[BUG] MCP tool schemas still consuming context tokens after all connectors disabled

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

After fully disabling/removing all connectors (Claude in Chrome, GitHub Integration, Higgsfield, Vercel) in Settings → Connectors, then fully quitting (Cmd+Q) and relaunching the desktop app and starting a brand-new conversation, /context still reports MCP tools consuming 12.7k tokens (12.7% of the 93k/100k window). Expected value is 0 tokens once every connector is disabled.

Full context breakdown observed (93k/100k window, 93% full):

| Category | Tokens | % of window |
|---|---|---|
| Autocompact buffer | 33k | 33.0% |
| System tools | 23.8k | 23.8% |
| MCP tools (loaded/active) | 12.7k | 12.7% |
| System prompt | 11.6k | 11.6% |
| Free space | 7k | 7.0% |
| Memory files | 6.4k | 6.4% |
| Skills | 5.5k | 5.5% |
| Messages | 8 | 0.0% |

Not part of the 100% above, shown separately as not-yet-loaded:

• MCP tools deferred: 26.9k tokens
• System tools deferred: 16.7k tokens
• 71 = total tool definitions across all connectors (loaded + deferred)
• 2 = memory files loaded

Steps to reproduce

1. Disable/remove every connector in Settings → Connectors.
2. Fully quit (Cmd+Q) and relaunch the app.
3. Start a brand-new conversation, run /context.
4. MCP tools (active) still shows 12.7k tokens instead of 0.

Expected behavior
With zero connectors enabled, MCP tools (active) should show 0 tokens.

Environment

• OS: macOS (Darwin 25.6.0)
• App: Claude desktop app
• Account: abeltransmu@hotmail.com

Submit at https://github.com/anthropics/claude-code/issues → New issue. Attach a screenshot of /context and the Connectors settings page if you can.

What Should Happen?

According to Claude helping. With all connectors disabled, there shouldn't be little token usage. Similar to what is experienced in the CLI terminal. There are no plugins/connectors. And Claude's diagnostics identifies Github as the potential source.

Error Messages/Logs

Steps to Reproduce

1. Disable/remove every connector in Settings → Connectors (Claude in Chrome, GitHub Integration, Higgsfield, Vercel).
2. Fully quit the desktop app (Cmd+Q) and relaunch it.
3. Start a brand-new conversation.
4. Run /context.
5. Observe: MCP tools (active) still shows 12.7k tokens (12.7%) instead of 0.

Claude Model

Sonnet (default)

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.1.261

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_