The issue is that Brunch has special handling for assets. They are treated differently from the files you wish to compile - copied as-is into your public directory.
The simplest way to solve the issue you're describing would be to move that coffeescript somewhere else under app
, but not in assets
.
Alternately, you could reconfigure what is treated as an asset in your brunch config under conventions.assets
. https://github.com/brunch/brunch/blob/stable/docs/config.md#conventions