From 2b814d9556ecc57cfc94aa652eb0c6043f3f984a Mon Sep 17 00:00:00 2001
From: "Toast (gastown)" <Toast@gastown.local>
Date: Thu, 2 Apr 2026 09:49:04 +0000
Subject: [PATCH] De-duplicate README.md - remove overlapping second section

- Removed entire duplicate second section (lines 708-1166, 459 lines)
- Ported unique content from second section into appropriate locations:
  - Programmatic API examples (TokenAnalyzer/MethodAnalyzer)
  - Method-level filtering with pattern syntax table
  - Use Cases & Examples (5 practical scenarios)
  - Requirements, Contributing, Support sections
  - Created by attribution
- Trimmed internal duplication (Include vs Exclude, LLM Context examples, Configuration)
- Reduced from 1166 lines to 600 lines (48% reduction)
- Buy Me A Coffee section and QR code preserved at top
---
 README.md | 738 +++++++-----------------------------------------------
 1 file changed, 86 insertions(+), 652 deletions(-)

diff --git a/README.md b/README.md
index 850ad15..d29a519 100644
--- a/README.md
+++ b/README.md
@@ -29,6 +29,7 @@ If you find this tool helpful, consider buying me a coffee! Your support helps m
 ## Features
 
 ### 🚀 Platform Features (v3.0.0)
+
 - 🔌 **Plugin Architecture** - Modular, extensible system for languages and exporters
 - 🔀 **Git Integration** - Analyze only changed files, diff analysis, author tracking
 - 👁️ **Watch Mode** - Real-time file monitoring and auto-analysis
@@ -37,23 +38,27 @@ If you find this tool helpful, consider buying me a coffee! Your support helps m
 - 🏗️ **Modular Core** - Scanner, Analyzer, ContextBuilder, Reporter
 
 ### 🎨 User Interface
+
 - 🧙 **Interactive Wizard Mode** - User-friendly guided setup (default)
 - 💻 **CLI Mode** - Traditional command-line interface (--cli flag)
 - 📤 **Interactive export** - Prompts for export choice when no options specified
 
 ### 🔢 Token Analysis
+
 - ✅ **Exact token counting** using tiktoken (GPT-4 compatible)
 - 🌍 **Multi-language support** - 14+ languages: JavaScript, TypeScript, Python, PHP, Ruby, Java, Kotlin, C#, Go, Rust, Swift, C/C++, Scala
 - 🎯 **Method-level analysis** - Analyze tokens per function/method
 - 📊 **Detailed reporting** - by file type, largest files, statistics
 
 ### 🎯 Filtering & Configuration
+
 - 🚫 **Dual ignore system** - respects both `.gitignore` and context ignore rules
 - 📋 **Include/Exclude modes** - `.contextinclude` takes priority over `.contextignore`
 - 🔍 **Method filtering** - `.methodinclude` and `.methodignore` for granular control
 - 🎯 **Core application focus** - configured to analyze only essential code files
 
 ### 📤 Export Options
+
 - 🤖 **LLM context export** - generate optimized file lists for LLM consumption
 - 📋 **Clipboard integration** - copy context directly to clipboard
 - 💾 **JSON/YAML/CSV/XML exports** - multiple format options
@@ -64,12 +69,14 @@ If you find this tool helpful, consider buying me a coffee! Your support helps m
 ## Quick Start
 
 ### 🧙 Interactive Wizard Mode (Default)
+
 ```bash
 # Launch interactive wizard (guides you through options)
 context-manager
 ```
 
 The wizard provides a user-friendly interface to:
+
 - Select your use case (Bug Fix, Feature, Code Review, etc.)
 - Choose target LLM (Claude, GPT-4, Gemini, etc.)
 - Pick output format (TOON, JSON, YAML, etc.)
@@ -77,6 +84,7 @@ The wizard provides a user-friendly interface to:
 **Note:** Wizard mode uses Ink terminal UI. If you experience visual artifacts, use CLI mode with `--cli` flag.
 
