How do I equip my crew? How do I know what all the traits, jobs, and equipment does? Can I switch jobs on my crewmen? Certain times clicking on my entire crew in a cluster will give orders to the captain only, other times it's to the entire crew. What's the difference between those? Why did my crew level up during travel time when nothing else was happening?
You don't equip your crew, that functionality doesn't exist yet. They use the weapons they spawn with, and that's it. I don't think traits do anything yet, they're just there as a placeholder. Equipment stats can be viewed when mousing over the equipped item when your captain is holding it (the only intentionally selectable pirate at this time). As for jobs, you basically just have to know or guess what each job is supposed to do. You cannot switch jobs on anyone. Right-clicking is used for issuing orders to your crew via the pop-up menu, and will issue orders in an area around where you clicked, left-clicking is used to tell the captain.
Traveling experience is just there because they're out living the piratical life and doing something, and therefor gaining experience. It lets your otherwise not-particularly-fighty crewmen get experience in your crew without having to kill people that often.
Sometimes I click around to explore on a friendly island and my captain randomly stabs someone, then gets mauled and dies.
Left-clicking will tell your captain to either move to the point clicked, or attack any non-crewman person standing at that point. If, when you click, the little confirmation circle is red instead of green, you know you issued an attack order. Try clicking a bit above the heads of people if you want to move through a crowd.
Does food have portions or duration? If yes, how many or how long? (I read "nutrition value" as how long after eating it takes to get hungry again, not how long the food itself lasts)
Yes, food has a certain amount it fills before it gets used up. Food that isn't eaten does not appear to spoil on its own. Now quit reading "nutrition value" that way and read it the proper way! (hunger increases at the same rate regardless of what type of food was eaten, a food's value just determines how much of it can be eaten before it disappears)
Why do some of my crew run past a fight already in progress, to go pick another fight? There doesn't seem to be a limit to how many people can be fighting at once, so why did they ignore one fight and go start another?
When first attacking, crewmen will default to one-on-one combat with the enemy, rather than everyone lumping up on the same guy and butchering him. Any crewmen "left over" will then find someone to gang up on. This makes the number of combatants actually fairly important, as even a small size difference between forces will have a compound effect. Note that you appear to have some greater amount of control in deciding who your captain fights with, and he will occasionally listen to you if you single out specific opponents for him to slice.
EDIT: Found another something that needs fixing. If you have some type of food that needs preparing, a cook may come and start preparing it but get distracted before he gets very far. This leaves it with a very low "food" rank and a very high "stock" rank, as one would expect.
However, if a pirate takes a bite of it when it's in that state, when the "food" bar is empty the item is removed, ignoring the remaining stock.
EDIT2: Cannons, tables, sails and masts all cost 0gp to purchase, whereas bowsprits cost some 198gp per section. A stack of 5 bombs costs 98, making cannons prohibitively expensive both in money and space to use "normally". Also, if you have multiple cannons, the cannoneer will keep reloading the first one until all others are loaded... Which, naturally, doesn't happen. So, he ends up stacking one cannon full of 10+ shots which he will then fire (one at a time, thankfully/sadly) at the enemy in the next combat.
Thanks for putting in the safeguard that makes them stop shooting if the enemy is on your boat... That's very highly appreciated. It'd be nice if that extended to enemies that are in the process of grappling over to your boat, when they are impossible to hit.
EDIT3: Aaand now I've run into a strange bug where my save file apparently keeps getting reset. So the extended ship I *did* build (twice now) is gone, as is my treasure and experience. I'm not entirely sure what causes this, but I think it might have something to do with exiting/reloading the game to fix locked travel scenes.
EDIT4: Yep, there is some SERIOUS savegame weirdness going on here. I'd just tricked out my ship with a couple expansions, and while doing a back-and-forth dance with the bombs in order to get the brand new cannons properly loaded, I accidentally hit the "exit game" button. I loaded the file right back up again, and found that I was back in the old unexpanded boat with none of the spare parts I had, the 2gp I had left over from buying the parts, and suddenly I was located at a port with two shops (thus not the port I *had* been parked at) with nobody manning them.