From 0833e1ca650924470486b54a10895ce9306db58d Mon Sep 17 00:00:00 2001
From: Florian BRUNIAUX <florian@bruniaux.com>
Date: Mon, 12 Jan 2026 08:37:01 +0100
Subject: [PATCH] fix(audit): correct MCP detection to check ~/.claude.json
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The audit script was looking for MCP config in ~/.claude/mcp.json which
doesn't exist. Claude Code actually stores MCP config in ~/.claude.json
under projects.<path>.mcpServers.

Changes:
- audit-scan.sh: Multi-source MCP detection (3 locations with priority)
- audit-scan.sh: Fixed count_pattern() bug causing "0\n0" output
- claude-setup-audit-prompt.md: Updated bash commands for MCP detection
- Version bump: 2.8 → 2.9

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
---
 CHANGELOG.md                   | 33 +++++++++++++
 README.md                      |  2 +-
 claude-setup-audit-prompt.md   | 47 ++++++++++++++-----
 examples/scripts/audit-scan.sh | 86 ++++++++++++++++++++++++++++------
 4 files changed, 141 insertions(+), 27 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 09feca0..e828d92 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,39 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
 ## [Unreleased]
 
+## [2.9.0] - 2026-01-12
+
+### Fixed
+- **MCP detection bug in audit-scan.sh** (~60 lines modified)
+  - **Root cause**: Script searched for `~/.claude/mcp.json` which doesn't exist
+  - **Actual location**: Claude Code stores MCP config in `~/.claude.json` under `projects.<path>.mcpServers`
+  - **Solution**: Multi-source detection with priority:
+    1. `~/.claude.json` → `projects.<cwd>.mcpServers` (most common)
+    2. `./.claude/mcp.json` (project-level)
+    3. `~/.claude/mcp.json` (legacy global)
+  - JSON output now includes detailed `mcp` section (configured, count, servers, source)
+  - Human output shows server count and source location
+- **Bug `0\n0` in `claude_md_refs`** (~8 lines)
+  - **Root cause**: `grep -c ... || echo "0"` could produce double output
+  - **Solution**: Rewritten `count_pattern()` function to properly capture and return count
+
+### Changed
+- **audit-scan.sh** enhanced (~50 lines)
+  - Added `MCP_SOURCE` variable to track where MCP config was found
+  - Added `MCP_COUNT` variable for server count
+  - Global `mcp.json` message changed from error to info (not required)
+  - JSON output restructured with separate `mcp` object
+- **claude-setup-audit-prompt.md** updated (~40 lines)
+  - Phase 1.1: Now checks `~/.claude.json` instead of `~/.claude/mcp.json`
+  - Phase 1.2: Complete MCP detection rewrite covering all 3 locations
+  - Glossary: Updated MCP definition to explain config locations
+  - Version: 2.8 → 2.9
+
+### Stats
+- 2 files modified (audit-scan.sh, claude-setup-audit-prompt.md)
+- Bug impact: Scripts now correctly detect MCP servers (was showing "No MCP" even when configured)
+- Tested: Verified on Méthode Aristote project with 9 MCP servers
+
 ## [2.8.0] - 2026-01-11
 
 ### Added
diff --git a/README.md b/README.md
index 8c53ed0..fea2234 100644
--- a/README.md
+++ b/README.md
@@ -315,7 +315,7 @@ If this guide saved you time, helped you master Claude Code, or inspired your wo
 
 ---
 
-*Version 2.8 | January 2026 | Crafted with Claude*
+*Version 2.9 | January 2026 | Crafted with Claude*
 
