Running module in IDE says module not found

[xkr47]

ceylon run: Module test/1 not found in the following repositories:
 /home/xyz/.IdeaIC2016.2/config/plugins/CeylonIDEA/classes/embeddedDist/repo
 /home/xyz/.ceylon/repo
 /home/xyz/.ceylon/cache
 https://modules.ceylon-lang.org/repo/1
 [Maven] Aether
 [NPM] NPM

However, I noticed that the test.iml file was located in the .idea/ subdirectory instead of the project root directory as it usually is. Moved the test.iml file to the project root directory and updated references in .idea/modules.xml manually, reopened project => problem fixed!

So to reproduce, reverse my fix procedure. Don't know how my project's iml file ended up in the .idea/ directory in the first place though..

[bjansen]

I fixed it by setting the working directory to "the parent folder of modules" instead of "the parent folder of the .iml file".