MCP tool manifest for a project-scoped remote connector doesn't refresh across --continue or a fresh launch

What happened

A remote streamable-HTTP MCP server (project-scoped — connected in-session but not listed in /mcp's server panel, which showed 21 user/claude.ai connectors, none matching this one) had two new tools deployed to it (simulate_delete_quote, delete_quote, added to an existing, already-connected server).

Tool discovery (ToolSearch with exact-name select: queries) returned "No matching deferred tools found" for both new tools, across four separate attempts:

1. The original session, immediately after the deploy.
2. After checking /mcp — the connector wasn't listed there at all (21 servers shown: 2 "User MCPs" + 19 claude.ai connectors), so no reconnect action was available for it.
3. After claude --continue (same session resumed in a new process).
4. After a fully fresh claude launch with no resume flag at all (new process, no restored session state).

None of the four picked up the new tools.

Root cause narrowed down

Calling the same server directly over raw HTTP — bypassing the CLI's MCP client entirely, using the same Bearer credential the CLI's own connector uses — returned both tools correctly on tools/list and tools/call on the very first attempt. This confirms:

• The deployed server was correctly serving the new tools the whole time.
• The staleness is entirely on the CLI/client side.
• Whatever caches this connector's tool manifest is not invalidated by session resume (--continue) or by a brand-new process launch — which is surprising, since a fresh process launch would normally be expected to re-run the MCP handshake from scratch.

The connector's absence from /mcp's own server listing (point 2 above) suggests it may be registered/managed through a different path than user-managed MCP servers, which may be where the caching that survives a process restart lives.

Repro

1. Have an active session connected to a project-scoped remote MCP server.
2. Deploy a new tool to that server (add a tool registration, redeploy).
3. From the same session, try to discover/call the new tool. Confirmed stale.
4. Try claude --continue. Still stale.
5. Try a fresh claude launch (no flags). Still stale.
6. Call the server directly over HTTP with the same auth the CLI uses. Tool is there immediately.

Environment

• CLI version: v2.1.247 (from the fresh-launch startup banner)
• Server: a Supabase Edge Function acting as an MCP server (streamable-HTTP transport), confirmed ACTIVE and serving the correct, current source at the time of every failed discovery attempt.

Impact

A user has no way to get newly-deployed tools on an already-connected project-scoped MCP server to become visible short of bypassing the CLI's own MCP client and hitting the server directly with raw HTTP — which most users can't do, and which shouldn't be necessary given /mcp didn't even offer a reconnect path for this connector.