Merge pull request 'development' (#328) from development into main

Reviewed-on: #328

.claude-plugin/marketplace.json

@@ -20,7 +20,6 @@
       },
       "homepage": "https://gitea.hotserv.cloud/personal-projects/leo-claude-mktplace/src/branch/main/plugins/projman/README.md",
       "repository": "https://gitea.hotserv.cloud/personal-projects/leo-claude-mktplace.git",
-      "mcpServers": ["./.mcp.json"],
       "category": "development",
       "tags": ["sprint", "agile", "gitea", "project-management"],
       "license": "MIT"
@@ -84,7 +83,6 @@
       },
       "homepage": "https://gitea.hotserv.cloud/personal-projects/leo-claude-mktplace/src/branch/main/plugins/cmdb-assistant/README.md",
       "repository": "https://gitea.hotserv.cloud/personal-projects/leo-claude-mktplace.git",
-      "mcpServers": ["./.mcp.json"],
       "category": "infrastructure",
       "tags": ["cmdb", "netbox", "dcim", "ipam", "data-quality", "validation"],
       "license": "MIT"
@@ -145,7 +143,6 @@
       },
       "homepage": "https://gitea.hotserv.cloud/personal-projects/leo-claude-mktplace/src/branch/main/plugins/pr-review/README.md",
       "repository": "https://gitea.hotserv.cloud/personal-projects/leo-claude-mktplace.git",
-      "mcpServers": ["./.mcp.json"],
       "category": "development",
       "tags": ["code-review", "pull-requests", "security", "quality"],
       "license": "MIT"
@@ -161,7 +158,6 @@
       },
       "homepage": "https://gitea.hotserv.cloud/personal-projects/leo-claude-mktplace/src/branch/main/plugins/data-platform/README.md",
       "repository": "https://gitea.hotserv.cloud/personal-projects/leo-claude-mktplace.git",
-      "mcpServers": ["./.mcp.json"],
       "category": "data",
       "tags": ["pandas", "postgresql", "postgis", "dbt", "data-engineering", "etl"],
       "license": "MIT"
@@ -177,7 +173,6 @@
       },
       "homepage": "https://gitea.hotserv.cloud/personal-projects/leo-claude-mktplace/src/branch/main/plugins/viz-platform/README.md",
       "repository": "https://gitea.hotserv.cloud/personal-projects/leo-claude-mktplace.git",
-      "mcpServers": ["./.mcp.json"],
       "category": "visualization",
       "tags": ["dash", "plotly", "mantine", "charts", "dashboards", "theming", "dmc"],
       "license": "MIT"
@@ -193,7 +188,6 @@
       },
       "homepage": "https://gitea.hotserv.cloud/personal-projects/leo-claude-mktplace/src/branch/main/plugins/contract-validator/README.md",
       "repository": "https://gitea.hotserv.cloud/personal-projects/leo-claude-mktplace.git",
-      "mcpServers": ["./.mcp.json"],
       "category": "development",
       "tags": ["validation", "contracts", "compatibility", "agents", "interfaces", "cross-plugin"],
       "license": "MIT"

.mcp.json

@@ -0,0 +1,24 @@
+{
+  "mcpServers": {
+    "gitea": {
+      "command": "/home/lmiranda/.claude/plugins/marketplaces/leo-claude-mktplace/mcp-servers/gitea/run.sh",
+      "args": []
+    },
+    "netbox": {
+      "command": "/home/lmiranda/.claude/plugins/marketplaces/leo-claude-mktplace/mcp-servers/netbox/run.sh",
+      "args": []
+    },
+    "viz-platform": {
+      "command": "/home/lmiranda/.claude/plugins/marketplaces/leo-claude-mktplace/mcp-servers/viz-platform/run.sh",
+      "args": []
+    },
+    "data-platform": {
+      "command": "/home/lmiranda/.claude/plugins/marketplaces/leo-claude-mktplace/mcp-servers/data-platform/run.sh",
+      "args": []
+    },
+    "contract-validator": {
+      "command": "/home/lmiranda/.claude/plugins/marketplaces/leo-claude-mktplace/mcp-servers/contract-validator/run.sh",
+      "args": []
+    }
+  }
+}

CLAUDE.md

@@ -40,8 +40,76 @@ Run `./scripts/verify-hooks.sh`. If changes affect MCP servers or hooks, inform
 
 **Valid hook events:** `PreToolUse`, `PostToolUse`, `UserPromptSubmit`, `SessionStart`, `SessionEnd`, `Notification`, `Stop`, `SubagentStop`, `PreCompact`
 
+### ⛔ MANDATORY: Before Any Code Change
+
+**Claude MUST show this checklist BEFORE editing any file:**
+
+#### 1. Impact Search Results
+Run and show output of:
+```bash
+grep -rn "PATTERN" --include="*.sh" --include="*.md" --include="*.json" --include="*.py" | grep -v ".git"
+```
+
+#### 2. Files That Will Be Affected
+Numbered list of every file to be modified, with the specific change for each.
+
+#### 3. Files Searched But Not Changed (and why)
+Proof that related files were checked and determined unchanged.
+
+#### 4. Documentation That References This
+List of docs that mention this feature/script/function.
+
+**User verifies this list before Claude proceeds. If Claude skips this, STOP IMMEDIATELY.**
+
+#### After Changes
+Run the same grep and show results proving no references remain unaddressed.
+
 ---
 
+## ⚠️ Development Context: We Build AND Use These Plugins
+
+**This is a self-referential project.** We are:
+1. **BUILDING** a plugin marketplace (source code in `plugins/`)
+2. **USING** the installed marketplace to build it (dogfooding)
+
+### Plugins ACTIVELY USED in This Project
+
+These plugins are installed and should be used during development:
+
+| Plugin | Used For |
+|--------|----------|
+| **projman** | Sprint planning, issue management, lessons learned |
+| **git-flow** | Commits, branch management |
+| **pr-review** | Pull request reviews |
+| **doc-guardian** | Documentation drift detection |
+| **code-sentinel** | Security scanning, refactoring |
+| **clarity-assist** | Prompt clarification |
+| **claude-config-maintainer** | CLAUDE.md optimization |
+| **contract-validator** | Cross-plugin compatibility |
+
+### Plugins NOT Used Here (Development Only)
+
+These plugins exist in source but are **NOT relevant** to this project's workflow:
+
+| Plugin | Why Not Used |
+|--------|--------------|
+| **data-platform** | For data engineering projects (pandas, PostgreSQL, dbt) |
+| **viz-platform** | For dashboard projects (Dash, Plotly) |
+| **cmdb-assistant** | For infrastructure projects (NetBox) |
+
+**Do NOT suggest** `/ingest`, `/profile`, `/chart`, `/cmdb-*` commands - they don't apply here.
+
+### Key Distinction
+
+| Context | Path | What To Do |
+|---------|------|------------|
+| **Editing plugin source** | `~/claude-plugins-work/plugins/` | Modify code, add features |
+| **Using installed plugins** | `~/.claude/plugins/marketplaces/` | Run commands like `/sprint-plan` |
+
+When user says "run /sprint-plan", use the INSTALLED plugin.
+When user says "fix the sprint-plan command", edit the SOURCE code.
+
+---
 
 ## Project Overview
 
@@ -76,7 +144,7 @@ A plugin marketplace for Claude Code containing:
 ./scripts/post-update.sh   # Rebuild venvs, verify symlinks
 ```
 
-### Plugin Commands by Category
+### Plugin Commands - USE THESE in This Project
 
 | Category | Commands |
 |----------|----------|
@@ -88,12 +156,19 @@ A plugin marketplace for Claude Code containing:
 | **Docs** | `/doc-audit`, `/doc-sync`, `/changelog-gen`, `/doc-coverage`, `/stale-docs` |
 | **Security** | `/security-scan`, `/refactor`, `/refactor-dry` |
 | **Config** | `/config-analyze`, `/config-optimize`, `/config-diff`, `/config-lint` |
-| **Data** | `/ingest`, `/profile`, `/schema`, `/explain`, `/lineage`, `/lineage-viz`, `/run`, `/dbt-test`, `/data-quality` |
-| **Visualization** | `/component`, `/chart`, `/chart-export`, `/dashboard`, `/theme`, `/theme-new`, `/theme-css`, `/accessibility-check`, `/breakpoints` |
 | **Validation** | `/validate-contracts`, `/check-agent`, `/list-interfaces`, `/dependency-graph` |
-| **CMDB** | `/cmdb-search`, `/cmdb-device`, `/cmdb-ip`, `/cmdb-site`, `/cmdb-audit`, `/cmdb-register`, `/cmdb-sync`, `/cmdb-topology`, `/change-audit`, `/ip-conflicts` |
 | **Debug** | `/debug-report`, `/debug-review` |
 
+### Plugin Commands - NOT RELEVANT to This Project
+
+These commands are being developed but don't apply to this project's workflow:
+
+| Category | Commands | For Projects Using |
+|----------|----------|-------------------|
+| **Data** | `/ingest`, `/profile`, `/schema`, `/lineage`, `/dbt-test` | pandas, PostgreSQL, dbt |
+| **Visualization** | `/component`, `/chart`, `/dashboard`, `/theme` | Dash, Plotly dashboards |
+| **CMDB** | `/cmdb-search`, `/cmdb-device`, `/cmdb-sync` | NetBox infrastructure |
+
 ## Repository Structure
 
 ```
@@ -108,7 +183,7 @@ leo-claude-mktplace/
 ├── plugins/
 │   ├── projman/                  # Sprint management
 │   │   ├── .claude-plugin/plugin.json
-│   │   ├── .mcp.json
+│   │   # .mcp.json removed - now at marketplace root
 │   │   ├── mcp-servers/gitea -> ../../../mcp-servers/gitea  # SYMLINK
 │   │   ├── commands/             # 14 commands (incl. setup, debug, suggest-version)
 │   │   ├── hooks/                # SessionStart: mismatch detection + sprint suggestions
@@ -120,7 +195,7 @@ leo-claude-mktplace/
 │   │   └── agents/
 │   ├── pr-review/                # Multi-agent PR review
 │   │   ├── .claude-plugin/plugin.json
-│   │   ├── .mcp.json
+│   │   # .mcp.json removed - now at marketplace root
 │   │   ├── mcp-servers/gitea -> ../../../mcp-servers/gitea  # SYMLINK
 │   │   ├── commands/             # 6 commands (incl. setup)
 │   │   ├── hooks/                # SessionStart mismatch detection
@@ -131,14 +206,14 @@ leo-claude-mktplace/
 │   │   └── agents/
 │   ├── data-platform/            # Data engineering (NEW v4.0.0)
 │   │   ├── .claude-plugin/plugin.json
-│   │   ├── .mcp.json
+│   │   # .mcp.json removed - now at marketplace root
 │   │   ├── mcp-servers/          # pandas, postgresql, dbt MCPs
 │   │   ├── commands/             # 7 commands
 │   │   ├── hooks/                # SessionStart PostgreSQL check
 │   │   └── agents/               # 2 agents
 │   ├── viz-platform/             # Visualization (NEW v4.0.0)
 │   │   ├── .claude-plugin/plugin.json
-│   │   ├── .mcp.json
+│   │   # .mcp.json removed - now at marketplace root
 │   │   ├── mcp-servers/          # viz-platform MCP
 │   │   ├── commands/             # 7 commands
 │   │   ├── hooks/                # SessionStart DMC check
@@ -354,4 +429,4 @@ The script will:
 
 ---
 
-**Last Updated:** 2026-01-28
+**Last Updated:** 2026-01-30

docs/CANONICAL-PATHS.md

@@ -163,12 +163,11 @@ leo-claude-mktplace/
 │       └── claude-md-integration.md
 ├── scripts/                    # Setup and maintenance scripts
 │   ├── setup.sh                # Initial setup (create venvs, config templates)
-│   ├── post-update.sh          # Post-update (rebuild venvs, verify symlinks)
-│   ├── check-venv.sh           # Check if venvs exist (for hooks)
+│   ├── post-update.sh          # Post-update (clear cache, show changelog)
+│   ├── check-venv.sh           # Check if venvs exist (read-only)
 │   ├── validate-marketplace.sh # Marketplace compliance validation
 │   ├── verify-hooks.sh         # Verify all hooks use correct event types
-│   ├── setup-venvs.sh          # Setup/repair MCP server venvs
-│   ├── venv-repair.sh          # Repair broken venv symlinks
+│   ├── setup-venvs.sh          # Setup MCP server venvs (create only, never delete)
 │   └── release.sh              # Release automation with version bumping
 ├── CLAUDE.md
 ├── README.md

docs/CONFIGURATION.md

@@ -501,9 +501,8 @@ If you get 401, regenerate your token in Gitea.
 # Check venv exists
 ls /path/to/mcp-servers/gitea/.venv
 
-# Reinstall if missing
+# If missing, create venv (do NOT delete existing venvs)
 cd /path/to/mcp-servers/gitea
-rm -rf .venv
 python3 -m venv .venv
 source .venv/bin/activate
 pip install -r requirements.txt

docs/UPDATING.md

@@ -132,10 +132,8 @@ When updating, review if changes affect the setup workflow:
 ### Dependencies fail to install
 
 ```bash
-# Rebuild virtual environment
+# Install missing dependencies (do NOT delete .venv)
 cd mcp-servers/gitea
-rm -rf .venv
-python3 -m venv .venv
 source .venv/bin/activate
 pip install -r requirements.txt
 deactivate

mcp-servers/gitea/mcp_server/server.py

@@ -144,7 +144,7 @@ class GiteaMCPServer:
                         "type": "object",
                         "properties": {
                             "issue_number": {
-                                "type": "integer",
+                                "type": ["integer", "string"],
                                 "description": "Issue number"
                             },
                             "repo": {
@@ -189,7 +189,7 @@ class GiteaMCPServer:
                         "type": "object",
                         "properties": {
                             "issue_number": {
-                                "type": "integer",
+                                "type": ["integer", "string"],
                                 "description": "Issue number"
                             },
                             "title": {
@@ -211,7 +211,7 @@ class GiteaMCPServer:
                                 "description": "New labels"
                             },
                             "milestone": {
-                                "type": "integer",
+                                "type": ["integer", "string"],
                                 "description": "Milestone ID to assign"
                             },
                             "repo": {
@@ -229,7 +229,7 @@ class GiteaMCPServer:
                         "type": "object",
                         "properties": {
                             "issue_number": {
-                                "type": "integer",
+                                "type": ["integer", "string"],
                                 "description": "Issue number"
                             },
                             "comment": {
@@ -424,7 +424,7 @@ class GiteaMCPServer:
                                 "description": "Tags to filter by (optional)"
                             },
                             "limit": {
-                                "type": "integer",
+                                "type": ["integer", "string"],
                                 "default": 20,
                                 "description": "Maximum results"
                             },
@@ -462,7 +462,7 @@ class GiteaMCPServer:
                         "type": "object",
                         "properties": {
                             "milestone_id": {
-                                "type": "integer",
+                                "type": ["integer", "string"],
                                 "description": "Milestone ID"
                             },
                             "repo": {
@@ -506,7 +506,7 @@ class GiteaMCPServer:
                         "type": "object",
                         "properties": {
                             "milestone_id": {
-                                "type": "integer",
+                                "type": ["integer", "string"],
                                 "description": "Milestone ID"
                             },
                             "title": {
@@ -541,7 +541,7 @@ class GiteaMCPServer:
                         "type": "object",
                         "properties": {
                             "milestone_id": {
-                                "type": "integer",
+                                "type": ["integer", "string"],
                                 "description": "Milestone ID"
                             },
                             "repo": {
@@ -560,7 +560,7 @@ class GiteaMCPServer:
                         "type": "object",
                         "properties": {
                             "issue_number": {
-                                "type": "integer",
+                                "type": ["integer", "string"],
                                 "description": "Issue number"
                             },
                             "repo": {
@@ -578,11 +578,11 @@ class GiteaMCPServer:
                         "type": "object",
                         "properties": {
                             "issue_number": {
-                                "type": "integer",
+                                "type": ["integer", "string"],
                                 "description": "Issue that will depend on another"
                             },
                             "depends_on": {
-                                "type": "integer",
+                                "type": ["integer", "string"],
                                 "description": "Issue that blocks issue_number"
                             },
                             "repo": {
@@ -600,11 +600,11 @@ class GiteaMCPServer:
                         "type": "object",
                         "properties": {
                             "issue_number": {
-                                "type": "integer",
+                                "type": ["integer", "string"],
                                 "description": "Issue that depends on another"
                             },
                             "depends_on": {
-                                "type": "integer",
+                                "type": ["integer", "string"],
                                 "description": "Issue being depended on"
                             },
                             "repo": {
@@ -782,7 +782,7 @@ class GiteaMCPServer:
                         "type": "object",
                         "properties": {