 ### 💻 CLI Mode
+
 ```bash
 # Use CLI mode instead of wizard
 context-manager --cli
@@ -97,6 +105,7 @@ context-manager --cli -g -s  # GitIngest digest + detailed report
 ```
 
 ### 🤖 LLM Optimization (v2.3.7)
+
 ```bash
 # Auto-detect LLM from environment
 export ANTHROPIC_API_KEY=sk-...
@@ -121,6 +130,7 @@ context-manager --cli --target-model claude-sonnet-4.5
 ```
 
 Supported LLM models (9+ models):
+
 - **Anthropic**: Claude Sonnet 4.5, Claude Opus 4
 - **OpenAI**: GPT-4 Turbo, GPT-4o, GPT-4o Mini
 - **Google**: Gemini 1.5 Pro, Gemini 2.0 Flash
@@ -129,6 +139,7 @@ Supported LLM models (9+ models):
 Custom models supported via `.context-manager/custom-profiles.json`
 
 ### 🔀 Git Integration (v3.0.0)
+
 ```bash
 # Analyze only uncommitted changes
 context-manager --changed-only
@@ -150,6 +161,7 @@ context-manager --changed-only --with-authors
 ```
 
 ### 👁️ Watch Mode (v3.0.0)
+
 ```bash
 # Start watch mode
 context-manager watch
@@ -168,6 +180,7 @@ context-manager watch --debounce 2000
 ```
 
 ### 🌐 API Server (v3.0.0)
+
 ```bash
 # Start API server
 context-manager serve
@@ -189,14 +202,6 @@ curl http://localhost:3000/api/v1/methods?file=src/server.js
 curl http://localhost:3000/api/v1/diff?since=main
 ```
 
-### Wrapper Script Usage
-```bash
-# Using the NPM package globally
-context-manager
-context-manager --save-report
-context-manager --context-clipboard
-```
-
 ## 🧪 Testing & Validation
 
 ### Test Repositories
@@ -224,6 +229,7 @@ See [test-repos/README.md](test-repos/README.md) for complete testing guide.
 Complete manual testing guide available at [docs/MANUAL-TESTING-v3.0.md](docs/MANUAL-TESTING-v3.0.md)
 
 Includes:
+
 - ✅ 50+ test scenarios for all v3.0.0 features
 - ✅ API endpoint validation
 - ✅ Git integration testing
@@ -244,145 +250,63 @@ npm run test:api
 npm run test:watch
 ```
 
-## Current Configuration
-
-The tool is configured to focus on **core application logic only**:
-
-### ✅ Included (64 JS files, ~181k tokens)
-- Core MCP server implementation (`utility-mcp/src/`)
-- Authentication and security layers
-- Request handlers and routing
-- Transport protocols and communication
-- Utilities and validation logic
-- Configuration management
-- Error handling and monitoring
-
-### 🚫 Excluded via context ignore rules
-- Documentation files (`.md`, `.txt`)
-- Configuration files (`.json`, `.yml`)
-- Infrastructure and deployment files
-- Testing and script directories
-- Build artifacts and dependencies
-- Workflow orchestration files (`utility-mcp/src/workflows/**`)
-- Testing utilities (`utility-mcp/src/testing/**`)
-- All non-essential supporting files
-
 ## Usage
 
-### Basic Analysis
 ```bash
-# Interactive analysis with export selection
-context-manager
-
-# Quiet mode (no file listing)
-context-manager --no-verbose
-
-# With detailed JSON report
-context-manager --save-report
-
-# Generate LLM context file list
-context-manager --context-export
-
-# Copy context directly to clipboard
-context-manager --context-clipboard
+context-manager                    # Interactive wizard (default)
+context-manager --cli              # CLI mode
+context-manager --cli -s           # Save detailed JSON report
+context-manager --cli --context-clipboard  # Copy context to clipboard
+context-manager --cli -m           # Method-level analysis
+context-manager --cli -g           # GitIngest digest
 ```
 
-### Interactive Export Selection
-
-When you run the tool without specifying export options (`--save-report`, `--context-export`, or `--context-clipboard`), it will automatically prompt you to choose an export option after the analysis:
-
-```bash
-# Run analysis and get prompted for export options
-context-manager
-
-# The tool will show:
-# 📤 Export Options:
-# 1) Save detailed JSON report (token-analysis-report.json)
-# 2) Generate LLM context file (llm-context.json)
-# 3) Copy LLM context to clipboard
-# 4) No export (skip)
-# 
-# 🤔 Which export option would you like? (1-4):
-```
-
-This interactive mode ensures you never miss the opportunity to export your analysis results in the format you need.
+When no export options are specified, the tool prompts for export selection interactively.
 
 ## Include vs Exclude Modes
 
-The token calculator supports two complementary filtering modes:
-
-### EXCLUDE Mode (.contextignore)
-- **Default mode** when only `.contextignore` exists
-- Includes all files **except** those matching ignore patterns
-- Traditional gitignore-style exclusion logic
-
-### INCLUDE Mode (.contextinclude) 
-- **Priority mode** - when `.contextinclude` exists, `.contextignore` is ignored
-- Includes **only** files matching include patterns
-- More precise control for specific file selection
-- Perfect for creating focused analysis sets
-
-### Mode Priority
-1. If `.contextinclude` exists → **INCLUDE mode** (ignore `.contextignore`)
-2. If only `.contextignore` exists → **EXCLUDE mode**
-3. If neither exists → Include all files (respect `.gitignore` only)
-
-### Example Usage
-```bash
-# EXCLUDE mode: Include everything except patterns in .contextignore
-rm .contextinclude  # Remove include file
-context-manager
-
-# INCLUDE mode: Include only patterns in .contextinclude
-# (automatically ignores .contextignore)
-context-manager
-```
-
-### Help and Options
-```bash
-context-manager --help
-```
+When `.contextinclude` exists, it activates **INCLUDE mode** (ignoring `.contextignore`). Otherwise, **EXCLUDE mode** uses `.contextignore` patterns. See the Configuration section below for details and examples.
 
 ### Available Options
+
 - `--save-report`, `-s` - Save detailed JSON report
 - `--no-verbose` - Disable file listing (verbose is default)
 - `--context-export` - Generate LLM context file list (saves as llm-context.json)
 - `--context-clipboard` - Copy LLM context directly to clipboard
 - `--detailed-context` - Use detailed context format (8.6k chars, default is compact 1.2k)
+- `--method-level`, `-m` - Enable method-level analysis
 - `--help`, `-h` - Show help message
 
 ## LLM Context Export
 
-The token calculator can generate optimized file lists for LLM consumption, with two format options:
+The token calculator generates optimized file lists for LLM consumption, with two format options:
 
 ### Ultra-Compact Format (Default)
+
 - **Size**: ~2.3k characters (structured JSON)
 - **Content**: Project metadata and organized file paths without token counts
-- **Format**: Identical to llm-context.json file - complete JSON structure
-- **Perfect for**: LLM consumption, programmatic processing, structured data needs
+- **Perfect for**: LLM consumption, programmatic processing
 - **Usage**: `--context-clipboard` or `--context-export`
 
 ### Detailed Format (Legacy)
+
 - **Size**: ~8.6k characters (comprehensive)
 - **Content**: Full paths, categories, importance scores, directory stats
 - **Perfect for**: Initial project analysis, comprehensive documentation
 - **Usage**: `--detailed-context --context-clipboard`
 
 ### Features
+
 - **Smart file selection** - Top files by token count and importance
 - **Directory grouping** - Common prefix compression saves space
 - **Token abbreviation** - "12k" instead of "12,388 tokens"
-- **Extension removal** - ".js" removed to save characters
 - **Cross-platform clipboard** - Works on macOS, Linux, and Windows
-- **Multiple output formats** - JSON file or clipboard ready text
-
-### Usage
 
