Deal with workspaces containing workspaces

Currently, #1 (Multiple declarations bug) will still affect projects that are structured like this:

```
root
├───bin << This (empty) folder is actually ignored instead of the other bin folder
├───build.gradle
└───subdir
├───bin << These (compiler-generated) copies of the source files should be ignored
│ └───main
│ └───kotlin
│ └───App.kt << Issues "Conflicting overload error"
├───build.gradle
└───src
└───main
└───kotlin
└───App.kt << Issues "Conflicting overload error"
```