I had a similar problem recently with Grunt when building my AngularJS app. Here’s a question I posted.
What I ended up doing is to explicitly list the files in order in the grunt config. The config file will then look like this:
[
'/path/to/app.js',
'/path/to/mymodule/mymodule.js',
'/path/to/mymodule/mymodule/*.js'
]
Grunt is able to figure out which files are duplicates and not include them. The same technique will work with Gulp as well.