 ```bash
-# Generate minimal LLM context and save to llm-context.json (2.3k chars JSON)
+# Generate minimal LLM context and save to llm-context.json
 context-manager --context-export
 
-# Copy minimal context directly to clipboard (2.3k chars JSON - identical to file)
+# Copy minimal context directly to clipboard
 context-manager --context-clipboard
 
 # Copy detailed context to clipboard (8.6k chars)
@@ -392,459 +316,88 @@ context-manager --detailed-context --context-clipboard
 context-manager --save-report --context-clipboard
 ```
 
-### Output Format Examples
-
-**Compact Format (JSON - 2.3k chars):**
-```json
-{
-  "project": {
-    "root": "cloudstack-go-mcp-proxy",
-    "totalFiles": 64,
-    "totalTokens": 181480
-  },
-  "paths": {
-    "utility-mcp/src/server/": [
-      "CloudStackUtilityMCP.js"
-    ],
-    "utility-mcp/src/handlers/": [
-      "workflow-handlers.js",
-      "tool-handlers.js",
-      "analytics-handler.js"
-    ],
-    "utility-mcp/src/utils/": [
-      "security.js",
-      "usage-tracker.js",
-      "cache-warming.js"
-    ]
-  }
-}
-```
-
-**Detailed Format (8.6k chars):**
-```
-# cloudstack-go-mcp-proxy Codebase Context
-
-**Project:** 64 files, 181,480 tokens
-
-**Core Files (Top 20):**
-1. `utility-mcp/src/server/CloudStackUtilityMCP.js` (12,388 tokens, server)
-2. `utility-mcp/src/handlers/workflow-handlers.js` (11,007 tokens, handler)
-...
-
-**All Files:**
-```json
-[{"path": "file.js", "t": 1234, "c": "core", "i": 85}]
-```
-
-**Use Cases**
-
-**Compact Format (2.3k chars JSON):**
-1. **LLM Integration** - Structured data for AI assistants with complete project context
-2. **Programmatic Processing** - JSON format for automated tools and scripts  
-3. **Context Sharing** - Identical format in clipboard and file exports
-4. **Development Workflows** - Consistent structure for CI/CD and automation
-
-**Detailed Format (8.6k chars):**
-1. **Architecture Planning** - Comprehensive project overview for major decisions
-2. **New Team Member Onboarding** - Complete codebase understanding
-3. **Documentation Generation** - Full project structure analysis
-4. **Code Review Preparation** - Detailed file relationships and importance
-
-**General Use Cases:**
-- Development workflow integration
-- CI/CD pipeline context generation
-- Automated documentation updates
-- Project health monitoring
-
 ## GitIngest Format Export
 
-Context-manager now supports generating GitIngest-style digest files - a single, prompt-friendly text file perfect for LLM consumption.
-
-### What is GitIngest Format?
-
-GitIngest format consolidates your entire codebase into a single text file with:
-- Project summary and statistics
-- Visual directory tree structure
-- Complete file contents with clear separators
-- Token count estimates
-
-This format is inspired by [GitIngest](https://github.com/coderamp-labs/gitingest), implemented purely in JavaScript with zero additional dependencies.
-
-### Usage
+Generate a single, prompt-friendly text file with your entire codebase for LLM consumption. Inspired by [GitIngest](https://github.com/coderamp-labs/gitingest).
 
