I've modified the components.js file I found under the theme folder to include a js file but it is not being included in the deployed index file.
Here is the output of the deployment, my file is sitting in the themes folder called mycustom.js:
{"files":{"css":["lib/bootstrap/css/bootstrap.min.css","mxclientsystem/mxui/ui/mxui.css","styles/css/lib/lib.css","styles/css/custom/custom.css"],"js":["mxclientsystem/mxui/mxui.js","mycustom.js"]},"cachebust":"636380598526532366","downloadResources":false}