Desktop app: an extension joinSession() call removes all plugin skills from the session

Start by reproducing the issue with the minimal ~/.copilot/extensions/noop-join/extension.mjs example and compare session.rpc.skills.list() before and after joinSession(). Trace the join, extension relaunch, and session resume paths, then verify that enabled plugin skills remain available after each path without requiring a later plugins.reload({ reloadMcp: false, reloadCustomAgents: true, reloadHooks: false, reloadExtensions: false }) workaround.

Describe the bug

In the GitHub Copilot desktop app, when any extension calls joinSession() from @github/copilot-sdk/extension, the session loses every skill whose source is plugin. session.rpc.plugins.list() still lists every enabled plugin, and user skills, custom agents, plugin MCP servers, and custom instructions all stay. So the plugins look installed and enabled, but <available_skills> has none of their skills and the skill tool returns Skill not found for them.

I think this is one concrete trigger for the symptom in github/copilot-cli#2753.

Affected version

• GitHub Copilot desktop app 1.1.23, bundled runtime 1.0.87-0
• Windows 11 x64
• Not yet tested on runtime 1.0.88-0 or later

Steps to reproduce the behavior

1. Install and enable one or more plugins that contribute skills.
2. Create a user extension at ~/.copilot/extensions/noop-join/extension.mjs:

   import { joinSession } from "@github/copilot-sdk/extension";
   await joinSession({});
   

3. Start a new session in the desktop app, or run extensions_reload in an existing session.
4. Ask the agent to list its available skills, or call session.rpc.skills.list() from an extension after the join and count the entries with source: "plugin".
5. Disable the extension and start another new session for comparison.

Result: with the extension, the count of plugin skills is zero and stays at zero. session.rpc.plugins.list() is unchanged. Without the extension, the plugin skills are present.

Expected behavior

The session keeps the skills of its enabled plugins after an extension joins.

Additional context

Join paths that reproduce it. Each of these relaunches the extensions, and each one removed the plugin skills in my tests: a new session, extensions_reload, creating an extension in the middle of a session, reopening an idle session (session.resume with sessionWasActive: false), and a full app restart followed by a session resume.

Control. With no extensions enabled, sessions kept their plugin skills through a one-hour soak.

Hourly re-trigger. On a machine with a Copilot device policy (HKLM\SOFTWARE\Policies\GitHubCopilot), the runtime runs a managed-settings refresh about every 60 minutes. The log shows this sequence:

[managedSettings] self-fetch
session.managed_settings_resolved
mcp graph load: reload {"force":true}   (policy_already_applied: true)
full replace_host path

About 4 seconds later every extension in every session relaunches and joins again, so the plugin skills disappear again, also in idle sessions. Honestly I feel like this explains the "healthy at first, degraded later" pattern in github/copilot-cli#2753. The policy did not change between refreshes, so the forced host replace looks unnecessary to me. I have not checked whether machines without a device policy do this too.

What did not work. joinSession({ enableConfigDiscovery: true }) keeps the plugin skills, but the extension then relaunched about 35 times in 80 seconds and the plugin list changed from 17 to 14 plugins.

Contrast. A standalone runtime of the same version, with an isolated home directory, did not lose plugin skills on join. My guess is that the resume that a join sends rebuilds the skill catalog without a discovery source that the desktop host depends on, but I have not confirmed that in source, so please treat it as an inference.

Workaround. Calling this from an extension a few seconds after each join restores the plugin skills within a few seconds:

await session.rpc.plugins.reload({
  reloadMcp: false,
  reloadCustomAgents: true,
  reloadHooks: false,
  reloadExtensions: false,
});

It is a band-aid, because the next join removes the skills again. Also, when many sessions relaunched at the same time (the hourly refresh), some of these reloads took longer than 35 seconds.

Impact. Plugin skills can be missing from the first prompt, after any extension relaunch, and about every hour. plugins.list() still looks complete, so the loss is hard to notice.