Don't deduplicate files in include with different paths but a same name

[akkyie]

XcodeGen removes duplication among included files by their file names, not paths.
This could be problematic, when you want to define multiple targets in their respective specs:

- project.yml (root spec)
- Modules
 \- App
   \- targets.yml
   \- Sources
   \- Tests
 \- UI
   \- targets.yml
   \- Sources
   \- Tests
 \- Core
   \- targets.yml
   \- Sources
   \- Tests
...

When you include three targets.ymls from the project.yml, only the first in the include: list is actually included while the others are just ignored.

This changes that by allowing SpecFile use the full path of subspecs to merge them.
Test changes included.

Related: #599

[yonaskolb]

Thanks @akkyie!