diff --git a/CLAUDE.md b/CLAUDE.md
index d80ad4f..8cb14d6 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -31,11 +31,16 @@ This file provides guidance to Claude Code when working with code in this reposi
 - If user asks for output, show the OUTPUT
 - **Don't interpret or summarize unless asked**
 
-### 5. AFTER PLUGIN UPDATES - ALWAYS CLEAR CACHE
-```bash
-rm -rf ~/.claude/plugins/cache/leo-claude-mktplace/
-./scripts/verify-hooks.sh
-```
+### 5. AFTER PLUGIN UPDATES - VERIFY AND RESTART
+
+**⚠️ DO NOT clear cache mid-session** - this breaks MCP tools that are already loaded.
+
+1. Run `./scripts/verify-hooks.sh` to check hook types
+2. If changes affect MCP servers or hooks, inform the user:
+   > "Plugin changes require a session restart to take effect. Please restart Claude Code."
+3. Cache clearing is ONLY safe **before** starting a new session (not during)
+
+See `docs/DEBUGGING-CHECKLIST.md` for details on cache timing.
 
 **FAILURE TO FOLLOW THESE RULES = WASTED USER TIME = UNACCEPTABLE**
 
@@ -125,7 +130,9 @@ leo-claude-mktplace/
 │   └── project-hygiene/
 ├── scripts/
 │   ├── setup.sh, post-update.sh
-│   └── validate-marketplace.sh   # Marketplace compliance validation
+│   ├── validate-marketplace.sh   # Marketplace compliance validation
+│   ├── verify-hooks.sh           # Verify all hooks are command type
+│   └── check-venv.sh             # Check MCP server venvs exist
 └── docs/
     ├── CANONICAL-PATHS.md        # Single source of truth for paths
     └── CONFIGURATION.md          # Centralized configuration guide
@@ -172,12 +179,12 @@ leo-claude-mktplace/
 
 | Category | Tools |
 |----------|-------|
-| Issues | `list_issues`, `get_issue`, `create_issue`, `update_issue`, `add_comment` |
-| Labels | `get_labels`, `suggest_labels`, `create_label` |
-| Milestones | `list_milestones`, `get_milestone`, `create_milestone`, `update_milestone` |
-| Dependencies | `list_issue_dependencies`, `create_issue_dependency`, `get_execution_order` |
-| Wiki | `list_wiki_pages`, `get_wiki_page`, `create_wiki_page`, `create_lesson`, `search_lessons` |
-| **Pull Requests** | `list_pull_requests`, `get_pull_request`, `get_pr_diff`, `get_pr_comments`, `create_pr_review`, `add_pr_comment` *(NEW v3.0.0)* |
+| Issues | `list_issues`, `get_issue`, `create_issue`, `update_issue`, `add_comment`, `aggregate_issues` |
+| Labels | `get_labels`, `suggest_labels`, `create_label`, `create_label_smart` |
+| Milestones | `list_milestones`, `get_milestone`, `create_milestone`, `update_milestone`, `delete_milestone` |
+| Dependencies | `list_issue_dependencies`, `create_issue_dependency`, `remove_issue_dependency`, `get_execution_order` |
+| Wiki | `list_wiki_pages`, `get_wiki_page`, `create_wiki_page`, `update_wiki_page`, `create_lesson`, `search_lessons` |
+| **Pull Requests** | `list_pull_requests`, `get_pull_request`, `get_pr_diff`, `get_pr_comments`, `create_pr_review`, `add_pr_comment` |
 | Validation | `validate_repo_org`, `get_branch_protection` |
 
 ### Hybrid Configuration
diff --git a/docs/DEBUGGING-CHECKLIST.md b/docs/DEBUGGING-CHECKLIST.md
index e0a442a..e4eb2ad 100644
--- a/docs/DEBUGGING-CHECKLIST.md
+++ b/docs/DEBUGGING-CHECKLIST.md
@@ -197,6 +197,51 @@ echo -e "\n=== Config Files ==="
 
 ---
 
+## Cache Clearing: When It's Safe vs Destructive
+
+**⚠️ CRITICAL: Never clear plugin cache mid-session.**
+
+### Why Cache Clearing Breaks MCP Tools
+
+When Claude Code starts a session:
+1. MCP tools are loaded from the cache directory
+2. Tool definitions include **absolute paths** to the venv (e.g., `~/.claude/plugins/cache/.../venv/`)
+3. These paths are cached in the session memory
+4. Deleting the cache removes the venv, but the session still references the old paths
+5. Any MCP tool making HTTP requests fails with TLS certificate errors
+
+### When Cache Clearing is SAFE
+
+| Scenario | Safe? | Action |
+|----------|-------|--------|
+| Before starting Claude Code | ✅ Yes | Clear cache, then start session |
+| Between sessions | ✅ Yes | Clear cache after `/exit`, before next session |
+| During a session | ❌ NO | Never - will break MCP tools |
+| After plugin source edits | ❌ NO | Restart session instead |
+
+### Recovery: MCP Tools Broken Mid-Session
+
+If you accidentally cleared cache during a session and MCP tools fail:
+
+```
+Error: Could not find a suitable TLS CA certificate bundle, invalid path:
+/home/.../.claude/plugins/cache/.../certifi/cacert.pem
+```
+
+**Fix:**
+1. Exit the current session (`/exit` or Ctrl+C)
+2. Start a new Claude Code session
+3. MCP tools will reload from the reinstalled cache
+
+### Correct Workflow for Plugin Development
+
+1. Make changes to plugin source files
+2. Run `./scripts/verify-hooks.sh` (verifies hook types)
+3. Tell user: "Please restart Claude Code for changes to take effect"
+4. **Do NOT clear cache** - session restart handles reloading
+
+---
+
 ## Automated Diagnostics
 
 Use these commands for automated checking:
diff --git a/scripts/verify-hooks.sh b/scripts/verify-hooks.sh
index bb6fff8..7247493 100755
--- a/scripts/verify-hooks.sh
+++ b/scripts/verify-hooks.sh
@@ -15,11 +15,11 @@ for f in $(find ~/.claude -name "hooks.json" 2>/dev/null); do
     fi
 done
 
-# Check cache specifically
+# Note about cache (informational only - do NOT clear mid-session)
 if [ -d ~/.claude/plugins/cache/leo-claude-mktplace ]; then
-    echo "❌ CACHE EXISTS: ~/.claude/plugins/cache/leo-claude-mktplace"
-    echo "   Run: rm -rf ~/.claude/plugins/cache/leo-claude-mktplace/"
-    FAILED=1
+    echo "ℹ️  Cache exists: ~/.claude/plugins/cache/leo-claude-mktplace"
+    echo "   (This is normal - do NOT clear mid-session or MCP tools will break)"
+    echo "   To apply plugin changes: restart Claude Code session"
 fi
 
 # Verify installed hooks are command type