As a rule of thumb, if it's code written by you or someone on your team, it does not belong in this folder.  Instead, assets/dependencies/ is for your client-side dependencies such as Vue.js, Bootstrap, or jQuery.  This folder can include client-side JavaScript files, stylesheets, and even images.  (See the "Web App" template for an example.)
JavaScript files and stylesheets in the assets/dependencies/ folder are loaded first, before your other assets.  This conventional behavior is orchestrated by tasks/pipeline.js, so head over there if you need to tweak this behavior (for example, if some of your client-side dependencies need to load before others.)