MCP tools stop working when resuming a previous session

[pWoLiAn]

Description

When resuming a previous Copilot CLI session (via checkpoint restore), MCP server tools that were working in the original session are no longer available. Attempting to call any MCP tool returns:

Tool 'jira-jira_get_issue' does not exist.

The MCP config (~/.copilot/mcp-config.json) is still present and unchanged. The tools worked fine in the original session before checkpointing.

Steps to Reproduce

1. Start a Copilot CLI session with MCP servers configured (e.g., Jira, GitHub Enterprise)
2. Use MCP tools successfully (e.g., jira-jira_add_comment)
3. Exit the session
4. Resume the session from the checkpoint
5. Attempt to use the same MCP tools

Expected Behavior

MCP servers should be reconnected/restarted when a session is resumed, and all previously available tools should work.

Actual Behavior

MCP tools return Tool '...' does not exist errors. There is no way to restart MCP servers from within the session.

Environment

• Copilot CLI version: 1.0.11
• MCP servers: Docker-based (jira, github) and stdio-based (uvx)
• OS: Linux

[examon]

This should be resolved as of v1.0.12, with further MCP lifecycle improvements through v1.0.16. Session resume and switching now properly restart MCP servers, and several follow-on fixes addressed config loading and race conditions during MCP reconnection. If you're still seeing this on a current version, please feel free to reopen.