fix: write MCP config to ~/.claude.json instead of settings.json

Claude Code looks for global MCP servers in ~/.claude.json, not in
~/.claude/settings.json. Also migrates any existing entry from the
legacy location and cleans up duplicates.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

install.sh

@@ -231,22 +231,22 @@ info "Checking existing MCP configuration..."
 MCP_CONFIG_FILE=""
 EXISTING_ENTRY=""
 
-# Check global settings.json first (preferred location)
+# Check ~/.claude.json first (preferred location for global MCP servers)
-if [ -f "$CLAUDE_SETTINGS" ]; then
+if [ -f "$CLAUDE_JSON" ]; then
-  EXISTING_ENTRY=$(jq -r --arg name "$MCP_NAME" '.mcpServers[$name] // empty' "$CLAUDE_SETTINGS" 2>/dev/null || true)
-  if [ -n "$EXISTING_ENTRY" ]; then
-    MCP_CONFIG_FILE="$CLAUDE_SETTINGS"
-  fi
-fi
-
-# Check ~/.claude.json
-if [ -z "$EXISTING_ENTRY" ] && [ -f "$CLAUDE_JSON" ]; then
   EXISTING_ENTRY=$(jq -r --arg name "$MCP_NAME" '.mcpServers[$name] // empty' "$CLAUDE_JSON" 2>/dev/null || true)
   if [ -n "$EXISTING_ENTRY" ]; then
     MCP_CONFIG_FILE="$CLAUDE_JSON"
   fi
 fi
 
+# Check ~/.claude/settings.json (legacy location)
+if [ -z "$EXISTING_ENTRY" ] && [ -f "$CLAUDE_SETTINGS" ]; then
+  EXISTING_ENTRY=$(jq -r --arg name "$MCP_NAME" '.mcpServers[$name] // empty' "$CLAUDE_SETTINGS" 2>/dev/null || true)
+  if [ -n "$EXISTING_ENTRY" ]; then
+    MCP_CONFIG_FILE="$CLAUDE_SETTINGS"
+  fi
+fi
+
 # Check for project-level .mcp.json files
 FOUND_PROJECT_MCP=()
 while IFS= read -r -d '' mcp_file; do
@@ -268,9 +268,9 @@ if [ ${#FOUND_PROJECT_MCP[@]} -gt 0 ]; then
 
     if [ -z "$EXISTING_ENTRY" ]; then
       # No global config yet - migrate from project file
-      if ask_yes_no "  Migrate to global config ($CLAUDE_SETTINGS)?"; then
+      if ask_yes_no "  Migrate to global config ($CLAUDE_JSON)?"; then
         EXISTING_ENTRY=$(jq --arg name "$MCP_NAME" '.mcpServers[$name]' "$mcp_file")
-        MCP_CONFIG_FILE="$CLAUDE_SETTINGS"
+        MCP_CONFIG_FILE="$CLAUDE_JSON"
       fi
     fi
 
@@ -396,22 +396,22 @@ else
     }')
 fi
 
-# Write to settings.json (global/user level)
+# Write to ~/.claude.json (global MCP config location)
-mkdir -p "$(dirname "$CLAUDE_SETTINGS")"
+if [ ! -f "$CLAUDE_JSON" ]; then
-if [ ! -f "$CLAUDE_SETTINGS" ]; then
+  echo '{}' > "$CLAUDE_JSON"
-  echo '{}' > "$CLAUDE_SETTINGS"
 fi
 
 tmp=$(jq --arg name "$MCP_NAME" --argjson entry "$MCP_ENTRY" \
-  '.mcpServers[$name] = $entry' "$CLAUDE_SETTINGS")
+  '.mcpServers[$name] = $entry' "$CLAUDE_JSON")
-echo "$tmp" > "$CLAUDE_SETTINGS"
+echo "$tmp" > "$CLAUDE_JSON"
-ok "Written to $CLAUDE_SETTINGS"
+ok "Written to $CLAUDE_JSON"
 
-# Also register via claude CLI if available (belt and suspenders)
+# Clean up from settings.json if it exists there (legacy location)
-if command -v claude &>/dev/null; then
+if [ -f "$CLAUDE_SETTINGS" ]; then
-  # Check if claude mcp already has this entry to avoid duplicates
+  if jq -e --arg name "$MCP_NAME" '.mcpServers[$name] != null' "$CLAUDE_SETTINGS" &>/dev/null; then
-  if claude mcp list 2>/dev/null | grep -q "$MCP_NAME"; then
+    tmp=$(jq --arg name "$MCP_NAME" 'del(.mcpServers[$name])' "$CLAUDE_SETTINGS")
-    claude mcp remove "$MCP_NAME" --scope user 2>/dev/null || true
+    echo "$tmp" > "$CLAUDE_SETTINGS"
+    ok "Removed legacy entry from $CLAUDE_SETTINGS"
   fi
 fi
 
@@ -436,13 +436,13 @@ done < <(find "$HOME" -maxdepth 3 -name ".mcp.json" \
   -not -path "*/node_modules/*" \
   -print0 2>/dev/null || true)
 
-# Clean from ~/.claude.json if we wrote to settings.json
+# Clean from ~/.claude/settings.json if we wrote to ~/.claude.json
-if [ -f "$CLAUDE_JSON" ]; then
+if [ -f "$CLAUDE_SETTINGS" ]; then
-  if jq -e --arg name "$MCP_NAME" '.mcpServers[$name] != null' "$CLAUDE_JSON" &>/dev/null; then
+  if jq -e --arg name "$MCP_NAME" '.mcpServers[$name] != null' "$CLAUDE_SETTINGS" &>/dev/null; then
-    warn "Duplicate found in $CLAUDE_JSON"
+    warn "Duplicate found in $CLAUDE_SETTINGS"
-    if ask_yes_no "  Remove from $CLAUDE_JSON? (already in settings.json)"; then
+    if ask_yes_no "  Remove from $CLAUDE_SETTINGS? (already in $CLAUDE_JSON)"; then
-      tmp=$(jq --arg name "$MCP_NAME" 'del(.mcpServers[$name])' "$CLAUDE_JSON")
+      tmp=$(jq --arg name "$MCP_NAME" 'del(.mcpServers[$name])' "$CLAUDE_SETTINGS")
-      echo "$tmp" > "$CLAUDE_JSON"
+      echo "$tmp" > "$CLAUDE_SETTINGS"
       ok "Removed"
     fi
   fi