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Is there a difference between the corebook presented here, and the free version?

(+2)

The core book has all of the information for game runners, with NPC character sheets,  advice and rules for running cmpaigns, and extra information about the game's setting to help tell the story.

To play, you'll need the GM to have this book, but the players only need the free book to learn how to play, build their character, and learn enough about the setting to enjoy the game

In addition to what Gaeel said, purchasing this version also gives you the .lcp files for the NPC mechs for use in COMP/CON. And it appears that mech token images have been recently added to the downloads here too :)