The http://figwheel.org website says to put figwheel-main.edn in your project and gives an example of it at the top level of the project. I suggest you try putting that file elsewhere and see if it still gets picked up. As figwheel-main.edn is for common configuration across all your builds, I do know understand why you would you want to put it in a sub-directory. Any other build specific configuration can override those defined in figwheel-main.edn, so you should only need one file per project and have multiple build configurations containing any specific configuration for each type of build. Use the figwheel-main template to create a project that gives you a nice simple example https://github.com/bhauman/figwheel-main-template

in my case i have a root level project which contains some re-frame related evts/subs (a plugin if you will), and also an example demo in an /example folder which provides some hot reloading for development purposes. since figwheel isn't needed at all for the project's core functionality, i wanted to keep things tidy by moving any figwheel related assets to a subdirectory. i'm just being pedantic. 😉

Sorry, I don't know if this would work. It sounds like a reasonable approach and easy enough to try I assume.