It's not so much of an upgrade: Clippings had to be rewritten to be compatible with Firefox 57 and newer, which imposes new requirements for Firefox add-ons. Some features like the shortcut key list and colored labels didn't make it into Clippings 6, but will be considered for upcoming releases. I will continue to monitor feedback from other users before deciding on what to do with the search functionality in Clippings Manager (I assume this is the "search tool" you were talking about).
All those permissions are needed for Clippings to function. Go to the following page to learn more about the meaning of those permissions, and why they are needed: http://aecreations.sourceforge.net/clippings/permissions.php