 ```bash
-# Standard workflow - analyze and generate digest in one step
-context-manager --gitingest
-context-manager -g
-
-# Combine with other exports
-context-manager -g -s  # digest.txt + token-analysis-report.json
-
-# Two-step workflow - generate digest from existing JSON (fast, no re-scan)
-context-manager -s                                    # Step 1: Create report
-context-manager --gitingest-from-report               # Step 2: Generate digest
-
-# Or from LLM context
-context-manager --context-export                      # Step 1: Create context
-context-manager --gitingest-from-context              # Step 2: Generate digest
-
-# With custom filenames
-context-manager --gitingest-from-report my-report.json
-context-manager --gitingest-from-context my-context.json
-```
-
-**Why use JSON-based digest?**
-- ⚡ **Performance**: Instant digest generation without re-scanning
-- 🔄 **Reusability**: Generate multiple digests from one analysis
-- 📦 **Workflow**: Separate analysis from export steps
-- 🎯 **Flexibility**: Use different JSON sources for different purposes
-
-### Output Example
-
-The generated `digest.txt` file looks like:
-
+context-manager --gitingest         # Generate digest.txt
+context-manager -g -s               # digest.txt + token-analysis-report.json
+context-manager --gitingest-from-report  # Generate from existing JSON (no re-scan)
+context-manager --gitingest-from-context # Generate from LLM context file
 ```
-Directory: my-project
-Files analyzed: 42
-
-Estimated tokens: 15.2k
-Directory structure:
-└── my-project/
-    ├── src/
-    │   ├── index.js
-    │   └── utils.js
-    └── README.md
-
-
-================================================
-FILE: src/index.js
-================================================
-[complete file contents here]
-
-================================================
-FILE: src/utils.js
-================================================
-[complete file contents here]
-```
-
-### Key Features
-
-- **Single File**: Everything in one file for easy LLM ingestion
-- **Tree Visualization**: Clear directory structure
-- **Token Estimates**: Formatted as "1.2k" or "1.5M"
-- **Sorted Output**: Files sorted by token count (largest first)
-- **Filter Compatible**: Respects all `.gitignore` and context ignore rules
-
-### Use Cases
 
-1. **LLM Context Windows**: Paste entire codebase as single context
-2. **Code Reviews**: Share complete project snapshot
-3. **Documentation**: Single-file project reference
-4. **AI Analysis**: Perfect for ChatGPT, Claude, or other LLMs
-5. **Archival**: Simple project snapshot format
-
-### Version Tracking
-
-Context-manager implements GitIngest format v0.3.1. See [docs/GITINGEST_VERSION.md](docs/GITINGEST_VERSION.md) for implementation details and version history.
+Output includes project summary, directory tree, and complete file contents sorted by token count. See [docs/GITINGEST_VERSION.md](docs/GITINGEST_VERSION.md) for version details.
 
 ## Configuration
 
-### .contextignore File (EXCLUDE Mode)
-
-The `.contextignore` file is pre-configured for core application analysis:
+### File-Level Filtering
 
-```bash
-# Current focus: Only core JS files in utility-mcp/src/
-# Excludes:
-**/*.md              # All documentation
-**/*.json            # All configuration files
-**/*.yml             # All YAML files
-infrastructure/**    # Infrastructure code
-workflows/**         # Workflow definitions
-docs/**              # Documentation directory
-token-analysis/**    # Analysis tools themselves
-utility-mcp/scripts/** # Utility scripts
-utility-mcp/src/workflows/** # Workflow JS files
-utility-mcp/src/testing/**   # Testing utilities
-```
+**Priority Order:**
 
-### .contextinclude File (INCLUDE Mode)
+1. `.gitignore` (always respected)
+2. `.contextinclude` - INCLUDE mode (highest priority for files)
+3. `.contextignore` - EXCLUDE mode (fallback for files)
 
-The `.contextinclude` file provides precise file selection:
+**`.contextinclude`** (INCLUDE mode) - include only matching files:
 
