PC does not handle subdirectories in project file

[gcasa]

Procedure to reproduce:

1. Create a new project
2. Go to the command line and create a directory and a new file to add to the project
3. Go to ProjectCenter and add the file to the subdirectory
4. ProjectCenter will copy the file to the root of the project instead of referencing it where it is.

Expected:

PC should be able to get the file from its existing location.

Workaround: Create the file in the existing directory.

Why this workaround is unacceptable: For larger projects it might be necessary to incorporate code like this without creating a sub-project.