fix: remove destructive cache-clear instruction from CLAUDE.md

The CLAUDE.md mandatory rule instructed clearing the plugin cache
mid-session, which breaks all MCP tools that were already loaded.
MCP tools are loaded with absolute paths to the venv, and deleting
the cache removes the venv while the session still references it.

Changes:
- CLAUDE.md: Replace "ALWAYS CLEAR CACHE" with "VERIFY AND RESTART"
- verify-hooks.sh: Change cache existence from error to info message
- DEBUGGING-CHECKLIST.md: Add section explaining cache timing

Fixes #145

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

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