If you are new to MobileFrontend then is a great task to start on and get familiar with it!
Now that the resources files have been moved to the resources folder, it makes sense to change old module names too. For example, modules/search/SearchApi should be renamed to mobile.search.api/SearchApi, etc. (the text before the / is the name of the ResourceLoader module and the text after it the name of the class).
Old names should be deprecated like
M.define( 'mobile.search.api/SearchApi' ).deprecate( 'modules/search/SearchApi' )
Be careful to correctly deprecate modules as some other exntensions may be using them.