Deleted resources are not being removed from `.scala-build` and the classpath

[jchyb]

Version(s) 0.1.2, also on e968a10797b2a14b835c6555ffc6c3d7aad14b10

Describe the bug When --resource-dirs option or using directives is used resources are copied to the project directory in .scala-build, which is then put on a classpath. If the resource will then be deleted (or have it's name changed) and the project recompiled, the previous resource will not be removed from the .scala-build and can still be used in the program.

To Reproduce

reproduction/main.scala

//> using resourceDir "resources"

import java.nio.charset.StandardCharsets
import java.io.{BufferedReader, InputStreamReader}
import java.io.FileInputStream

@main def main(): Unit =
  val inputStream = getClass().getResourceAsStream("/resourcefile.txt")
  val text = new BufferedReader(
    new InputStreamReader(inputStream, StandardCharsets.UTF_8)
  ).readLine()
  println(text)

reproduction/resources/resource1

resource1

1. Run scala-cli project
2. Remove project/resources/resource1 file
3. Run scala-cli project

Expected behaviour Deleted resource files should be removed from .scala-build, and resource files with changed filenames should not be duplicated there - instead the previous version should be removed.

[jchyb]

I imagine this is caused by the copyResourceToClassesDir in Build.scala, but I would rather not attempt at fixing that yet - I imagine the solution would be manually walking through the .scala-build directory and removing files that are neither source nor resource, but with the recent additions (native-image) I'm unsure what exactly would constitute a source (besides the obvious class, scala, tasty, nir, sjsir)