Workflow setup

Struggling with the project setup.

My folder setup:
/src    => Source from which I compile my code 
/dist   => Compiled code that I upload to my Google App Engine

With a Gulp script I compile my code with task like handlebars to implement my language specific string, minifying several data and compiling some other stuff. This works great. Especially as I can compile it for my test environment, which is easier to debug as code is not minified and my debugging system is enabled. 

Now my problem is that I have a src folder where I need to code and the dist folder which I need to run my code and test if everything works like expected. Now I can exclude my dist folder so PHPstorm does not tell me that there is duplicate code etc etc. But that does not solve the workflow issue where I need to code (/src), run Gulp, run my compiled (/dist) code, test it and fix my source code (/src).

Is there any way to handle this? I have looked but I could not find a manual or advise. Can someone guide me in the right direction or give me a bit more insight?