Bumps the registry generation, so that extension API objects captured by old code signal
gptr_error_stale_api, and re-declares lazily activated plugins from their manifests (their
factories run again on first use). Discovery of declarative resources (skills, prompts, agents,
MCP configurations, plugin manifests) is keyed on the generation, so it runs again on next
use. Sessions whose prompt is already frozen are not changed. Refused from model code while a
run executes a tool, unless the user approved that call.