Great success!

Apparently I could simply add the file to the module.config file, like so:

<add name="epi-cms.widgets.base" path="my/modified/version/of/a/dojo/file.js" resourceType="Script"/>

And it will be used instead of the original function, I assume because the dojo system only load one "define(..." once, and mine is loaded before the original (in widgets.js). Though I fear this can sometimes break depending on the order the files are loaded.

This could lead to multiple define errors in the AMD loader. A better approach would be to use an alias. This is a bit of configuration in the module.config that says run my file instead, e.g.:

<?xml version="1.0" encoding="utf-8" ?>
<module>
  <dojo>
    <packages>
      <add name="my-app" location="ClientResources" />
    </packages>
    <aliases>
      <add from="epi-cms/widget/FileList" to="my-app/FileList" />
    </aliases>
  </dojo>
</module>

Nice, this seem like a cleaner approach.

Can you register a dojo alias programmatically?

Edit: Ah, I seem to be lost anyways on what exactly I should set. Could you possibly write up a complete modules.config example to replace:

[version]\ClientResources\epi-cms\widget\FileList.js

with

/ClientResources/myapp/FileList.js

The files will be identical, im just trying to understand exactly how the aliases work here.