                             "pr_number": {
-                                "type": "integer",
+                                "type": ["integer", "string"],
                                 "description": "Pull request number"
                             },
                             "repo": {
@@ -800,7 +800,7 @@ class GiteaMCPServer:
                         "type": "object",
                         "properties": {
                             "pr_number": {
-                                "type": "integer",
+                                "type": ["integer", "string"],
                                 "description": "Pull request number"
                             },
                             "repo": {
@@ -818,7 +818,7 @@ class GiteaMCPServer:
                         "type": "object",
                         "properties": {
                             "pr_number": {
-                                "type": "integer",
+                                "type": ["integer", "string"],
                                 "description": "Pull request number"
                             },
                             "repo": {
@@ -836,7 +836,7 @@ class GiteaMCPServer:
                         "type": "object",
                         "properties": {
                             "pr_number": {
-                                "type": "integer",
+                                "type": ["integer", "string"],
                                 "description": "Pull request number"
                             },
                             "body": {
@@ -855,7 +855,7 @@ class GiteaMCPServer:
                                     "type": "object",
                                     "properties": {
                                         "path": {"type": "string"},
-                                        "position": {"type": "integer"},
+                                        "position": {"type": ["integer", "string"]},
                                         "body": {"type": "string"}
                                     }
                                 },
@@ -876,7 +876,7 @@ class GiteaMCPServer:
                         "type": "object",
                         "properties": {
                             "pr_number": {
-                                "type": "integer",
+                                "type": ["integer", "string"],
                                 "description": "Pull request number"
                             },
                             "body": {

plugins/claude-config-maintainer/agents/maintainer.md

@@ -277,6 +277,39 @@ Every CLAUDE.md should have:
 1. **Project Overview** - What is this?
 2. **Quick Start** - How do I build/test/run?
 3. **Important Rules** - What must I NOT do?
+4. **Pre-Change Protocol** - Mandatory dependency check before code changes
+
+### Pre-Change Protocol Section (MANDATORY)
+
+**This section is REQUIRED in every CLAUDE.md.** It ensures Claude performs comprehensive dependency analysis before making any code changes.
+
+```markdown
+## ⛔ MANDATORY: Before Any Code Change
+
+**Claude MUST show this checklist BEFORE editing any file:**
+
+### 1. Impact Search Results
+Run and show output of:
+```bash
+grep -rn "PATTERN" --include="*.sh" --include="*.md" --include="*.json" --include="*.py" | grep -v ".git"
+```
+
+### 2. Files That Will Be Affected
+Numbered list of every file to be modified, with the specific change for each.
+
+### 3. Files Searched But Not Changed (and why)
+Proof that related files were checked and determined unchanged.
+
+### 4. Documentation That References This
+List of docs that mention this feature/script/function.
+
+**User verifies this list before Claude proceeds. If Claude skips this, stop immediately.**
+
+### After Changes
+Run the same grep and show results proving no references remain unaddressed.
+```
+
+**When analyzing a CLAUDE.md, flag as HIGH priority issue if this section is missing.**
 
 ### Optional Sections (as needed)
 

plugins/claude-config-maintainer/commands/analyze.md

@@ -59,6 +59,7 @@ Analyze the CLAUDE.md file in this project
 - Quick start commands documented
 - Critical rules highlighted
 - Key workflows covered
+- **Pre-Change Protocol section present** (MANDATORY - see below)
 
 ### Conciseness (25 points)
 - No unnecessary repetition
@@ -66,6 +67,42 @@ Analyze the CLAUDE.md file in this project
 - Appropriate length for project size
 - No generic filler content
 
+## Pre-Change Protocol Check (MANDATORY)
+
+**This check is CRITICAL.** The Pre-Change Protocol section ensures Claude performs comprehensive dependency analysis before making any code changes, preventing missed references and incomplete updates.
+
+### What to Check
+
+Search CLAUDE.md for:
+- Section header containing "Pre-Change" or "Before Any Code Change"
+- References to `grep -rn` or impact search
+- Checklist with "Files That Will Be Affected"
+- Requirement for user verification before proceeding
+
+### If Missing
+
+**Flag as HIGH PRIORITY issue:**
+
+```
+1. [HIGH] Missing Pre-Change Protocol section
+   CLAUDE.md lacks mandatory dependency-check protocol.
+   Impact: Claude may miss file references when making changes,
+   leading to broken dependencies and incomplete updates.
+
+   Recommendation: Add Pre-Change Protocol section immediately.
+   This is the #1 cause of cascading bugs from incomplete changes.
+```
+
+### Required Section Content
+
+The Pre-Change Protocol section must include:
+1. Requirement to run grep search and show results
+2. List of files that will be affected
+3. List of files searched but not changed (with reasoning)
+4. Documentation that references the change target
+5. User verification checkpoint before proceeding
+6. Post-change verification step
+
 ## Plugin Integration Analysis
 
 After the content analysis, the command detects and analyzes marketplace plugin integration:

plugins/claude-config-maintainer/commands/init.md

@@ -139,6 +139,7 @@ For small projects or when starting fresh:
 - Project Overview (required)
 - Quick Start (required)
 - Critical Rules (required)
+- **Pre-Change Protocol (required)**
 
 ### Standard Template (default)
 For typical projects:
@@ -146,6 +147,7 @@ For typical projects:
 - Quick Start
 - Architecture
 - Critical Rules
+- **Pre-Change Protocol**
 - Common Operations
 - File Structure
 
@@ -153,11 +155,44 @@ For typical projects:
 For large or complex projects:
 - All standard sections plus:
 - Detailed Architecture
+- **Pre-Change Protocol**
 - Troubleshooting
 - Integration Points
 - Development Workflow
 - Deployment Notes
 
+### Pre-Change Protocol Section (MANDATORY in ALL templates)
+
+**This section MUST be included in every generated CLAUDE.md:**
+
+```markdown
+## ⛔ MANDATORY: Before Any Code Change
+
+**Claude MUST show this checklist BEFORE editing any file:**
+
+### 1. Impact Search Results
+Run and show output of:
+\`\`\`bash
+grep -rn "PATTERN" --include="*.sh" --include="*.md" --include="*.json" --include="*.py" | grep -v ".git"
+\`\`\`
+
+### 2. Files That Will Be Affected
+Numbered list of every file to be modified, with the specific change for each.
+
+### 3. Files Searched But Not Changed (and why)
+Proof that related files were checked and determined unchanged.
+
+### 4. Documentation That References This
+List of docs that mention this feature/script/function.
+
+**User verifies this list before Claude proceeds. If Claude skips this, stop immediately.**
+
+### After Changes
+Run the same grep and show results proving no references remain unaddressed.
+```
+
+**Rationale:** This protocol prevents incomplete changes where Claude modifies some files but misses others that reference the same code, causing cascading bugs.
+
 ## Auto-Detection
 
 The command automatically detects:

plugins/claude-config-maintainer/commands/optimize.md

@@ -56,6 +56,7 @@ Or specify specific optimizations:
 
 ### Enhance
 - Add missing essential sections
+- **Add Pre-Change Protocol if missing (HIGH PRIORITY)**
 - Improve unclear instructions
 - Add helpful examples
 - Highlight critical rules
@@ -158,6 +159,49 @@ Backup saved to: .claude/backups/CLAUDE.md.2025-01-18
 | `--preserve-comments` | Keep all existing comments |
 | `--section=NAME` | Optimize specific section only |
 
+## Pre-Change Protocol (Mandatory Addition)
+
+**If CLAUDE.md is missing the Pre-Change Protocol section, optimization MUST add it.**
+
+This is the highest priority enhancement because it prevents cascading bugs from incomplete code changes.
+
+### Detection
+
+Search CLAUDE.md for:
+- "Pre-Change" or "Before Any Code Change" in headers
+- References to impact search or grep verification
+- User verification checkpoint
+
+### If Missing
+
+Add this section (position: after Critical Rules, before Common Operations):
+
+```markdown
+## ⛔ MANDATORY: Before Any Code Change
+
+**Claude MUST show this checklist BEFORE editing any file:**
+
+### 1. Impact Search Results
+Run and show output of:
+\`\`\`bash
+grep -rn "PATTERN" --include="*.sh" --include="*.md" --include="*.json" --include="*.py" | grep -v ".git"
+\`\`\`
+
+### 2. Files That Will Be Affected
+Numbered list of every file to be modified, with the specific change for each.
+
+### 3. Files Searched But Not Changed (and why)
+Proof that related files were checked and determined unchanged.
+
+### 4. Documentation That References This
+List of docs that mention this feature/script/function.
+
+**User verifies this list before Claude proceeds. If Claude skips this, stop immediately.**
+
+### After Changes
+Run the same grep and show results proving no references remain unaddressed.
+```
+
 ## When to Use
 
 Run `/config-optimize` when:

plugins/cmdb-assistant/.claude-plugin/plugin.json

@@ -19,6 +19,5 @@
     "data-quality",
     "validation"
   ],
-  "commands": ["./commands/"],
-  "mcpServers": ["./.mcp.json"]
+  "commands": ["./commands/"]
 }

plugins/cmdb-assistant/.mcp.json

@@ -1,8 +0,0 @@
-{
-  "mcpServers": {
-    "netbox": {
-      "command": "${CLAUDE_PLUGIN_ROOT}/mcp-servers/netbox/run.sh",
-      "args": []
-    }
-  }
-}

plugins/contract-validator/.claude-plugin/plugin.json

@@ -18,6 +18,5 @@
     "interfaces",
     "cross-plugin"
   ],
-  "commands": ["./commands/"],
-  "mcpServers": ["./.mcp.json"]
+  "commands": ["./commands/"]
 }

plugins/contract-validator/.mcp.json

@@ -1,9 +0,0 @@
-{
-  "mcpServers": {
-    "contract-validator": {
-      "type": "stdio",
-      "command": "${CLAUDE_PLUGIN_ROOT}/mcp-servers/contract-validator/run.sh",
-      "args": []
-    }
-  }
-}

plugins/data-platform/.claude-plugin/plugin.json

@@ -19,6 +19,5 @@
     "etl",
     "dataframe"
   ],
-  "commands": ["./commands/"],
-  "mcpServers": ["./.mcp.json"]
+  "commands": ["./commands/"]
 }

plugins/data-platform/.mcp.json

@@ -1,9 +0,0 @@
-{
-  "mcpServers": {
-    "data-platform": {
-      "type": "stdio",
-      "command": "${CLAUDE_PLUGIN_ROOT}/mcp-servers/data-platform/run.sh",
-      "args": []
-    }
-  }
-}

plugins/doc-guardian/hooks/notify.sh

@@ -1,11 +1,12 @@
 #!/bin/bash
 # doc-guardian notification hook
 # Tracks documentation dependencies and queues updates
-# This is a command hook - guaranteed not to block workflow
 #
-# IMPORTANT: Output is purely informational - uses passive language
-# to avoid triggering Claude to seek user confirmation.
-# Run /doc-sync to process the queue when ready.
+# SILENT BY DEFAULT - No output to avoid interrupting Claude's workflow.
+# Changes are queued to .doc-guardian-queue for later processing.
+# Run /doc-sync or /doc-audit to see and process pending updates.
+#
+# Set DOC_GUARDIAN_VERBOSE=1 to enable notification output.
 
 # Read tool input from stdin (JSON with file_path)
 INPUT=$(cat)
@@ -48,40 +49,26 @@ DEPENDENT_DOCS="${DOC_DEPS[$MODIFIED_TYPE]}"
 # Queue file for tracking pending updates
 QUEUE_FILE="${CLAUDE_PROJECT_ROOT:-.}/.doc-guardian-queue"
 
-# Debounce: skip notification if same type was logged in last 5 seconds
-# This prevents 4+ rapid notifications during batch edits
