Sponge has several services, which are interfaces all plugins can access but are actually implemented by another plugin. A good analog would be the economy service compared to Bukkit’s Vault plugin - a global interface for economy, so any plugin that requires an economy can interface with any plugin that provides an economy without either knowing the other exists. Permissions are done the same way. The default implementation of the permission service is very simple - the op system. If you’re an op, you have all the permissions; if you’re not, you have none. If you install another permissions system, such as LuckPerms, then you configure your permissions through the plugin, whatever system that happens to provide. LP in particular is designed to be edited through in-game commands, but one of its storage options is a text file, so you can still edit that directly if you want.
As for fire spread, for a simple solution you can do /gamerule doFireTick false, which will prevent fire spread or burning but will also prevent fires from going out. Alternatively, since you’ll probably end up using a protection plugin anyway, I know UniverseGuard has a flag for fire spread.