Deal with workspaces containing workspaces

[fwcd]

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"