 <!-- SEO Keywords -->
 <!-- claude code, claude code tutorial, anthropic cli, ai coding assistant, claude code mcp,
diff --git a/claude-setup-audit-prompt.md b/claude-setup-audit-prompt.md
index 0548aa4..9c86b23 100644
--- a/claude-setup-audit-prompt.md
+++ b/claude-setup-audit-prompt.md
@@ -95,9 +95,11 @@ https://github.com/FlorianBruniaux/claude-code-ultimate-guide/blob/main/english-
 ```bash
 bash -c '
 echo "=== GLOBAL CONFIG ==="
-for f in ~/.claude/CLAUDE.md ~/.claude/settings.json ~/.claude/mcp.json; do
+for f in ~/.claude/CLAUDE.md ~/.claude/settings.json; do
   [ -f "$f" ] && echo "✅ $(basename $f)" || echo "❌ $(basename $f)"
 done
+# Note: MCP config is now in ~/.claude.json, not ~/.claude/mcp.json
+[ -f ~/.claude.json ] && echo "✅ ~/.claude.json (contains MCP config)" || echo "❌ ~/.claude.json"
 
 echo -e "\n=== PROJECT CONFIG ==="
 for f in ./CLAUDE.md ./.claude/CLAUDE.md ./.claude/settings.json ./.claude/settings.local.json; do
@@ -141,18 +143,41 @@ else
   echo "❌ No hooks directory"
 fi
 
-# MCP servers
+# MCP servers (check all locations)
 echo -e "\n=== MCP SERVERS ==="
-if [ -f ~/.claude/mcp.json ]; then
-  if command -v jq &> /dev/null; then
-    jq -r ".mcpServers | keys[]" ~/.claude/mcp.json 2>/dev/null
-  else
-    grep -oE "\"[a-zA-Z0-9_-]+\"\\s*:" ~/.claude/mcp.json | sed "s/\"//g;s/://g"
+CURRENT_DIR=$(pwd)
+
+# Check 1: Project-specific MCP in ~/.claude.json (most common)
+if [ -f ~/.claude.json ] && command -v jq &> /dev/null; then
+  MCP=$(jq -r --arg path "$CURRENT_DIR" ".projects[\$path].mcpServers // {} | keys[]" ~/.claude.json 2>/dev/null)
+  if [ -n "$MCP" ]; then
+    echo "Source: ~/.claude.json (project)"
+    echo "$MCP"
   fi
-else
-  echo "❌ No mcp.json"
 fi
 
+# Check 2: Project-level .claude/mcp.json
+if [ -z "$MCP" ] && [ -f ./.claude/mcp.json ]; then
+  echo "Source: .claude/mcp.json"
+  if command -v jq &> /dev/null; then
+    jq -r ".mcpServers // {} | keys[]" ./.claude/mcp.json 2>/dev/null
+  else
+    grep -oE "\"[a-zA-Z0-9_-]+\"[[:space:]]*:" ./.claude/mcp.json | sed "s/\"//g;s/://g"
+  fi
+fi
+
+# Check 3: Legacy global ~/.claude/mcp.json
+if [ -z "$MCP" ] && [ -f ~/.claude/mcp.json ]; then
+  echo "Source: ~/.claude/mcp.json (global)"
+  if command -v jq &> /dev/null; then
+    jq -r ".mcpServers // {} | keys[]" ~/.claude/mcp.json 2>/dev/null
+  else
+    grep -oE "\"[a-zA-Z0-9_-]+\"[[:space:]]*:" ~/.claude/mcp.json | sed "s/\"//g;s/://g"
+  fi
+fi
+
+[ -z "$MCP" ] && echo "❌ No MCP servers configured for this project"
+
 # CLAUDE.md quality
 echo -e "\n=== MEMORY FILE QUALITY ==="
 if [ -f ./CLAUDE.md ]; then
@@ -448,7 +473,7 @@ Here's an example of what the audit report looks like:
 | **Memory Files** | CLAUDE.md files that provide persistent context to Claude across sessions |
 | **Single Source of Truth** | Pattern where conventions are documented once and referenced everywhere |
 | **Tool SEO** | Writing agent/command descriptions so Claude selects the right tool automatically |
-| **MCP Servers** | Model Context Protocol - external tools that extend Claude's capabilities |