 ```bash
-# Include only core JavaScript files
-# This should produce exactly 64 files
-
-# Include main entry point
-utility-mcp/index.js
-
-# Include all src JavaScript files EXCEPT workflows and testing
 utility-mcp/src/**/*.js
-
-# Exclude specific subdirectories (using negation)
 !utility-mcp/src/workflows/**
 !utility-mcp/src/testing/**
 ```
 
-### Creating Custom Configurations
-
-**For EXCLUDE mode** (edit `.contextignore`):
-```bash
-# Remove lines to include more file types
-# Add patterns to exclude specific files
-
-# Example: Include documentation
-# **/*.md    <- comment out or remove this line
-
-# Example: Exclude specific large files
-your-large-file.js
-specific-directory/**
-```
+**`.contextignore`** (EXCLUDE mode) - exclude matching files:
 
-**For INCLUDE mode** (create `.contextinclude`):
 ```bash
-# Include specific files or patterns
-src/**/*.js          # All JS files in src
-config/*.json        # Config files only
-docs/api/**/*.md     # API documentation only
-
-# Use negation to exclude from broad patterns
-src/**/*.js
-!src/legacy/**       # Exclude legacy code
-!src/**/*.test.js    # Exclude test files
-```
-
-## Configuration File Priority
-
-1. **`.gitignore`** (project root) - Standard git exclusions (always respected)
-2. **`.contextinclude`** (token-analysis/) - INCLUDE mode (highest priority)
-3. **`.contextignore`** (token-analysis/) - EXCLUDE mode (used when no include file)
-4. **`.contextignore`** (project root) - Fallback EXCLUDE mode location
-
-## Installation
-
-For exact token counting, install tiktoken:
-
-```bash
-npm install tiktoken
+**/*.md
+**/*.json
+**/*.yml
+node_modules/**
+**/*.test.js
 ```
 
-Without tiktoken, the tool uses smart estimation (~95% accuracy).
+Use negation (`!pattern`) to exclude from broad include patterns.
 
 ## Output Example
 
 ```
 🎯 PROJECT TOKEN ANALYSIS REPORT
-================================================================================
 📊 Total files analyzed: 64
 🔢 Total tokens: 181,480
 💾 Total size: 0.78 MB
 📄 Total lines: 28,721
-📈 Average tokens per file: 2,836
-🚫 Files ignored by .gitignore: 11,912
-📋 Files ignored by calculator rules: 198
-
-📋 BY FILE TYPE:
---------------------------------------------------------------------------------
-Extension         Files      Tokens   Size (KB)     Lines
---------------------------------------------------------------------------------
-.js                  64     181,480       799.8    28,721
-
-🏆 TOP 5 LARGEST FILES BY TOKEN COUNT:
---------------------------------------------------------------------------------
- 1.   12,388 tokens (6.8%) - utility-mcp/src/server/CloudStackUtilityMCP.js
- 2.   11,007 tokens (6.1%) - utility-mcp/src/handlers/workflow-handlers.js
- 3.    7,814 tokens (4.3%) - utility-mcp/src/utils/security.js
- 4.    6,669 tokens (3.7%) - utility-mcp/src/handlers/tool-handlers.js
- 5.    5,640 tokens (3.1%) - utility-mcp/src/ci-cd/pipeline-integration.js
-```
-
-## Context Management
 
-Perfect for LLM context window optimization:
-- **181k tokens** = Core application logic only
-- **Clean analysis** = No noise from docs, configs, or build files
-- **Focused development** = Essential code for AI-assisted development
-- **Context efficiency** = Maximum useful code per token
-- **Dual mode flexibility** = Precise include/exclude control
-- **Ultra-minimal export** = 1k chars (89% reduction) for frequent AI interactions
-- **Detailed export** = 8.6k chars for comprehensive analysis when needed
-
-## Integration
-
-You can integrate this tool into:
-- CI/CD pipelines for code size monitoring
-- Pre-commit hooks for token budget checks
-- Documentation generation workflows
-- Code quality gates
-- LLM context preparation workflows
-- Development environment setup
+🏆 TOP 5 LARGEST FILES:
+ 1. 12,388 tokens - utility-mcp/src/server/CloudStackUtilityMCP.js
+ 2. 11,007 tokens - utility-mcp/src/handlers/workflow-handlers.js
+ 3.  7,814 tokens - utility-mcp/src/utils/security.js
+```
 
