metals reports "best effort mode" error on nonexistent files

[scarf005]

Expected behaviour:

code compiles without errors, but a lot of errors doesn't seem to make sense for me.

for example: source file not found: /run/media/home/scarf/repo/aoc-scala/prelude/Boolean.scala but the file isn't referenced anywhere.
https://github.com/scarf005/aoc-scala/blob/877b652e571e2fa691a11641e8a0cdc374711c50/prelude/Boolean.scala

Operating system:
Linux

Java version:
23.0.1

Editor/extension:
Visual Studio Code v1.95.3

Metals version:
1.4.1

Extra context or search terms:

reports.zip
repo in question: https://github.com/scarf005/aoc-scala/tree/877b652e571e2fa691a11641e8a0cdc374711c50

Workspace information:

• Scala versions: 3.5.2
• Build tools: 0. scala-cli
• Build servers:
  0. scala-cli v1.5.4
• All build tools in workspace: