Interactive autopilot stops after 600s while a background subagent is still running (regression in 1.0.102) #5223

Describe the bug

Since 1.0.102, interactive autopilot stops whenever a background subagent runs for more than 600 seconds. The subagent is still working normally when this happens. The CLI shows:

Autopilot stopped after 600s waiting for background tasks. Set COPILOT_TASK_WAIT_TIMEOUT_SECONDS to change the limit.

A common pattern is for the main agent to start a background agent (for example, to implement part of a feature) and then end its turn to wait for the result. Any subagent that needs more than 10 minutes now ends the autopilot run, and I have to continue it manually.

This worked in 1.0.101 and 1.0.100. The 1.0.102 changelog doesn't mention any change to this behavior, so it looks unintended.

Affected version

1.0.102

Steps to reproduce the behavior

1. Start Copilot CLI interactively and turn on autopilot (/autopilot or shift+tab).
2. Give it a task where the main agent starts a background subagent (task with mode: "background") that takes more than 10 minutes.
3. Let the main agent end its turn to wait for the subagent.
4. After 600 seconds, autopilot stops with the message above, even though the subagent is still running.

Expected behavior

Interactive autopilot keeps waiting for in-flight background agents and continues when they finish, as it did in 1.0.101. If a cap is needed, a running subagent that is making progress shouldn't count as stuck, or the cap should be opt-in for interactive sessions.

Additional context

• In 1.0.101, COPILOT_TASK_WAIT_TIMEOUT_SECONDS / autopilot_background_timeout appear to apply only to prompt mode (-p). In 1.0.102 the native runtime adds new autopilot continuation logic, and the stop message and autopilot_background_timeout warning first appear there.
• Workaround: export COPILOT_TASK_WAIT_TIMEOUT_SECONDS=3600 (or higher) before launching.
• The limit can't be turned off. COPILOT_TASK_WAIT_TIMEOUT_SECONDS=0 gives a 0 ms wait, not an unlimited one. Negative or non-numeric values fall back to 600 s.
• Related but different: Autopilot background-task timeout exits active parent after subagent completes #4628 (prompt mode on 1.0.80, closed).