 ## Troubleshooting
 
 ### Include vs Exclude Mode Issues
-- **INCLUDE mode active**: Remove `.contextinclude` to use EXCLUDE mode
-- **Wrong files included**: Check if `.contextinclude` exists (takes priority)
-- **Mode confusion**: Use verbose mode to see which mode is active
+
+- Remove `.contextinclude` to use EXCLUDE mode
+- Check if `.contextinclude` exists (takes priority)
+- Use verbose mode to see which mode is active
 
 ### Patterns Not Working
+
 - Ensure no inline comments in ignore/include pattern files
 - Use file patterns (`docs/**`) instead of directory patterns (`docs/`)
-- Test specific patterns with verbose mode
 - Check pattern syntax: `**` for recursive, `*` for single level
 
 ### Token Count Issues
+
 - **Too high**: Review included files with verbose mode, add exclusion patterns
 - **Too low**: Check if important files are excluded, review patterns
 - **Inconsistent**: Verify which mode is active (include vs exclude)
 
-### Missing Expected Files
-- Check if files are excluded by `.gitignore` (always respected)
-- Verify calculator ignore/include patterns
-- Ensure files are recognized as text files
-- Use verbose mode to see exclusion reasons
-
-# Context Manager
-
-LLM context manager with method-level filtering and token optimization. The ultimate tool for AI-assisted development.
-
-*Created by Hakkı Sağdıç*
-
-## 🚀 Features
-
-✅ **File-level token analysis** - Analyze entire files and directories
-🔧 **Method-level analysis** - Extract and analyze specific methods from JavaScript/TypeScript/Rust/C#/Go/Java
-📋 **Dual filtering system** - Include/exclude files and methods with pattern matching  
-📊 **LLM context optimization** - Generate ultra-compact context for AI assistants  
-🎯 **Exact token counting** - Uses tiktoken for GPT-4 compatible counts  
-📤 **Multiple export formats** - JSON reports, clipboard, file exports  
-📦 **NPM package** - Use programmatically or as global CLI tool  
-🔍 **Pattern matching** - Wildcards and regex support for flexible filtering  
-⚡ **Performance optimized** - 36% smaller codebase with enhanced functionality  
-
-## 📦 Installation
-
-### Option 1: NPM Package (Recommended)
-```bash
-# Local installation
-npm install @hakkisagdic/context-manager
-
-# Global installation
-npm install -g @hakkisagdic/context-manager
-
-# Run globally
-context-manager --help
-```
-
-### Option 2: Direct Usage
-```bash
-# Clone and use directly
-git clone <repository>
-cd token-analysis
-node token-calculator.js --help
-```
-
-## 🎯 Quick Start
-
-### Basic Analysis
-```bash
-# Interactive analysis with export selection
-context-manager
-
-# File-level analysis with clipboard export
-context-manager --context-clipboard
-
-# Method-level analysis
-context-manager --method-level --context-export
-
-# Analysis with reports
-context-manager --method-level --save-report --verbose
-```
-
-### Advanced Usage
-```bash
-# Focus on specific methods only
-echo "calculateTokens\nhandleRequest\n*Validator" > .methodinclude
-context-manager --method-level
-
-# Exclude test methods
-echo "*test*\n*debug*\nconsole" > .methodignore
-context-manager --method-level --context-clipboard
-```
-
-## Usage
-
-### Command Line Interface
-
-```bash
-# Basic analysis
-context-manager
-
-# Method-level analysis
-context-manager --method-level
-
-# Save detailed report
-context-manager --save-report
-
-# Copy context to clipboard
-context-manager --context-clipboard
-
-# Combine options
-context-manager --method-level --save-report --verbose
-```
-
-### Programmatic Usage
-
-```javascript
-const { TokenAnalyzer } = require('@hakkisagdic/context-manager');
-
-// Basic file-level analysis
-const analyzer = new TokenAnalyzer('./src', {
-    methodLevel: false,
-    verbose: true
-});
-
-// Method-level analysis
-const methodAnalyzer = new TokenAnalyzer('./src', {
-    methodLevel: true,
-    saveReport: true
-});
-
-analyzer.run();
-```
-
-## 🔧 Configuration
-
-### File-Level Filtering
-
-**Priority Order:**
-1. `.gitignore` (project root) - Standard git exclusions (always respected)
-2. `.contextinclude` - INCLUDE mode (highest priority for files)
-3. `.contextignore` - EXCLUDE mode (fallback for files)
-
-**`.contextinclude`** - Include only these files:
-```bash
-# Include only core JavaScript files
-utility-mcp/src/**/*.js
-!utility-mcp/src/testing/**
-!utility-mcp/src/workflows/**
-```
-
-**`.contextignore`** - Exclude these files:  
-```bash
-# Exclude documentation and config
-**/*.md
-**/*.json
-node_modules/**
-test/
-**/*.test.js
-**/*.spec.js
-```
-
-### Method-Level Filtering
+### Advanced Method Filtering
 
