1) Where do i write ship descriptions, nothing in the csv or the .ship file.
You'll need to make a descriptions.csv file in a strings folder in data.
For example: C:\Program Files (x86)\Fractal Softworks\Starfarer\mods\<YOURMOD>\data\strings\descriptions.csv
Easiest thing to do is copy what's in the core files and just remove everything but the title row and work from there with your stuff
2) Does the game automatically compile the .java files in .classes when it runs?
I don't think the classes are needed for custom things, at least I've never had any trouble without them, should be safe with just the .java stuff you've written
3) If i wanted to modify certain aspects of ship systems besides what's offered in the CSV, would i need to decompile/recompile the scripts, or just introduce values in the .system files? I'm seeing functionality placed all over from the CSV to .system to .class, with graphical options limited to .systems. Technically i would be interested in modding for example the fortress shield to give a speed buff aswell.
Not entirely sure on this one, I'll be honest, but I'd guess you would just have to chuck some of the burner lines into your custom fortress shield system, namely these lines
"accelerationBonusFlat":800,
"accelerationBonusPercent":800,
"decelerationBonusFlat":0,
"decelerationBonusPercent":0,
"turnAccelerationBonusFlat":0,
"turnAccelerationBonusPercent":400,
"speedBonusFlat":50,
"speedBonusPercent":50,
"turnRateBonusFlat":0,
"turnRateBonusPercent":50,
Again, not 100% on this one
4) How much if at all does 'weight' affect handling?
Not sure if it does. I was under the impression that it was more to do with ship to ship collisions as to which one "wins out". Someone else may shed more light on this, I have little-to-no experience with the weight system
5) I'm seeing some times that the game ignores the boundaries and uses the collision radius, when and why does that happen? I'm having issues with long ships that if i set the radius too small, asteroids sometimes get 'inside' the ship boundaries before rebounding of the collision. Also, if i'm not mistaken, that's also used by fighters, so if i put the collision bigger than the shield coverage, i assume fighters would bypass the shields per se?
Can't say I've noticed that happening at all, so I can't help you there I'm afraid
6) Could i define a different 'center' of a ship to be used for movement and another for collision? I'd like to get some ships the feeling that they handle more like a front-wheel-drive car rather than a 4x4.
The centre variable should be enough for that. As long as the collision covers the entire ship, it doesn't matter how much it goes over one of the sides IIRC
7) Can i set-up a certain command parameter to automatically load a mission or ideally the simulator? I'm seeing a lot of back and forth in playtesting and balancing my ship/s with me starting up the game, selecting missions, going to my test mission, selecting Refit and then finally 'Simulate'
You could use devmode, which means changing the third line of the settings.json in the config folder to true. It adds a simulate thing to use
Hopefully that's helped you slightly, though there are some things that I'm still unsure about, so I apologise if I didn't help there