-DEBOUNCE_SECONDS=5
+# Add to queue (always, for deduplication we check file+type combo)
+# Format: timestamp | type | file_path | dependent_docs
+QUEUE_ENTRY="$(date +%Y-%m-%dT%H:%M:%S) | $MODIFIED_TYPE | $FILE_PATH | $DEPENDENT_DOCS"
+
+# Check if this exact file+type combo already exists in queue (dedup)
 if [ -f "$QUEUE_FILE" ]; then
-    LAST_ENTRY=$(tail -1 "$QUEUE_FILE" 2>/dev/null || true)
-    LAST_TYPE=$(echo "$LAST_ENTRY" | cut -d'|' -f2 | tr -d ' ')
-    LAST_TIME=$(echo "$LAST_ENTRY" | cut -d'|' -f1 | tr -d ' ')
-
-    if [ "$LAST_TYPE" = "$MODIFIED_TYPE" ] && [ -n "$LAST_TIME" ]; then
-        # Convert timestamps to seconds for comparison
-        LAST_EPOCH=$(date -d "$LAST_TIME" +%s 2>/dev/null || echo "0")
-        NOW_EPOCH=$(date +%s)
-        DIFF=$((NOW_EPOCH - LAST_EPOCH))
-
-        if [ "$DIFF" -lt "$DEBOUNCE_SECONDS" ]; then
-            # Still add to queue, but skip notification
-            {
-                echo "$(date +%Y-%m-%dT%H:%M:%S) | $MODIFIED_TYPE | $FILE_PATH | $DEPENDENT_DOCS"
-            } >> "$QUEUE_FILE" 2>/dev/null || true
-            exit 0
-        fi
+    if grep -qF "| $MODIFIED_TYPE | $FILE_PATH |" "$QUEUE_FILE" 2>/dev/null; then
+        # Already queued, skip silently
+        exit 0
     fi
 fi
 
-# Add to queue (create if doesn't exist, append if does)
-{
-    echo "$(date +%Y-%m-%dT%H:%M:%S) | $MODIFIED_TYPE | $FILE_PATH | $DEPENDENT_DOCS"
-} >> "$QUEUE_FILE" 2>/dev/null || true
+# Add to queue
+echo "$QUEUE_ENTRY" >> "$QUEUE_FILE" 2>/dev/null || true
 
-# Count pending updates
-PENDING_COUNT=$(wc -l < "$QUEUE_FILE" 2>/dev/null | tr -d ' ' || echo "1")
-
-# Output passive notification (no action implied)
-# Uses "queued" instead of "update needed" to avoid triggering Claude to ask about it
-echo "[doc-guardian] drift queued: $MODIFIED_TYPE → $DEPENDENT_DOCS ($PENDING_COUNT total)"
+# SILENT by default - only output if DOC_GUARDIAN_VERBOSE is set
+# This prevents Claude from stopping to ask about documentation updates
+if [ "${DOC_GUARDIAN_VERBOSE:-0}" = "1" ]; then
+    PENDING_COUNT=$(wc -l < "$QUEUE_FILE" 2>/dev/null | tr -d ' ' || echo "1")
+    echo "[doc-guardian] queued: $MODIFIED_TYPE ($PENDING_COUNT pending)"
+fi
 
 exit 0

plugins/pr-review/.claude-plugin/plugin.json

@@ -17,6 +17,5 @@
     "performance",
     "multi-agent"
   ],
-  "commands": ["./commands/"],
-  "mcpServers": ["./.mcp.json"]
+  "commands": ["./commands/"]
 }

plugins/pr-review/.mcp.json

@@ -1,8 +0,0 @@
-{
-  "mcpServers": {
-    "gitea": {
-      "command": "${CLAUDE_PLUGIN_ROOT}/mcp-servers/gitea/run.sh",
-      "args": []
-    }
-  }
-}

plugins/projman/.claude-plugin/plugin.json

@@ -17,6 +17,5 @@
     "agile",
     "lessons-learned"
   ],
-  "commands": ["./commands/"],
-  "mcpServers": ["./.mcp.json"]
+  "commands": ["./commands/"]
 }

plugins/projman/.mcp.json

@@ -1,8 +0,0 @@
-{
-  "mcpServers": {
-    "gitea": {
-      "command": "${CLAUDE_PLUGIN_ROOT}/mcp-servers/gitea/run.sh",
-      "args": []
-    }
-  }
-}

plugins/projman/commands/clear-cache.md

@@ -0,0 +1,24 @@
+# /clear-cache
+
+Clear plugin cache to force fresh configuration reload. Run this after marketplace updates.
+
+## When to Use
+
+- After updating the marketplace (`git pull` or reinstall)
+- When MCP servers show stale configuration
+- When plugin changes don't take effect
+
+## What It Does
+
+1. Clears `~/.claude/plugins/cache/leo-claude-mktplace/`
+2. Forces Claude Code to re-read `.mcp.json` files on next session
+
+## Instructions
+
+Run this command, then **restart your Claude Code session** for changes to take effect.
+
+```bash
+rm -rf ~/.claude/plugins/cache/leo-claude-mktplace/
+```
+
+After clearing, inform the user: "Cache cleared. Restart Claude Code for changes to take effect."

plugins/projman/hooks/startup-check.sh

@@ -7,42 +7,6 @@ PREFIX="[projman]"
 
 # Calculate paths
 PLUGIN_ROOT="${CLAUDE_PLUGIN_ROOT:-$(dirname "$(dirname "$(realpath "$0")")")}"
-# Marketplace root is 2 levels up from plugin root (plugins/projman -> .)
-MARKETPLACE_ROOT="$(dirname "$(dirname "$PLUGIN_ROOT")")"
-VENV_REPAIR_SCRIPT="$MARKETPLACE_ROOT/scripts/venv-repair.sh"
-PLUGIN_CACHE="$HOME/.claude/plugins/cache/leo-claude-mktplace"
-
-# ============================================================================
-# Clear stale plugin cache (MUST run before MCP servers load)
-# ============================================================================
-# The cache at ~/.claude/plugins/cache/ holds versioned .mcp.json files.
-# After marketplace updates, cached configs may point to old paths.
-# Clearing forces Claude to read fresh configs from installed marketplace.
-
-if [[ -d "$PLUGIN_CACHE" ]]; then
-    rm -rf "$PLUGIN_CACHE"
-    # Don't output anything - this should be silent and automatic
-fi
-
-# ============================================================================
-# Auto-repair MCP venvs (runs before other checks)
-# ============================================================================
-
-if [[ -x "$VENV_REPAIR_SCRIPT" ]]; then
-    # Run venv repair - this creates symlinks to cached venvs
-    # Only outputs messages if something needed fixing
-    "$VENV_REPAIR_SCRIPT" 2>/dev/null || {
-        echo "$PREFIX MCP venv setup failed - run: cd $MARKETPLACE_ROOT && ./scripts/setup-venvs.sh"
-        exit 0
-    }
-else
-    # Fallback: just check if venv exists
-    VENV_PATH="$PLUGIN_ROOT/mcp-servers/gitea/.venv/bin/python"
-    if [[ ! -f "$VENV_PATH" ]]; then
-        echo "$PREFIX MCP venvs missing - run setup.sh from installed marketplace"
-        exit 0
-    fi
-fi
 
 # Check git remote vs .env config (only if .env exists)
 if [[ -f ".env" ]]; then

plugins/viz-platform/.claude-plugin/plugin.json

@@ -20,6 +20,5 @@
     "visualization",
     "dmc"
   ],
-  "commands": ["./commands/"],
-  "mcpServers": ["./.mcp.json"]
+  "commands": ["./commands/"]
 }

plugins/viz-platform/.mcp.json

@@ -1,9 +0,0 @@
-{
-  "mcpServers": {
-    "viz-platform": {
-      "type": "stdio",
