I don't really care that it changes when the user manually makes updates to skills or MCP servers. I do however care that it changes with the current date and the current working directory. Note that it includes both the project directory and the current working directory. Any time a command is run that changes the working directory and doesn't change it back, the whole transcript has to be reprocessed. Other stuff like CLAUDE/AGENTS.md being re-read from scratch each turn I'm still not a huge fan of, but it's not as big of a problem.

IMO, the system messages should not change retroactively during the normal course of the session, only with the agent configuration. That does include skills and tools and etc., but should not include anything like the current working directory, which can change constantly during a session!