Claude in Chrome: 18 of 20 MCP tools blocked by enabledMcpTools despite connector being enabled

Description

After reinstalling both Claude Code (v2.1.44) and the Claude in Chrome extension (v1.0.63), only 2 out of 20 Claude in Chrome MCP tools are available: tabs_close_mcp and file_upload. The remaining 18 tools (including read_page, navigate, click, find, javascript_tool, etc.) are blocked.

Root Cause Analysis

The enabledMcpTools field in session JSON files (AppData/Roaming/Claude/claude-code-sessions/) has all 18 Chrome tools set to false:

"local:Claude in Chrome:read_page": false,
"local:Claude in Chrome:navigate": false,
"local:Claude in Chrome:find": false,
// ... all 18 tools = false

tabs_close_mcp and file_upload work because they are not listed in enabledMcpTools at all (unlisted = no filter = works).

What we verified

• Native Messaging Host: registry entry exists, chrome-native-host.exe present and functional
• Chrome extension permissions: all correct (nativeMessaging, debugger, tabs, scripting, <all_urls>)
• Extension ID matches allowed_origins in native host manifest
• main.log shows replaceEnabledMcpTools: toolCount=23 — the app recognizes all 23 tools
• Claude in Chrome connector is enabled in Desktop app settings
• Toggling the connector off/on does not change enabledMcpTools values

What we tried (all failed)

1. Setting all Chrome tools to true in session JSON files — Desktop app overwrites them back to false
2. Deleting Chrome tool entries from enabledMcpTools entirely — tools still blocked (filtering happens in-memory, not from files)
3. Reinstalling Chrome extension
4. Reinstalling Claude Code
5. Toggling Claude in Chrome connector off then on

Expected Behavior

All Claude in Chrome MCP tools should be enabled when the connector is set to "enabled" in settings.

Environment

• OS: Windows 11 Pro 10.0.26200
• Claude Code: v2.1.44
• Claude in Chrome extension: v1.0.63
• Chrome Profile: Profile 1
• Extension ID: fcoeoabgfenejglbffodgkkbkcdhcgfn
• Plan: Claude Max 20x