Here are the most common methods you can use to manage modules:
reloadAll() : Reload all modules in the application. This clears out all module settings, re-registers from disk, re-configures them and activates them
reload(module) : Target a module reload by name
unloadAll() : Unload all modules
unload(module) : Target a module unload by name
registerAllModules() : Registers all module configurations
registerModule(moduleName,[instantiationPath]) : Target a module configuration registration
activateAllModules() : Activate all registered modules
activateModule(moduleName) : Target activate a module that has been registered already
getLoadedModules() : Get an array of loaded module names
rebuildModuleRegistry() : Rescan all the module locations for newly installed modules and rebuild the registry so these modules can be registered and activated.
registerAndActivateModule(moduleName,[instantiationPath]) : Register and Activate a new module
With these methods you can get creative and target the reloading, unloading or loading of specific modules. These methods really open the opportunity to build an abstraction API where you can install modules in your application on the fly and then register and activate them. You can also do the inverse and deactivate modules in a running application.