diff --git a/Docs/User-Guide/agents.md b/Docs/User-Guide/agents.md
index 7eea815..39a0d5a 100644
--- a/Docs/User-Guide/agents.md
+++ b/Docs/User-Guide/agents.md
@@ -509,7 +509,7 @@ Task Analysis →
 **Level 3: Expert Support (30+ min)**
 ```bash
 # Deep agent analysis
-SuperClaude diagnose --agents
+SuperClaude install --diagnose
 # Check agent coordination patterns
 # Review multi-domain keyword strategies
 ```
diff --git a/Docs/User-Guide/commands.md b/Docs/User-Guide/commands.md
index 42c50d3..30f1ea3 100644
--- a/Docs/User-Guide/commands.md
+++ b/Docs/User-Guide/commands.md
@@ -19,8 +19,8 @@ SuperClaude --version
 # Expected: SuperClaude Framework v4.0+
 
 # Check MCP server connectivity
-SuperClaude status --mcp
-# Expected: At least context7 and sequential-thinking connected
+SuperClaude install --list-components | grep mcp
+# Expected: Shows installed MCP components
 ```
 
 ### 💬 Claude Code Testing (Type in Claude Code Chat)
@@ -499,7 +499,7 @@ ps aux | grep SuperClaude  # Check for hung processes
 ```bash
 # Problem: MCP servers not responding
 # Quick Fix: Verify server status and restart
-SuperClaude status --mcp                    # Check all servers
+ls ~/.claude/.claude.json                    # Check MCP config exists
 /sc:command --no-mcp                       # Bypass MCP temporarily
 node --version                             # Verify Node.js v16+
 npm cache clean --force                    # Clear NPM cache
@@ -546,7 +546,7 @@ killall node                         # Reset MCP servers
 **Level 2: Detailed Help (5-15 min)**
 ```bash
 # Comprehensive diagnostics
-SuperClaude diagnose --verbose
+SuperClaude install --diagnose
 /sc:help troubleshoot
 cat ~/.claude/logs/superclaude.log | tail -50
 ```
@@ -555,7 +555,7 @@ cat ~/.claude/logs/superclaude.log | tail -50
 **Level 3: Expert Support (30+ min)**
 ```bash
 # Deep system analysis
-SuperClaude diagnose --full-system
+SuperClaude install --diagnose
 strace -e trace=file /sc:command 2>&1 | grep ENOENT
 lsof | grep SuperClaude
 # Check GitHub Issues for known problems
diff --git a/Docs/User-Guide/flags.md b/Docs/User-Guide/flags.md
index eae5851..041e752 100644
--- a/Docs/User-Guide/flags.md
+++ b/Docs/User-Guide/flags.md
@@ -659,7 +659,7 @@ SuperClaude's intelligent flag system automatically detects task complexity and
 - **Reset flags**: Remove all flags and let auto-detection work
 - **Check compatibility**: Use `/sc:help flags` for valid combinations
 - **Restart session**: Exit and restart Claude Code to reset flag state
-- **Verify setup**: Run `SuperClaude status --flags` to check flag system
+- **Verify setup**: Check `/sc:help flags` for available flag options
 
 ### Flag-Specific Troubleshooting
 
@@ -668,7 +668,7 @@ SuperClaude's intelligent flag system automatically detects task complexity and
 # Problem: "Unknown flag --invalid-flag"
 # Quick Fix: Check flag spelling and availability
 /sc:help flags                         # List all valid flags
-python3 -m SuperClaude --help flags    # System-level flag help
+python3 -m SuperClaude --help          # System-level help
 # Common typos: --brainstrom → --brainstorm, --seq → --sequential
 ```
 
