This is a quick, basic guide on how to mod Black Geyser.
No special skills or programs required, just Notepad++, WinRAR and some attentiveness to syntax.

I will not spell out everything: this guide is for showing the method, rest is up to you.

Kudos to user wendigo211 for the idea that started the ball rolling.

I. General modding method

1. Go to your steam library Black Geyser folder
   
   
2. Make a backup copy of data.bgd
   
   
3. Rename data.bgd to data.rar, and open with WinRAR
   
   At this point, you can unpack the entire archive to your hard drive, and explore it. I did it just to learn the structure and browse the files more easily, as well as have backup individual files. However, for changes to appear in game, the altered files need to be packed back into the archive. I found it easiest (and fastest) to edit files straight from the archive, saving them when done.
   
   
4. Once you find the file you want to edit (more on specific files below), open it with Notepad++ and change what you want. Be very careful with the syntax - keep the same structure, any mistake will make the game hang up on launch (but that's why you have backups).
   
   
5. Save the changes in Notepad, then save changes in WinRAR to the archive
   
   
6. Rename the archive back to data.bgd
   
   
7. Launch the game, changes should be in game

Be aware that every time the game updates data.bgd, your mod will be overwritten. So be prepared to add it again (by keeping some copies of edited files, or just knowing what to change and where).

Now to specifics:

II. Class and starting equipment modding

1. Follow the guide in Part I to open the archive
   
2. Classes files are - surprisingly - in the "classes" folder, races are in "races"
   
3. Open the relevant file (e.g. necromancer.cla) and edit to your heart's content.

It's pretty self-explanatory once you see the internal file structure. Some stats are simply numbers that can be increased or decreased. New abilities, proficiencies etc. need to be written in - the best way to do so is by copying from another class which has these abilities. E.g. you can copy heavy armor proficiency from fighter to necromancer this way, by expanding the node "UsableArmors" like this:

"UsableArmors":[
{
"Type":"BGModel.RuleSystemNS.UsableArmorEntry"
},
{
"ArmorType":"Medium",
"Type":"BGModel.RuleSystemNS.UsableArmorEntry"
},
{
"ArmorType":"Heavy",
"Type":"BGModel.RuleSystemNS.UsableArmorEntry"
}
],

Be aware that sometimes it's necessary to edit not one, but two or more nodes in different places to make it work. E.g. to add heavy armor to a necromancer (or any wizard class), in addition to editing the "UsableArmors" node, you'd have to remove the node "ExplicitlyDisabledMulticlassArmors".

You can also add starting equipment in the relevant section of the file, although for adding items it's quicker to just use the developer's console (however, that may be immersion-breaking to some).

This way you can tweak abilities, spells, skills, usable armor and weapons, and many more aspects of both classes and races. Ever wanted a non-Human Templar/Wintermage? Or a full-plate wearing, greatsword swinging, necromancy casting Death Knight? All possible.

III. Companion modding

Foreword: you have to do it BEFORE meeting the companion. So if you want to mod everyone, then do it before starting a new game, or while still at the prologue Estate. If you've already met/recruited some of the companions but not others, only the latter will be moddable.

1. Follow the guide in Part I to open the archive
   
2. Go to data/creatures and find the companion *.cre file (e.g. Jade_TheNecroGoth.cre)
   
3. Open the file with Notepad++ and edit what you want (the CRE file allows to alter race, sex, appearance, portrait, sound set and basic items)
   
   
4. Save changes to the file and to the archive
   
   
5. Go to data\initial_state\entities\creatures\ and find the companion *.iscr file (e.g. Jade_the_NecroGoth.iscr)
   
   
6. Again, open the file in Notepad++ and edit to your heart's content (the ISCR file allows to alter stats, class, proficiencies, skills, and abilities)
   
   
7. Save in Notepad and in WinRAR, close all files
   
   
8. Rename data.rar back to data.bgd
   
   
9. Start game, go meet the companion and recruit them, they should have new stats.

If anything bugs out, just revert to the backed up original data.bgd and start over.

Using this method, I turned Jade into a Fighter/Necromancer (which allowed me to finally get rid of Siracca and made Jade immensely more fun).

This can be used to make good companions better, to make utterly worthless companions playable, or simply to compose your "dream party" while still retaining companion personalities and personal quests.

There may be some limits to the edits (e.g. I was unable to successfully add Abolish Curses to a class that didn't have it, but whether it was due to some syntax mistake or a hard-coded conflict is unclear). But most of the important things seem to be editable. Finally, we can have sensible stat allocations and good race/class combos for companions. Enjoy!

IV. Portrait modding

Replacing your portrait after you've already started the game

It's possible (and quite easy) to change the in-game main character portrait, IF you're using a custom portrait (as you should, as the ones offered by the game are fugly). All you have to do is replace the relevant files in your "portrait" folder (the ones you put there for a custom portrait) with new ones, and voila - your character will have a new portrait when you next load the game. I have tested it, and it works.

It should ALSO possible to change a non-custom portrait, but that will require some more effort.

The portrait references are located in data.bgd in your main game folder (steam/common/Black Geyser). Rename the file to data.rar and open with WinRAR (back up original first), then browse to data/portraits, where you will see a whole lot of portrait reference files (*.por). These are not the actual portraits, but point towards them. You can open these files in Notepad++ and edit the references. Example:

Open data\portraits\elf_01.por
Edit the following lines by changing the 1 at the end to 2
textures/ui/portraits/loadgame/CharacterGen_variables/ELF/40x50_1
textures/ui/portraits/mainframe/CharacterGen_variables/ELF/80x100_1
textures/ui/portraits/characterInfo/CharacterGen_variables/ELF/100x125_1
textures/ui/portraits/inventory/CharacterGen_variables/ELF/182x216_1

As a result, the "elf_01" portrait should switch to "elf_02".

You will have to experiment to find the exact portraits you need, and I have not actually tested if this works in game, but feel free to try it out.