Resource precedence for extensions, skills, prompts, themes, and slash-command name collisions is now project-first (cwd/.pi) before user-global (~/.pi/agent). If you relied on global resources overriding project resources with the same names, rename or reorder your resources.
Extension registration conflicts no longer unload the entire later extension. All extensions stay loaded, and conflicting command/tool/flag names are resolved by first registration in load order.