+| **MCP Servers** | Model Context Protocol - external tools that extend Claude's capabilities. Config stored in `~/.claude.json` per project, or `.claude/mcp.json` at project level |
 | **Serena** | MCP server for codebase indexation and session memory persistence |
 | **Context7** | MCP server for official library documentation lookup |
 | **Hooks** | Scripts that run automatically on Claude events (PreToolUse, PostToolUse, etc.) |
@@ -528,4 +553,4 @@ Here's an example of what the audit report looks like:
 
 ---
 
-*Last updated: January 2026 | Version 2.8 - Optimized with bash scanning*
+*Last updated: January 2026 | Version 2.9 - Fixed MCP detection (now checks ~/.claude.json)*
diff --git a/examples/scripts/audit-scan.sh b/examples/scripts/audit-scan.sh
index b48ba82..66b36c9 100755
--- a/examples/scripts/audit-scan.sh
+++ b/examples/scripts/audit-scan.sh
@@ -68,7 +68,13 @@ get_file_lines() {
 }
 
 count_pattern() {
-  [[ -f "$1" ]] && grep -c "$2" "$1" 2>/dev/null || echo "0"
+  if [[ -f "$1" ]]; then
+    local count
+    count=$(grep -c "$2" "$1" 2>/dev/null) || count="0"
+    echo "$count"
+  else
+    echo "0"
+  fi
 }
 
 # Expand home directory
@@ -114,18 +120,62 @@ if [[ -d "./.claude/hooks" ]]; then
   grep -l "PreToolUse" ./.claude/hooks/* 2>/dev/null >/dev/null && HAS_SECURITY_HOOKS="true"
 fi
 
-# MCP servers (check global config)
+# MCP servers detection
+# Claude Code stores MCP config in multiple locations:
+# 1. ~/.claude.json under projects.<cwd>.mcpServers (per-project, most common)
+# 2. ~/.claude/mcp.json (legacy global)
+# 3. ./.claude/mcp.json (project-level)
 MCP_SERVERS=""
-if [[ -f "${GLOBAL_DIR}/mcp.json" ]]; then
-  # Extract server names (works with or without jq)
+MCP_SOURCE=""
+CURRENT_DIR=$(pwd)
+
+# Check 1: Project-specific MCP in ~/.claude.json
+if [[ -f "${HOME}/.claude.json" ]]; then
   if command -v jq &> /dev/null; then
-    MCP_SERVERS=$(jq -r '.mcpServers | keys[]' "${GLOBAL_DIR}/mcp.json" 2>/dev/null | tr '\n' ',' | sed 's/,$//')
-  else
-    # Fallback: simple grep
-    MCP_SERVERS=$(grep -oE '"[a-zA-Z0-9_-]+"\\s*:' "${GLOBAL_DIR}/mcp.json" 2>/dev/null | sed 's/"//g;s/://g' | tr '\n' ',' | sed 's/,$//')
+    # Get MCP servers for current project path
+    MCP_SERVERS=$(jq -r --arg path "$CURRENT_DIR" '.projects[$path].mcpServers // {} | keys[]' "${HOME}/.claude.json" 2>/dev/null | tr '\n' ',' | sed 's/,$//')
+    if [[ -n "$MCP_SERVERS" ]]; then
+      MCP_SOURCE="~/.claude.json (project)"
+    fi
   fi
 fi
 
+# Check 2: Project-level .claude/mcp.json
+if [[ -z "$MCP_SERVERS" && -f "./.claude/mcp.json" ]]; then
+  if command -v jq &> /dev/null; then
+    MCP_SERVERS=$(jq -r '.mcpServers // {} | keys[]' "./.claude/mcp.json" 2>/dev/null | tr '\n' ',' | sed 's/,$//')
+    if [[ -n "$MCP_SERVERS" ]]; then
+      MCP_SOURCE=".claude/mcp.json (project)"
+    fi
+  else
+    MCP_SERVERS=$(grep -oE '"[a-zA-Z0-9_-]+"[[:space:]]*:' "./.claude/mcp.json" 2>/dev/null | head -20 | sed 's/"//g;s/://g' | tr '\n' ',' | sed 's/,$//')
+    if [[ -n "$MCP_SERVERS" ]]; then
