I use PHP Storm too but ironically my dev tools are a XF add on so my tools use their REST API to minify on the fly as the add on is exported and it's files are packaged up.
My add ons (starting with XMG 2.1) are all going to contain the full and minified versions. The full runs with debug mode on. The min versions run in normal operation. That's all controlled by a custom template helper and also generates a separate cache buster to the default XF one based on the add on version ID and the XF JS version debug option value.