security checks → review vulnerabilities → check suspicious patterns → AI analysis
+**Check for:** API keys, hardcoded credentials, network calls, obfuscation, malicious patterns
+
+### Pre-Deployment
+```bash
+repomix --include "src/**,config/**" --style xml -o pre-deploy-audit.xml
+```
+**Checklist:** No sensitive data, no test credentials, env vars correct, security practices, no debug code
+
+### Dependency Audit
+```bash
+repomix --include "**/package.json,**/package-lock.json" -o deps.md --style markdown
+repomix --include "node_modules/suspicious-package/**" -o dep-audit.xml
+```
+**Use:** Suspicious dependency, security advisory, license compliance, vulnerability assessment
+
+### Compliance
+```bash
+repomix --include "src/**,LICENSE,README.md,docs/**" --style markdown -o compliance.md
+```
+**Include:** Source, licenses, docs, configs. **Exclude:** Test data, dependencies
+
+## Documentation
+
+### Doc Context
+```bash
+repomix --include "src/**,docs/**,*.md" --style markdown -o doc-context.md
+```
+**Use:** API docs, architecture docs, user guides, onboarding
+**Tips:** Include existing docs, include source, use markdown
+
+### API Documentation
+```bash
+repomix --include "src/api/**,src/routes/**,src/controllers/**" --remove-comments -o api-context.xml
+```
+**Include:** Routes, controllers, schemas, middleware
+**Workflow:** Package → AI → OpenAPI/Swagger → endpoint docs → examples
+
+### Architecture
+```bash
+repomix --include "src/**/*.ts,*.md" -i "**/*.test.ts" --style markdown -o architecture.md
+```
+**Focus:** Module structure, dependencies, design patterns, data flow
+
+### Examples
+```bash
+repomix --include "examples/**,demos/**,*.example.js" --style markdown -o examples.md
+```
+
+## Library Evaluation
+
+### Quick Assessment
+```bash
+npx repomix --remote owner/library --style markdown -o library-eval.md
+```
+**Evaluate:** Code quality, architecture, dependencies, tests, docs, maintenance
+
+### Feature Comparison
+```bash
+npx repomix --remote owner/lib-a --style xml -o lib-a.xml
+npx repomix --remote owner/lib-b --style xml -o lib-b.xml
+```
+**Compare:** Features, API design, performance, bundle size, dependencies, maintenance
+
+### Integration Feasibility
+```bash
+npx repomix --remote vendor/library --include "src/**,*.md" -o library.xml
+repomix --include "src/integrations/**" -o our-integrations.xml
+```
+Analyze compatibility between target library and your integration points
+
+### Migration Planning
+```bash
+repomix --include "node_modules/old-lib/**" -o old-lib.xml
+npx repomix --remote owner/new-lib -o new-lib.xml
+```
+Compare current vs target library, analyze usage patterns
+
+## Workflow Integration
+
+### CI/CD
+```yaml
+# GitHub Actions
+- name: Generate Snapshot
+  run: |
+    npm install -g repomix
+    repomix --style markdown -o release-snapshot.md
+- name: Upload Artifact
+  uses: actions/upload-artifact@v3
+  with: {name: repo-snapshot, path: release-snapshot.md}
+```
+**Use:** Release docs, compliance archives, change tracking, audit trails
+
+### Git Hooks
+```bash
+#!/bin/bash
+# .git/hooks/pre-commit
+git diff --cached --name-only > staged-files.txt
+repomix --include "$(cat staged-files.txt | tr '\n' ',')" -o .context/latest.xml
+```
+
+### IDE (VS Code)
+```json
+{"version": "2.0.0", "tasks": [{"label": "Package for AI", "type": "shell", "command": "repomix --include 'src/**' --remove-comments --copy"}]}
+```
+
+### Claude Code
+```bash
+repomix --style markdown --copy  # Then paste into Claude
+```
+
+## Language-Specific Patterns
+
+### TypeScript
+```bash
+repomix --include "**/*.ts,**/*.tsx" --remove-comments --no-line-numbers
+```
+**Exclude:** `**/*.test.ts`, `dist/`, `coverage/`
+
+### React
+```bash
+repomix --include "src/**/*.{js,jsx,ts,tsx},public/**" -i "build/,*.test.*"
+```
+**Include:** Components, hooks, utils, public assets
+
+### Node.js Backend
+```bash
+repomix --include "src/**/*.js,config/**" -i "node_modules/,logs/,tmp/"
+```
+**Focus:** Routes, controllers, models, middleware, configs
+
+### Python
+```bash
+repomix --include "**/*.py,requirements.txt,*.md" -i "**/__pycache__/,venv/"
+```
+**Exclude:** `__pycache__/`, `*.pyc`, `venv/`, `.pytest_cache/`
+
+### Monorepo
+```bash
+repomix --include "packages/*/src/**" -i "packages/*/node_modules/,packages/*/dist/"
+```
+**Consider:** Package-specific patterns, shared deps, cross-package refs, workspace structure
+
+## Troubleshooting
+
+### Output Too Large
+**Problem:** Exceeds LLM token limits
+**Fix:**
+```bash
+repomix -i "node_modules/**,dist/**,coverage/**" --include "src/core/**" --remove-comments --no-line-numbers
+```
+
+### Missing Files
+**Problem:** Expected files not included
+**Debug:**
+```bash
+cat .gitignore .repomixignore  # Check ignore patterns
+repomix --no-gitignore --no-default-patterns --verbose
+```
+
+### Sensitive Data Warnings
+**Problem:** Security scanner flags secrets
+**Actions:** Review files → add to `.repomixignore` → remove sensitive data → use env vars
+```bash
+repomix --no-security-check  # Use carefully for false positives
+```
+
+### Performance Issues
+**Problem:** Slow on large repo
+**Optimize:**
+```bash
+repomix --include "src/**/*.ts" -i "node_modules/**,dist/**,vendor/**"
+```
+
+### Remote Access
+**Problem:** Cannot access remote repo
+**Fix:**
+```bash
+npx repomix --remote https://github.com/owner/repo  # Full URL
+npx repomix --remote https://github.com/owner/repo/commit/abc123  # Specific commit
+# For private: clone first, run locally
+```
+
+## Best Practices
+
+**Planning:** Define scope → identify files → check token limits → consider security
+
+**Execution:** Start broad, refine narrow → use appropriate format → enable security checks → monitor tokens
+
+**Review:** Verify no sensitive data → check completeness → validate format → test with LLM
+
+**Iteration:** Refine patterns → adjust format → optimize tokens → document patterns