 **`.methodinclude`** - Include only these methods:
+
 ```bash
 # Core business logic methods
 calculateTokens
@@ -862,6 +415,7 @@ TokenCalculator.* # All methods in TokenCalculator class
 ```
 
 **`.methodignore`** - Exclude these methods:
+
 ```bash
 # Utility and debug methods
 console
@@ -876,98 +430,19 @@ server.printStatus
 utils.debugLog
 ```
 
-### Pattern Syntax
-
-| Pattern | Description | Example |
-|---------|-------------|----------|
-| `methodName` | Exact match | `calculateTokens` |
-| `*pattern*` | Contains pattern | `*Handler` matches `requestHandler` |
-| `Class.*` | All methods in class | `TokenCalculator.*` |
-| `file.method` | Specific file method | `server.handleRequest` |
-| `!pattern` | Negation (exclude) | `!*test*` |
-
-## 📤 Output Formats
-
-### 1. File-Level Context (Default)
-**Use case:** General codebase analysis, file organization
-
-```json
-{
-  "project": {
-    "root": "my-project",
-    "totalFiles": 64,
-    "totalTokens": 181480
-  },
-  "paths": {
-    "src/core/": ["server.js", "handler.js"],
-    "src/utils/": ["helper.js", "validator.js"]
-  }
-}
-```
-
-### 2. Method-Level Context (`--method-level`)
-**Use case:** Focused analysis, debugging specific methods, LLM context optimization
-
-```json
-{
-  "project": {
-    "root": "my-project",
-    "totalFiles": 64,
-    "totalTokens": 181480
-  },
-  "methods": {
-    "src/server.js": [
-      {"name": "handleRequest", "line": 15, "tokens": 234},
-      {"name": "validateInput", "line": 45, "tokens": 156}
-    ],
-    "src/utils.js": [
-      {"name": "processData", "line": 12, "tokens": 89}
-    ]
-  },
-  "methodStats": {
-    "totalMethods": 150,
-    "includedMethods": 23,
-    "totalMethodTokens": 5670
-  }
-}
-```
-
-### 3. Detailed Report (JSON)
-**Use case:** Comprehensive analysis, CI/CD integration, historical tracking
-
-```json
-{
-  "metadata": {
-    "generatedAt": "2024-01-15T10:30:00.000Z",
-    "projectRoot": "/path/to/project",
-    "gitignoreRules": ["node_modules/**", "*.log"],
-    "calculatorRules": ["src/**/*.js", "!src/test/**"]
-  },
-  "summary": {
-    "totalFiles": 64,
-    "totalTokens": 181480,
-    "byExtension": {".js": {"count": 64, "tokens": 181480}},
-    "largestFiles": [...]
-  },
-  "files": [...]
-}
-```
-
-## CLI Options
+#### Method Pattern Syntax
 
-| Option | Short | Description |
-|--------|-------|-------------|
-| `--save-report` | `-s` | Save detailed JSON report |
-| `--verbose` | `-v` | Show included files and directories |
-| `--context-export` | | Generate LLM context file |
-| `--context-clipboard` | | Copy context to clipboard |
-| `--method-level` | `-m` | Enable method-level analysis |
-| `--help` | `-h` | Show help message |
+| Pattern       | Description          | Example                             |
+| ------------- | -------------------- | ----------------------------------- |
+| `methodName`  | Exact match          | `calculateTokens`                   |
+| `*pattern*`   | Contains pattern     | `*Handler` matches `requestHandler` |
+| `Class.*`     | All methods in class | `TokenCalculator.*`                 |
+| `file.method` | Specific file method | `server.handleRequest`              |
+| `!pattern`    | Negation (exclude)   | `!*test*`                           |
 
 ## 📊 Use Cases & Examples
 
-### 1. 🤖 LLM Context Optimization
-**Goal:** Generate minimal context for AI assistants
+### 1. LLM Context Optimization
 
 ```bash
 # Ultra-compact method-level context
@@ -978,10 +453,7 @@ echo "handleRequest\nprocessData\nvalidateInput" > .methodinclude
 context-manager --method-level --context-export
 ```
 