-      "command": "${CLAUDE_PLUGIN_ROOT}/mcp-servers/viz-platform/run.sh",
-      "args": []
-    }
-  }
-}

scripts/post-update.sh

@@ -6,9 +6,10 @@
 #
 # This script:
 # 1. Clears Claude plugin cache (forces fresh .mcp.json reads)
-# 2. Restores MCP venv symlinks (instant if cache exists)
-# 3. Creates venvs in external cache if missing (first run only)
-# 4. Shows recent changelog updates
+# 2. Shows recent changelog updates
+#
+# NOTE: This script does NOT touch .venv directories.
+# If venvs are missing, run ./scripts/setup.sh manually.
 #
 
 set -euo pipefail
@@ -22,13 +23,11 @@ REPO_ROOT="$(dirname "$SCRIPT_DIR")"
 GREEN='\033[0;32m'
 YELLOW='\033[1;33m'
 BLUE='\033[0;34m'
-RED='\033[0;31m'
 NC='\033[0m'
 
 log_info() { echo -e "${BLUE}[INFO]${NC} $1"; }
 log_success() { echo -e "${GREEN}[OK]${NC} $1"; }
 log_warn() { echo -e "${YELLOW}[WARN]${NC} $1"; }
-log_error() { echo -e "${RED}[ERROR]${NC} $1"; }
 
 check_changelog() {
     if [[ -f "$REPO_ROOT/CHANGELOG.md" ]]; then
@@ -52,35 +51,21 @@ main() {
 
     # Clear Claude plugin cache to force fresh .mcp.json reads
     # This cache holds versioned copies that become stale after updates
+    # NOTE: This does NOT touch .venv directories
     if [[ -d "$CLAUDE_PLUGIN_CACHE" ]]; then
         log_info "Clearing Claude plugin cache..."
         rm -rf "$CLAUDE_PLUGIN_CACHE"
         log_success "Plugin cache cleared"
     fi
 
-    # Run venv-repair.sh to restore symlinks to external cache
-    # This is instant if cache exists, or does full setup on first run
-    if [[ -x "$SCRIPT_DIR/venv-repair.sh" ]]; then
-        log_info "Restoring MCP venv symlinks..."
-        if "$SCRIPT_DIR/venv-repair.sh"; then
-            log_success "MCP venvs ready"
-        else
-            log_error "MCP venv setup failed"
-            log_warn "Run: $SCRIPT_DIR/setup-venvs.sh for full setup"
-            exit 1
-        fi
-    else
-        log_error "venv-repair.sh not found at $SCRIPT_DIR"
-        exit 1
-    fi
-
     check_changelog
 
     echo ""
     log_success "Post-update complete!"
     echo ""
     echo "IMPORTANT: Restart Claude Code for changes to take effect."
-    echo "MCP servers will work immediately on next session start."
+    echo ""
+    echo "If MCP servers are not working, run: ./scripts/setup.sh"
 }
 
 main "$@"

scripts/validate-marketplace.sh

@@ -158,9 +158,106 @@ for plugin_dir in "$PLUGINS_DIR"/*/; do
         echo "WARNING: Missing README.md in $plugin_name/"
     fi
 
+    # CRITICAL: Validate file references exist (mcpServers, hooks, commands)
+    # This prevents broken references that silently break plugin loading
+
+    # Check mcpServers references
+    mcp_servers=$(jq -r '.mcpServers // [] | .[]' "$plugin_json" 2>/dev/null)
+    for mcp_ref in $mcp_servers; do
+        mcp_path="$plugin_dir/$mcp_ref"
+        if [[ ! -f "$mcp_path" ]]; then
+            echo "ERROR: BROKEN REFERENCE in $plugin_name/plugin.json"
+            echo "       mcpServers references '$mcp_ref' but file does not exist at:"
+            echo "       $mcp_path"
+            echo ""
+            echo "       FIX: Either create the file or remove the mcpServers entry"
+            exit 1
+        fi
+        echo "  ✓ mcpServers reference: $mcp_ref exists"
+    done
+
+    # Check hooks references (can be array of file paths OR object with handlers)
+    hooks_type=$(jq -r '.hooks | type' "$plugin_json" 2>/dev/null)
+    if [[ "$hooks_type" == "array" ]]; then
+        # Array format: ["./hooks/hooks.json"]
+        hooks=$(jq -r '.hooks[]' "$plugin_json" 2>/dev/null)
+        for hook_ref in $hooks; do
+            hook_path="$plugin_dir/$hook_ref"
+            if [[ ! -f "$hook_path" ]]; then
+                echo "ERROR: BROKEN REFERENCE in $plugin_name/plugin.json"
+                echo "       hooks references '$hook_ref' but file does not exist at:"
+                echo "       $hook_path"
+                echo ""
+                echo "       FIX: Either create the file or remove the hooks entry"
+                exit 1
+            fi
+            echo "  ✓ hooks reference: $hook_ref exists"
+        done
+    elif [[ "$hooks_type" == "object" ]]; then
+        # Object format: { "PostToolUse": [...] } - inline hooks, no file reference to validate
+        echo "  ✓ hooks: inline object format (no file references)"
+    fi
+
+    # Check commands directory references
+    commands=$(jq -r '.commands // [] | .[]' "$plugin_json" 2>/dev/null)
+    for cmd_ref in $commands; do
+        cmd_path="$plugin_dir/$cmd_ref"
+        if [[ ! -d "$cmd_path" ]] && [[ ! -f "$cmd_path" ]]; then
+            echo "ERROR: BROKEN REFERENCE in $plugin_name/plugin.json"
+            echo "       commands references '$cmd_ref' but path does not exist at:"
+            echo "       $cmd_path"
+            echo ""
+            echo "       FIX: Either create the path or remove the commands entry"
+            exit 1
+        fi
+        echo "  ✓ commands reference: $cmd_ref exists"
+    done
+
     echo "✓ $plugin_name valid"
 done
 
+# CRITICAL: Validate marketplace.json file references
+echo ""
+echo "=== Validating Marketplace File References (CRITICAL) ==="
+
+for i in $(seq 0 $((PLUGIN_COUNT - 1))); do
+    PLUGIN_NAME=$(jq -r ".plugins[$i].name" "$MARKETPLACE_JSON")
+    PLUGIN_SOURCE=$(jq -r ".plugins[$i].source" "$MARKETPLACE_JSON")
+    PLUGIN_DIR="$ROOT_DIR/$PLUGIN_SOURCE"
+
+    # Check mcpServers in marketplace.json
+    mcp_servers=$(jq -r ".plugins[$i].mcpServers // [] | .[]" "$MARKETPLACE_JSON" 2>/dev/null)
+    for mcp_ref in $mcp_servers; do
+        mcp_path="$PLUGIN_DIR/$mcp_ref"
+        if [[ ! -f "$mcp_path" ]]; then
+            echo "ERROR: BROKEN REFERENCE in marketplace.json for $PLUGIN_NAME"
+            echo "       mcpServers references '$mcp_ref' but file does not exist at:"
+            echo "       $mcp_path"
+            echo ""
+            echo "       FIX: Either create the file or remove the mcpServers entry from marketplace.json"
+            exit 1
+        fi
