Fix nested namespace directories

[ds5678]

Resolves #3448

Problem

31bbcf4 introduced a regression, preventing the UseNestedDirectoriesForNamespaces from functioning as intended.

Solution

• Any comments on the approach taken, its consistency with surrounding code, etc.
  • As part of my testing, I added two API methods to WholeProjectDecompiler.
• Which part of this PR is most in need of attention/improvement?
  • BamlResourceNodeFactory::WriteResourceToFile also uses this method, which I think is incorrect, but I'm not sure what to change it to.
• At least one test covering the code changed