@@ -676,7 +676,7 @@ python3 -m SuperClaude --help flags    # System-level flag help
 ```bash
 # Problem: --magic, --morph, --c7 not working
 # Quick Fix: Check MCP server status
-SuperClaude status --mcp              # Verify server connections
+ls ~/.claude/.claude.json              # Check MCP config exists
 node --version                        # Ensure Node.js v16+
 npm cache clean --force               # Clear package cache
 /sc:command --no-mcp                  # Bypass MCP temporarily
@@ -765,7 +765,7 @@ SuperClaude install --components mcp --force  # Reinstall MCP
 **Level 2: Detailed Help (5-15 min)**
 ```bash
 # Flag-specific diagnostics
-SuperClaude diagnose --flags
+SuperClaude install --diagnose
 /sc:help flags --verbose
 cat ~/.claude/logs/flag-system.log
 # Test individual flags one at a time
@@ -792,13 +792,13 @@ strace -e trace=execve /sc:command --verbose 2>&1
 After applying flag fixes, test with:
 - [ ] `/sc:help flags` (should list all available flags)
 - [ ] `/sc:command --basic-flag` (should work without errors)
-- [ ] `SuperClaude status --mcp` (MCP flags should work if servers connected)
+- [ ] `ls ~/.claude/.claude.json` (MCP config should exist if installed)
 - [ ] Flag combinations follow priority rules correctly
 - [ ] Auto-detection works for simple commands
 
 ## Quick Troubleshooting (Legacy)
-- **Flag not recognized** → Check spelling: `SuperClaude --help flags`
-- **MCP flag fails** → Check server status: `SuperClaude status --mcp`
+- **Flag not recognized** → Check spelling: `python3 -m SuperClaude --help`
+- **MCP flag fails** → Check MCP config: `ls ~/.claude/.claude.json`
 - **Auto-flags wrong** → Use manual override: `--no-mcp` or specific flags
 - **Performance issues** → Reduce complexity: `--scope file` or `--concurrency 1`
 - **Flag conflicts** → Check priority rules in documentation
diff --git a/Docs/User-Guide/mcp-servers.md b/Docs/User-Guide/mcp-servers.md
index 1724cf1..b6b2c48 100644
--- a/Docs/User-Guide/mcp-servers.md
+++ b/Docs/User-Guide/mcp-servers.md
@@ -11,9 +11,9 @@
 Before using this guide, verify MCP servers are working:
 
 ```bash
-# Test server connectivity
-SuperClaude status --mcp
-# Expected: Shows connected servers (at minimum context7, sequential-thinking)
+# Test MCP configuration exists
+ls ~/.claude/.claude.json
+# Expected: Shows MCP server configuration file
 
 # Test Context7 server
 /sc:explain "React useEffect"
@@ -744,9 +744,9 @@ ls ~/.claude/.claude.json
 node --version  
 # Should show: v16.x.x or higher
 
-# Test basic MCP connectivity
-SuperClaude status --mcp
-# Should show connected servers (at least context7, sequential-thinking)
+# Test basic MCP configuration
+ls ~/.claude/.claude.json
+# Should show MCP server configuration file exists
 ```
 
 **Step 2: Common Fixes (1-2 minutes)**
@@ -787,9 +787,9 @@ chmod -R 755 ~/.claude/
 # Detailed MCP server logs
 tail -f ~/.claude/logs/mcp-*.log
 
-# Test individual server connections
-SuperClaude test-mcp --server context7
-SuperClaude test-mcp --server sequential-thinking
+# Test individual server functionality
+/sc:explain "test" --c7  # Test Context7 server
+/sc:analyze test/ --seq  # Test Sequential server
 
 # Check for port conflicts
 netstat -tulpn | grep :3000
@@ -891,9 +891,10 @@ SuperClaude restart --mcp                    # Restart MCP system
 **Level 2: Detailed Help (5-15 min)**
 ```bash
 # MCP-specific diagnostics
-SuperClaude diagnose --mcp
+SuperClaude install --diagnose
 tail -f ~/.claude/logs/mcp-*.log
-SuperClaude test-mcp --all-servers
+# Test all MCP servers with commands
+/sc:explain "test" --c7 && /sc:analyze test/ --seq
 ```
 - See [Common Issues Guide](../Reference/common-issues.md) for MCP installation problems
 - See [MCP Server Guide](../Reference/mcp-server-guide.md) for detailed server troubleshooting
@@ -901,7 +902,7 @@ SuperClaude test-mcp --all-servers
 **Level 3: Expert Support (30+ min)**
 ```bash
 # Deep MCP analysis
-SuperClaude diagnose --mcp --full-system
+SuperClaude install --diagnose
 lsof | grep mcp
 netstat -tulpn | grep node
 # Check individual server configurations
@@ -916,7 +917,7 @@ netstat -tulpn | grep node
 ### Success Validation
 
 After applying MCP fixes, test with:
-- [ ] `SuperClaude status --mcp` (should show connected servers)
+- [ ] `ls ~/.claude/.claude.json` (should show MCP configuration exists)
 - [ ] `/sc:explain "test" --c7` (context7 should fetch documentation)
 - [ ] `/sc:analyze test/ --seq` (sequential should show reasoning)
 - [ ] MCP flags work: `--magic`, `--play` (if configured)
@@ -926,15 +927,15 @@ After applying MCP fixes, test with:
 
 **MCP Server Status Check:**
 ```bash
-# Check all server health
-SuperClaude status --mcp
+# Check MCP configuration exists
+ls ~/.claude/.claude.json
 
 # Test individual servers
-SuperClaude test-mcp --server context7
-SuperClaude test-mcp --server sequential
+/sc:explain "test" --c7  # Test Context7
+/sc:analyze test/ --seq  # Test Sequential
 
 # Detailed diagnostics
-SuperClaude diagnose --verbose
+SuperClaude install --diagnose
 ```
 
 **Log Analysis:**
diff --git a/Docs/User-Guide/modes.md b/Docs/User-Guide/modes.md
index 3f6e2d5..0ebc73b 100644
--- a/Docs/User-Guide/modes.md
+++ b/Docs/User-Guide/modes.md
@@ -518,7 +518,7 @@ Standard Approach: Consistent, professional baseline for all tasks
 **Level 3: Expert Support (30+ min)**
 ```bash
 # Deep mode analysis
-SuperClaude diagnose --modes
+SuperClaude install --diagnose
 # Check mode activation patterns
 # Review behavioral triggers and thresholds
 ```
diff --git a/Docs/User-Guide/session-management.md b/Docs/User-Guide/session-management.md
index e3a28db..d9dc767 100644
--- a/Docs/User-Guide/session-management.md
+++ b/Docs/User-Guide/session-management.md
@@ -24,12 +24,12 @@ Before using this guide, verify session commands work:
 # Expected: Shows current session status and progress
 ```
 
-**If tests fail**: Check Serena MCP installation: `SuperClaude status --mcp serena`
+**If tests fail**: Check Serena MCP installation: `SuperClaude install --list-components | grep serena`
 
 ## 🚨 Quick Troubleshooting
 
 ### Common Issues (< 2 minutes)
-- **Session won't load**: Check Serena MCP server connection: `SuperClaude status --mcp serena`
+- **Session won't load**: Check Serena MCP installed: `SuperClaude install --list-components | grep serena`
 - **Save fails**: Verify write permissions to `~/.claude/` directory
 - **Memory issues**: Clear old sessions with `/sc:reflect --type session-cleanup`
 - **Slow loading**: Use `--scope file` for large projects or `--fast` flag
@@ -71,8 +71,8 @@ Test your setup before starting:
 # Verify SuperClaude is working
 SuperClaude --version
 
-# Check Serena MCP connection
-SuperClaude status --mcp serena
+# Check Serena MCP installed
+SuperClaude install --list-components | grep serena
 ```
 
 **Time Investment:**
@@ -189,7 +189,7 @@ cd /path/to/your/project
 **Test:** Session should remember changes when resumed later  
 **Check:** `/sc:reflect` should show accurate progress tracking
 
-**Need Help?**: If any step fails, check your setup by running `SuperClaude status --mcp serena` to verify the Serena MCP server is working correctly.
+**Need Help?**: If any step fails, check your setup by running `SuperClaude install --list-components | grep serena` to verify the Serena MCP component is installed.
 
 
 ## Session Commands
@@ -519,7 +519,7 @@ delete_memory(key)       # Clean up old data
 # Problem: "/sc:load project/ fails with error"
 # Quick Fix: Verify project and dependencies
 ls -la project/                           # Check project exists
-SuperClaude status --mcp serena          # Verify Serena MCP
+SuperClaude install --list-components | grep serena  # Verify Serena MCP
 /sc:load . --refresh                     # Force fresh analysis
 /sc:load . --scope module                # Reduce load scope
 ```
@@ -585,7 +585,7 @@ cat ~/.claude/logs/serena.log | tail -50 # Check Serena logs
 **Level 3: Expert Support (30+ min)**
 ```bash
 # Deep session analysis
-SuperClaude diagnose --sessions
+SuperClaude install --diagnose
 ls -la ~/.claude/serena/                 # Check Serena state
 uv run serena diagnose                   # Serena diagnostics
 # Reset session system completely