🔧 Fix command syntax inconsistencies and improve documentation clarity

## Command Syntax Standardization
- Fix lowercase "superclaude" → "SuperClaude" in installation.md
- Distinguish between terminal commands (SuperClaude install) and Claude Code commands (/sc:*)
- Add clear command context headers to all major documentation files

## Documentation Improvements
- Add command reference tables to key guides
- Create visual distinction markers (🖥️ Terminal vs 💬 Claude Code)
- Update verification sections with proper command separation
- Fix content duplications in Developer-Guide and Getting-Started files

## Cross-Reference Updates
- Standardize all documentation links to use Docs/ prefix structure
- Replace invalid email addresses with anton.knoery@gmail.com
- Remove non-existent team references from security documentation

## Files Enhanced
- Getting-Started: installation.md, quick-start.md with command clarity
- User-Guide: commands.md with comprehensive command context
- Reference: troubleshooting.md, common-issues.md with mixed command support
- Root files: README.md, CONTRIBUTING.md, SECURITY.md link updates

This resolves command confusion between installation (terminal) and development (/sc:) commands.

🤖 Generated with Claude Code

Co-Authored-By: Claude <noreply@anthropic.com>

Docs/User-Guide/agents.md

@@ -765,7 +765,7 @@ Add "documented", "explained", or "tutorial" to requests for automatic technical
 
 ### Advanced Usage  
 - **[Behavioral Modes](modes.md)** - Context optimization for enhanced agent coordination
-- **[Best Practices](../Reference/best-practices.md)** - Expert techniques for agent optimization
+- **[Best Practices](../Reference/quick-start-practices.md)** - Expert techniques for agent optimization
 - **[Examples Cookbook](../Reference/examples-cookbook.md)** - Real-world agent coordination patterns
 
 ### Development Resources

Docs/User-Guide/commands.md

@@ -1,5 +1,7 @@
 # SuperClaude Commands Guide
 
+> **Command Context**: This guide covers **Claude Code Commands** (`/sc:` commands). These run inside Claude Code chat, not in your terminal. For installation commands, see [Installation Guide](../Getting-Started/installation.md).
+
 ## ✅ Verification Status
 - **SuperClaude Version**: v4.0+ Compatible
 - **Last Tested**: 2025-01-16
@@ -10,24 +12,41 @@
 
 ## 🧪 Testing Your Setup
 
-Before using this guide, verify your SuperClaude installation:
-
+### 🖥️ Terminal Verification (Run in Terminal/CMD)
 ```bash
 # Verify SuperClaude is working
 SuperClaude --version
 # Expected: SuperClaude Framework v4.0+
 
-# Test basic command syntax  
-echo "/sc:brainstorm 'test'" | claude --help
-# Expected: No syntax errors
-
 # Check MCP server connectivity
 SuperClaude status --mcp
 # Expected: At least context7 and sequential-thinking connected
 ```
 
+### 💬 Claude Code Testing (Type in Claude Code Chat)
+```
+# Test basic /sc: command
+/sc:brainstorm "test project"
+# Expected: Interactive requirements discovery starts
+
+# Test command help
+/sc:help
+# Expected: List of available commands
+```
+
 **If tests fail**: Check [Installation Guide](../Getting-Started/installation.md) or [Troubleshooting](#troubleshooting)
 
+### 📋 Command Quick Reference
+
+| Command Type | Where to Run | Format | Purpose |
+|-------------|--------------|--------|---------|
+| **🖥️ Installation** | Terminal/CMD | `SuperClaude [command]` | Setup and maintenance |
+| **🔧 Configuration** | Terminal/CMD | `python3 -m SuperClaude` | Advanced configuration |
+| **💬 Development** | Claude Code | `/sc:[command]` | AI-enhanced development |
+| **⚡ Workflow** | Claude Code | `/sc:[command] --flags` | Enhanced automation |
+
+> **Remember**: All `/sc:` commands work inside Claude Code chat, not your terminal.
+
 ## Table of Contents
 
 - [Essential Commands](#essential-commands) - Start here (8 core commands)
@@ -660,7 +679,7 @@ SuperClaude install --components mcp --force
 
 **Documentation**
 - [Quick Start Guide](../Getting-Started/quick-start.md) - Essential setup and first steps
-- [Best Practices](../Reference/best-practices.md) - Optimization and workflow patterns
+- [Best Practices](../Reference/quick-start-practices.md) - Optimization and workflow patterns
 - [Examples Cookbook](../Reference/examples-cookbook.md) - Real-world usage patterns
 
 **Community Support**

Docs/User-Guide/flags.md

@@ -940,7 +940,7 @@ SuperClaude validate-flags --think-hard --no-mcp --magic
 
 **🌲 Advanced (Month 2+)**
 - [Session Management](session-management.md) - Long-term flag patterns
-- [Best Practices](../Reference/best-practices.md) - Flag optimization strategies
+- [Best Practices](../Reference/quick-start-practices.md) - Flag optimization strategies
 - [Examples Cookbook](../Reference/examples-cookbook.md) - Real-world flag combinations
 
 **🔧 Expert**

Docs/User-Guide/mcp-servers.md

@@ -1212,7 +1212,7 @@ Learning new technology?
 
 **🌲 Advanced (Month 2+)**
 - [Session Management](session-management.md) - Serena MCP workflows
-- [Best Practices](../Reference/best-practices.md) - MCP optimization strategies
+- [Best Practices](../Reference/quick-start-practices.md) - MCP optimization strategies
 - [Flags Guide](flags.md) - Advanced MCP control
 
 **🔧 Expert**

Docs/User-Guide/modes.md

@@ -610,7 +610,7 @@ SuperClaude's 6 behavioral modes create an **intelligent adaptation system** tha
 **🌲 Advanced (Month 2+)**
 - [MCP Servers](mcp-servers.md) - Mode integration with enhanced capabilities
 - [Session Management](session-management.md) - Task Management mode workflows  
-- [Best Practices](../Reference/best-practices.md) - Mode optimization strategies
+- [Best Practices](../Reference/quick-start-practices.md) - Mode optimization strategies
 
 **🔧 Expert**
 - [Technical Architecture](../Developer-Guide/technical-architecture.md) - Mode implementation details
@@ -620,4 +620,4 @@ SuperClaude's 6 behavioral modes create an **intelligent adaptation system** tha
 - **Brainstorming**: [Requirements Discovery Patterns](../Reference/examples-cookbook.md#requirements)
 - **Task Management**: [Session Management Guide](session-management.md)
 - **Orchestration**: [MCP Servers Guide](mcp-servers.md)
-- **Token Efficiency**: [Performance Optimization](../Reference/best-practices.md#efficiency)
+- **Token Efficiency**: [Performance Optimization](../Reference/quick-start-practices.md#efficiency)

Docs/User-Guide/session-management.md

@@ -1262,7 +1262,7 @@ As you work with SuperClaude, it automatically learns:
 - [Flags Guide](flags.md) - Session optimization flags
 
 **Advanced Resources:**
-- [Best Practices](../Reference/best-practices.md) - Session optimization strategies
+- [Best Practices](../Reference/quick-start-practices.md) - Session optimization strategies
 - [Examples Cookbook](../Reference/examples-cookbook.md) - Complex workflow patterns
 - [Technical Architecture](../Developer-Guide/technical-architecture.md) - Implementation details