[Bug] New sessions created after launch bypass agency_mode until app restart

[tjegbejimba]

Short summary

When the Copilot desktop app is launched with agency gh-app, sessions restored during app startup use Agency, but sessions created afterward bypass Agency and launch copilot.exe directly. The new session does not receive Agency plugin directories or MCP configuration until the entire app is quit and relaunched.

Affected version or release

Observed on 2026-08-13 on Windows. The exact desktop app build was not captured during the investigation. Copilot CLI version: 1.0.79-9.

Installation context

GitHub Copilot desktop app on Windows, launched from a terminal with agency gh-app. Agency was enabled in the app settings, with external plugin directories and generated MCP configuration.

What happened?

Process ancestry and command lines showed two different launch paths:

• A session restored when the app starts uses github.exe -> agency.exe -> copilot.exe. Its copilot.exe command line includes the external plugin directories and --additional-mcp-config, and the Agency-provided tools are available.
• A new session created after the app is already running uses github.exe -> copilot.exe. There is no agency.exe parent, no external plugin directory arguments, and no Agency MCP configuration, so Agency-provided skills and tools are unavailable.

The same newly created session works after fully quitting the app (including the tray process), relaunching with agency gh-app, and reopening that session. At that point it is restored through Agency and receives the expected plugins and MCP configuration.

Steps to reproduce

1. Enable Agency in the Copilot app settings.
2. Fully quit the Copilot desktop app.
3. Launch it from a terminal with agency gh-app.
4. Confirm that a restored session runs as github.exe -> agency.exe -> copilot.exe and has Agency-provided plugins/tools.
5. While the app remains running, create a new project session or chat.
6. Inspect the new session backend process ancestry and command line.
7. Observe that it runs as github.exe -> copilot.exe without Agency plugin or MCP arguments.
8. Fully quit and relaunch with agency gh-app, then reopen the same session.
9. Observe that the restored session now runs through agency.exe and receives the Agency resources.

Expected behavior

When agency_mode is enabled by agency gh-app, every session backend launched by the app should use the Agency launch path, including sessions created after startup. Restored and newly created sessions should use the same process factory and receive the same plugin directories and MCP configuration.

Additional context

The current workaround is:

1. Create the session.
2. Fully quit the Copilot app, including its tray process.
3. Relaunch with agency gh-app.
4. Reopen the session.

Agency's launcher enables the desktop feature and starts github.exe; it does not remain as a supervisor for future app subprocesses. The app is therefore responsible for routing each session backend through Agency.

Related but distinct issues found during duplicate search:

• [General] Internally we use Agency, and we use it on the GH CLI, it would be good to so... #54 added initial Agency support and was closed with the guidance to run agency gh-app.
• [Bugs] agency_mode per-request spawn times out with many MCP servers (~2.5s deadline too tight) #1012 covers agency_mode per-request startup timeouts with many MCP servers.
• [Bug] 1.1.3 session repair health checks fail during concurrent CLI startup timeouts #2565 covers concurrent CLI startup timeouts and restored-session repair health checks.

None describes the create-vs-restore launch-path split above.