missing parent directory in absolute paths in 2.45.3

[MaksimG82]

Description

After upgrading from 2.44.1 to 2.45.3, XcodeGen generates incorrect absolute file paths — the parent directory is missing, causing all files to show as red (not found) in Xcode.

Setup

Directory structure:

ProjectRoot/
  ├── XcodeGen/
  │   └── project.yaml
  ├── Sources/
  └── Modules/

project.yaml:

options:
  createIntermediateGroups: true

targets:
  MyApp:
    sources:
      - ../Sources/  # Path relative to project.yaml

What happens

Expected (2.44.1):
Files resolve correctly:

/path/to/ProjectRoot/Sources
/path/to/ProjectRoot/Modules

Actual (2.45.3):
Parent directory is dropped:

/path/to/Sources      # ❌ Missing ProjectRoot
/path/to/Modules      # ❌ Missing ProjectRoot

All files appear red in Xcode's Project Navigator.

p.s. And while I'm at it — thanks for this amazing tool! =))