Unfortunately it's been kind of hodge-podge thus far, but there are a couple stickies in this very sub-forum that might help you get started. Alex has also posted two example mods I believe, that are probably still valid to illustrate how to add basic ship hulls, variants and missions. I would start by looking at the structure of the existing game data in starfarer-core. All mods follow the same structure, and at load-time are loaded on top of the core data and so can add to or replace any file in core.
Far and away, the bread-and-butter of most mods is the ability to add ships; these are represented by *.ship files. They go in [mod]/data/hulls/[yourship].ship Think of .ship as a hull definition; i.e., here's a ship, here's the picture to use, here's its bounding polygon and weapon hardpoint locations etc.
Every usable ship though also needs a .variant file (such as [mod]/data/variants/[yourshipsvariant].variant ), which defines very little apart from the loadout associated with a particular .ship. A variant puts weapons on the hull, and a few other things.
One other things is necessary before the game will recognize your ship, and that is to add the balance stats row for your hull in [mod]/data/hulls/ship_data.csv.
You can also add standalone missions, these are pretty simple. Look in starfarer-core/data/missions/ and If you know a bit of java, it'll help, but look at the existing missions for this. There's an api .jar you can load if you use an IDE.
Most folks want to add campaign content. This is somewhat more involved, but usually takes the form of adding a custom faction. You need two main things for this: a faction definition, which tells the game about its fleet configurations to be found in the wild, and random seeds for generating them. And some string data. With your faction definition in hand, you have to write them into the sector gens, also somewhat involved depending on how you want them to spawn. I think generally you spawn them at an entity like a planet or station, and setup their attitudes toward other factions and bam done.
To go even further it is possible to add custom weapons and sounds as well.
