[nicobailon]

After an extension unload removed the subagent tools and a later compaction ran, a session resumed with neither subagent nor subagents_enable, and restarting or forking it didn't help (#3198). Pi stores a checkpoint of the declared tools at compaction, and the activation replay read that checkpoint. The unload before it was folded away, so the existing unload recovery never ran.

When the compacted context starts with a checkpoint, the replay now reads the branch's system messages from before the latest compaction instead, the same history Pi core restores tools from. Without a compaction, sessions already behave this way.

Unchanged: a compaction without a checkpoint is still decided as a new session; tools you removed yourself stay removed; a session that never declared these tools gets nothing added; intact sessions make no new tool change on resume.

A fresh review checked this against real Pi 1.5.0 SessionManager sessions: two compactions, a kept range starting at a system message, a cold session, an unload that was later re-added, and a deliberate removal all give the same result as before. The new test fails on main.

Closes #3198. Thanks to @chuducandev for the report and the synthetic repro.

[greptile-apps]

Confidence Score: 5/5

[Medium impact] No blocking code defect was identified; merge readiness still requires confirmation of exact-head CI.

Summary

Restores tool selections hidden by a compaction checkpoint by replaying earlier system messages from the current branch.

• Compacted sessions restore subagent tools that an extension unload turned off.

_{Reviews (1) · Last reviewed commit: "fix(tool-activation): restore tools an u..." · Reviewed by Greptile}