-**Result:** 89% smaller context compared to full codebase
-
-### 2. 📊 Codebase Analysis  
-**Goal:** Understand project complexity and structure
+### 2. Codebase Analysis
 
 ```bash
 # Analysis with detailed reports
@@ -991,8 +463,7 @@ context-manager --save-report --verbose
 context-manager --method-level --save-report
 ```
 
-### 3. 🔍 Method-Level Debugging
-**Goal:** Focus on specific problematic methods
+### 3. Method-Level Debugging
 
 ```bash
 # Debug authentication methods only
@@ -1004,8 +475,7 @@ echo "*test*\n*debug*\nconsole\nlogger" > .methodignore
 context-manager --method-level
 ```
 
-### 4. 🚀 CI/CD Integration
-**Goal:** Monitor codebase growth and complexity
+### 4. CI/CD Integration
 
 ```bash
 # Daily token analysis for monitoring
@@ -1015,8 +485,7 @@ context-manager --save-report > reports/analysis-$(date +%Y%m%d).json
 context-manager --method-level --save-report
 ```
 
-### 5. 📈 Code Quality Gates
-**Goal:** Ensure code stays within token budgets
+### 5. Code Quality Gates
 
 ```bash
 # Check if codebase exceeds LLM context limits
@@ -1027,38 +496,6 @@ if [ $TOKENS -gt 100000 ]; then
 fi
 ```
 
-## 🛠️ CLI Reference
-
-### Core Options
-
-| Option | Short | Description | Example |
-|--------|-------|-------------|----------|
-| `--save-report` | `-s` | Save detailed JSON report | `context-manager -s` |
-| `--verbose` | `-v` | Show included files/methods | `context-manager -v` |
-| `--context-export` | | Generate LLM context file | `context-manager --context-export` |
-| `--context-clipboard` | | Copy context to clipboard | `context-manager --context-clipboard` |
-| `--method-level` | `-m` | Enable method-level analysis | `context-manager -m` |
-| `--help` | `-h` | Show help message | `context-manager -h` |
-
-### Usage Patterns
-
-```bash
-# Quick analysis with interactive export
-context-manager
-
-# Method-level analysis with all outputs
-context-manager --method-level --save-report --context-export --verbose
-
-# LLM-optimized context generation
-context-manager --method-level --context-clipboard
-
-# CI/CD monitoring
-context-manager --save-report --context-export
-
-# Development debugging
-context-manager --method-level --verbose
-```
-
 ## 💻 Programmatic API
 
 ### Basic Usage
@@ -1069,7 +506,7 @@ const { TokenAnalyzer } = require('@hakkisagdic/context-manager');
 // File-level analysis
 const analyzer = new TokenAnalyzer('./src', {
   verbose: true,
-  saveReport: true
+  saveReport: true,
 });
 
 analyzer.run();
@@ -1084,7 +521,7 @@ const { TokenAnalyzer, MethodAnalyzer } = require('@hakkisagdic/context-manager'
 const analyzer = new TokenAnalyzer('./src', {
   methodLevel: true,
   contextExport: true,
-  verbose: false
+  verbose: false,
 });
 
 analyzer.run();
@@ -1100,17 +537,17 @@ const methods = methodAnalyzer.extractMethods(fileContent, 'server.js');
 const analyzer = new TokenAnalyzer('./src', {
   // Enable method-level analysis
   methodLevel: true,
-  
+
   // Output options
   saveReport: true,
   contextExport: true,
   contextToClipboard: true,
-  
+
   // Verbosity
   verbose: true,
-  
+
   // Compact context (for LLM optimization)
-  compactContext: true
+  compactContext: true,
 });
 
 // Access results
@@ -1124,17 +561,14 @@ console.log('Analysis complete!');
 const { MethodAnalyzer, MethodFilterParser } = require('@hakkisagdic/context-manager');
 
 // Create custom method filter
-const filter = new MethodFilterParser(
-  './custom-methods.include',
-  './custom-methods.ignore'
-);
+const filter = new MethodFilterParser('./custom-methods.include', './custom-methods.ignore');
 
 // Analyze specific file
 const methodAnalyzer = new MethodAnalyzer();
 const methods = methodAnalyzer.extractMethods(content, filePath);
 
 // Filter methods
-const filteredMethods = methods.filter(method => 
+const filteredMethods = methods.filter((method) =>
   filter.shouldIncludeMethod(method.name, fileName)
 );
 ```
@@ -1163,4 +597,4 @@ MIT License - see LICENSE file for details
 
 ---
 
-*Created with ❤️ by Hakkı Sağdıç*
+_Created with ❤️ by Hakkı Sağdıç_