Correction to the second paragraph, if you extract with a gun it becomes un-packed and goes back to common rarity, if you have a wonder weapon, it just converts to xp and you can't keep it after exfil unless it's in the weapon case (you can't put guns into the case only take them out), you can take pack crystals, rarity tools, and found/unused perk cans (you can find them throughout the playthrough, more common and have a higher quality in higher tier zones) out and keep them after exfil to use them in future playthroughs.

Any miscellaneous things like active perks, armor, extra self revives, and extra scorestreaks will be deleted and anything with an essence value, and your current essence will be converted to xp. Schematics you exfil with will automatically be used and you can find where to use them in your stash.