+        echo "✓ $PLUGIN_NAME: mcpServers reference $mcp_ref exists"
+    done
+
+    # Check hooks in marketplace.json
+    hooks=$(jq -r ".plugins[$i].hooks // [] | .[]" "$MARKETPLACE_JSON" 2>/dev/null)
+    for hook_ref in $hooks; do
+        hook_path="$PLUGIN_DIR/$hook_ref"
+        if [[ ! -f "$hook_path" ]]; then
+            echo "ERROR: BROKEN REFERENCE in marketplace.json for $PLUGIN_NAME"
+            echo "       hooks references '$hook_ref' but file does not exist at:"
+            echo "       $hook_path"
+            echo ""
+            echo "       FIX: Either create the file or remove the hooks entry from marketplace.json"
+            exit 1
+        fi
+        echo "✓ $PLUGIN_NAME: hooks reference $hook_ref exists"
+    done
+done
+
+echo "✓ All file references validated"
+
 # v5.4.0: Validate agent model fields
 echo ""
 echo "=== Validating Agent Model Fields (v5.4.0+) ==="

scripts/venv-repair.sh

@@ -1,169 +0,0 @@
-#!/usr/bin/env bash
-#
-# venv-repair.sh - Fast MCP venv auto-repair for SessionStart hooks
-#
-# This script is designed to run at session start. It:
-# 1. Checks if venvs exist in external cache (~/.cache/claude-mcp-venvs/)
-# 2. Creates symlinks from marketplace to cache (instant operation)
-# 3. Only runs pip install if cache is missing (first install)
-#
-# Output format: All messages prefixed with [mcp-venv] for hook display
-#
-# Usage:
-#   ./scripts/venv-repair.sh           # Auto-repair (default)
-#   ./scripts/venv-repair.sh --silent  # Silent mode (no output unless error)
-#
-
-set -euo pipefail
-
-# ============================================================================
-# Configuration
-# ============================================================================
-
-PREFIX="[mcp-venv]"
-VENV_CACHE_DIR="${HOME}/.cache/claude-mcp-venvs/leo-claude-mktplace"
-SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
-REPO_ROOT="$(dirname "$SCRIPT_DIR")"
-
-# MCP servers
-MCP_SERVERS=(gitea netbox data-platform viz-platform contract-validator)
-
-# Parse args
-SILENT=false
-[[ "${1:-}" == "--silent" ]] && SILENT=true
-
-log() {
-    [[ "$SILENT" == true ]] && return
-    echo "$PREFIX $1"
-}
-
-log_error() {
-    echo "$PREFIX ERROR: $1" >&2
-}
-
-# ============================================================================
-# Check if all venvs exist in cache
-# ============================================================================
-
-cache_complete() {
-    for server in "${MCP_SERVERS[@]}"; do
-        local venv_python="$VENV_CACHE_DIR/$server/.venv/bin/python"
-        [[ ! -f "$venv_python" ]] && return 1
-    done
-    return 0
-}
-
-# ============================================================================
-# Create symlinks from marketplace to cache
-# ============================================================================
-
-create_symlink() {
-    local server_name="$1"
-    local server_path="$REPO_ROOT/mcp-servers/$server_name"
-    local venv_cache="$VENV_CACHE_DIR/$server_name/.venv"
-    local venv_link="$server_path/.venv"
-
-    # Skip if server doesn't exist
-    [[ ! -d "$server_path" ]] && return 0
-
-    # Skip if cache doesn't exist
-    [[ ! -d "$venv_cache" ]] && return 1
-
-    # Already correct symlink?
-    if [[ -L "$venv_link" ]]; then
-        local target
-        target=$(readlink "$venv_link")
-        [[ "$target" == "$venv_cache" ]] && return 0
-        rm "$venv_link"
-    elif [[ -d "$venv_link" ]]; then
-        # Old venv directory exists - back it up or remove
-        rm -rf "$venv_link"
-    fi
-
-    # Create symlink
-    ln -s "$venv_cache" "$venv_link"
-    return 0
-}
-
-create_all_symlinks() {
-    local created=0
-    for server in "${MCP_SERVERS[@]}"; do
-        if create_symlink "$server"; then
-            ((created++)) || true
-        fi
-    done
-    [[ $created -gt 0 ]] && log "Restored $created venv symlinks"
-}
-
-# ============================================================================
-# Full setup (only if cache missing)
-# ============================================================================
-
-setup_server() {
-    local server_name="$1"
-    local server_path="$REPO_ROOT/mcp-servers/$server_name"
-    local venv_path="$VENV_CACHE_DIR/$server_name/.venv"
-
-    [[ ! -d "$server_path" ]] && return 0
-
-    mkdir -p "$VENV_CACHE_DIR/$server_name"
-
-    # Create venv
-    if [[ ! -d "$venv_path" ]]; then
-        python3 -m venv "$venv_path"
-    fi
-
-    # Install dependencies
-    # shellcheck disable=SC1091
-    source "$venv_path/bin/activate"
-    pip install -q --upgrade pip
-
-    if [[ -f "$server_path/requirements.txt" ]]; then
-        pip install -q -r "$server_path/requirements.txt"
-    fi
-
-    if [[ -f "$server_path/pyproject.toml" ]]; then
-        pip install -q -e "$server_path"
-    fi
-
-    deactivate
-
-    # Save hash for future quick checks
-    local hash_file="$VENV_CACHE_DIR/$server_name/.requirements_hash"
-    {
-        if [[ -f "$server_path/requirements.txt" ]]; then
-            cat "$server_path/requirements.txt"
-        fi
-        if [[ -f "$server_path/pyproject.toml" ]]; then
-            cat "$server_path/pyproject.toml"
-        fi
-        echo ""  # Ensure non-empty input for sha256sum
-    } | sha256sum | cut -d' ' -f1 > "$hash_file"
-}
-
-full_setup() {
-    log "First run - setting up MCP venvs (this only happens once)..."
-    for server in "${MCP_SERVERS[@]}"; do
-        log "  Setting up $server..."
-        setup_server "$server"
-    done
-    log "Setup complete. Future sessions will be instant."
-}
-
-# ============================================================================
-# Main
-# ============================================================================
-
-main() {
-    # Fast path: cache exists, just ensure symlinks
-    if cache_complete; then
-        create_all_symlinks
-        exit 0
-    fi
-
-    # Slow path: need to create venvs (first install)
-    full_setup
-    create_all_symlinks
-}
-
-main "$@"