Thread-only tool pre-approvals are held back when the tools are not a thread's

Claude Code can pre-approve certain tools so they run without asking you for permission. Some of these pre-approvals are meant only for a conversation thread. The part of Claude Code that handles project replies over the bridge connection used to pre-approve every tool on its auto-allow list. It now watches the list of MCP tools (tools supplied by outside programs). When those tools do not belong to a thread, it holds back the thread-only pre-approvals and logs a note saying so.

The approval rules are also applied as soon as this reply handler starts, rather than later.