When using the Kanela runner it behaves a bit differently to other runners as the settings are not scoped correctly. The settings it uses such as baseDirectory should be scoped to Compile/run.

For example, if I set:

run / baseDirectory := "foo"

Then the Kanela runner will not use this and instead it will use baseDirectory which by default is the project base directory.

The settings used in kanelaRunnerTask are mostly raw which is good it's just where they are used in projectSettings is where the scoping problem is.

See how sbt does it:

https://github.com/sbt/sbt/blob/ce59ea754a12709a978ac1f54306a81c6c6d68d7/main/src/main/scala/sbt/Defaults.scala#L2582

inConfig(Compile)(compileSettings)

https://github.com/sbt/sbt/blob/ce59ea754a12709a978ac1f54306a81c6c6d68d7/main/src/main/scala/sbt/Defaults.scala#L994

inTask(run)(runnerSettings ++ newRunnerSettings)

The workaround is fairly straight forward:

inConfig(Compile) {
  inTask(run) {
    runner := SbtKanelaRunner.kanelaRunnerTask.value
  }
}