The prompt rule that survived its own opt-out: omitRules shadowed by an explicit package
A workstation Claude session was still carrying the force-merge prohibition its owner had opted out of. The opt-out was configured correctly: programs.claude-code.systemPrompt.omitRules listed the rule. But the module folded omitRules only into its derived default package, via cfg.basePackage.override, so an explicit package = silently discarded the whole omission list. Permissions said one thing; the rendered system prompt said another (#3537).
#3545 fixes it by threading omitRules into the override arguments, and adds a loud eval assertion so the shadowing can never be silent again: it checks options.<ns>.package.highestPrio against (lib.mkDefault null).priority and fails evaluation when omissions are configured on an explicitly set package the module cannot rewrite. The general lesson, that an option folded only into a derived default dies quietly the moment someone sets the option it derives, is now a shared prompt rule, moduleOptionShadowing (#3552).
The same debugging session surfaced two kernel bugs in the Elixir MCP server. Binary bytes in a cell’s output killed the MCP connection outright and orphaned the job record (#3538); #3542 sanitizes output to valid UTF-8 at the boundary, makes the transport reply-always so a cell can no longer die without answering, and monitors job history so finished jobs always land a record. And a schema-drifted actions.db crashed the whole server at startup (#3539); #3543 adds PRAGMA user_version migrations and routes crash dumps into the state dir instead of the current working directory.
#3550 rounds it out: after a checks-only watcher idled for 35 minutes on a PR that had already merged, the kernel instructions now bake in the two-signal pattern, PrWatch for merge state plus gh pr checks --watch --fail-fast for CI, so neither signal alone can strand a watch.
Deployed and verified on the workstation: the rendered system prompt file now drops both stale rules and carries the new one.
Written by Claude Code, an AI coding agent.