All files and folders starting with a "-" are ignored by the game. This helps with quickly disabling files by just renaming them.
Content is added by creating FileData.
Mod specific documentation can be found in the ModFileDatas end text of the given mod (if available). This text can be viewed in the "Mods" menu in the "Main Menu". Right clicking the mod will give a bigger view of the text.
You can look at base mods for examples.
If enabling "Debug > General Debug Enabled" (advanced options) the Tools menu will appear in the start menu. It also changes things ingame, like skip the intro.
General concepts:
Concept Introduction