+      MCP_SOURCE=".claude/mcp.json (project)"
+    fi
+  fi
+fi
+
+# Check 3: Legacy global ~/.claude/mcp.json
+if [[ -z "$MCP_SERVERS" && -f "${GLOBAL_DIR}/mcp.json" ]]; then
+  if command -v jq &> /dev/null; then
+    MCP_SERVERS=$(jq -r '.mcpServers // {} | keys[]' "${GLOBAL_DIR}/mcp.json" 2>/dev/null | tr '\n' ',' | sed 's/,$//')
+    if [[ -n "$MCP_SERVERS" ]]; then
+      MCP_SOURCE="~/.claude/mcp.json (global)"
+    fi
+  else
+    MCP_SERVERS=$(grep -oE '"[a-zA-Z0-9_-]+"[[:space:]]*:' "${GLOBAL_DIR}/mcp.json" 2>/dev/null | head -20 | sed 's/"//g;s/://g' | tr '\n' ',' | sed 's/,$//')
+    if [[ -n "$MCP_SERVERS" ]]; then
+      MCP_SOURCE="~/.claude/mcp.json (global)"
+    fi
+  fi
+fi
+
+# Count MCP servers
+MCP_COUNT=0
+if [[ -n "$MCP_SERVERS" ]]; then
+  MCP_COUNT=$(echo "$MCP_SERVERS" | tr ',' '\n' | grep -c . || echo "0")
+fi
+
 # Memory file quality (if exists)
 CLAUDE_MD_LINES="0"
 CLAUDE_MD_REFS="0"
@@ -143,13 +193,13 @@ fi
 # === OUTPUT ===
 
 if [[ "$OUTPUT_MODE" == "json" ]]; then
-  # JSON output
+  # JSON output - ensure all values are properly formatted
   cat <<EOF
 {
   "global": {
     "claude_md": $GLOBAL_CLAUDE_MD,
     "settings": $GLOBAL_SETTINGS,
-    "mcp": $GLOBAL_MCP
+    "mcp_json": $GLOBAL_MCP
   },
   "project": {
     "claude_md": $PROJECT_CLAUDE_MD,
@@ -169,8 +219,13 @@ if [[ "$OUTPUT_MODE" == "json" ]]; then
     "has_security_hooks": $HAS_SECURITY_HOOKS,
     "has_ssot_references": $HAS_SSOT,
     "claude_md_lines": $CLAUDE_MD_LINES,
-    "claude_md_refs": $CLAUDE_MD_REFS,
-    "mcp_servers": "$MCP_SERVERS"
+    "claude_md_refs": $CLAUDE_MD_REFS
+  },
+  "mcp": {
+    "configured": $([ -n "$MCP_SERVERS" ] && echo "true" || echo "false"),
+    "count": $MCP_COUNT,
+    "servers": "$MCP_SERVERS",
+    "source": "$MCP_SOURCE"
   }
 }
 EOF
@@ -181,7 +236,7 @@ else
   echo -e "${BLUE}📁 GLOBAL CONFIG${NC} (~/.claude/)"
   [[ "$GLOBAL_CLAUDE_MD" == "true" ]] && echo -e "  ${GREEN}✅${NC} CLAUDE.md" || echo -e "  ${RED}❌${NC} CLAUDE.md"
   [[ "$GLOBAL_SETTINGS" == "true" ]] && echo -e "  ${GREEN}✅${NC} settings.json" || echo -e "  ${RED}❌${NC} settings.json"
-  [[ "$GLOBAL_MCP" == "true" ]] && echo -e "  ${GREEN}✅${NC} mcp.json" || echo -e "  ${RED}❌${NC} mcp.json"
+  [[ "$GLOBAL_MCP" == "true" ]] && echo -e "  ${GREEN}✅${NC} mcp.json (legacy)" || echo -e "  ${YELLOW}⚠️${NC}  mcp.json (not required, MCP in ~/.claude.json)"
 
   echo -e "\n${BLUE}📁 PROJECT CONFIG${NC} (./)"
   [[ "$PROJECT_CLAUDE_MD" == "true" ]] && echo -e "  ${GREEN}✅${NC} CLAUDE.md" || echo -e "  ${YELLOW}⚠️${NC}  CLAUDE.md (recommended)"
@@ -210,9 +265,10 @@ else
   fi
 
   if [[ -n "$MCP_SERVERS" ]]; then
-    echo -e "  ${GREEN}✅${NC} MCP servers: $MCP_SERVERS"
+    echo -e "  ${GREEN}✅${NC} MCP servers ($MCP_COUNT): $MCP_SERVERS"
+    echo -e "      ${BLUE}Source:${NC} $MCP_SOURCE"
   else
-    echo -e "  ${YELLOW}⚠️${NC}  No MCP servers configured"
+    echo -e "  ${YELLOW}⚠️${NC}  No MCP servers configured for this project"
   fi
 
   echo -e "\n${BLUE}━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━${NC}"