@IXix
Limitation 2 just means that ReaPack won't accept to put stuff in C:\WINDOWS nor anywhere outside of <REAPER resource path>/Effects/<repo name>/ (for an effect package).
About the .jsfx extension, even if I add support for extension-less files, it might still break existing projects (or custom/cycle actions for ReaScripts) if ReaPack's install location differs from where the user put them before.
In my opinion this would be the best solution for that:
http://forum.cockos.com/showthread.php?t=53820.
@G-Sun
ReaPack v0.9 is incompatible with previous releases (I don't enforce backward compatibility since it's beta and things change frequently):
Delete <REAPER resource path>/ReaPack/registry.db and restart REAPER (note that this makes ReaPack forget anything it previously installed).