resources: files silently dropped when target has multiple/nested sources: entries

Summary

When a target declares a top-level resources: key and has more than one sources: entry (or a single sources: entry whose directory contains subdirectories), the files listed under resources: are silently dropped from the generated project — no PBXBuildFile/PBXResourcesBuildPhase entries are created for them at all. xcodegen generate exits 0 with no warning or error, and the resulting Xcode project builds successfully, but the resource files are simply missing from the app bundle at runtime.

This is a nasty failure mode because there's no diagnostic of any kind — I only found it because our app crashed on launch with Could not locate configuration file: 'GoogleService-Info.plist' (Firebase), even though the file was present on disk and listed under resources: in project.yml.

Environment

• XcodeGen 2.46.0 (Homebrew)
• macOS 26.6.2, Xcode 26.6 (17F113)

Minimal reproduction

Sources/App/App.swift
Sources/Models/Model.swift
Resources/config.plist
project.yml

project.yml:

name: Demo
options:
  deploymentTarget:
    iOS: "17.0"
targets:
  Demo:
    type: application
    platform: iOS
    sources:
      - path: Sources/App
      - path: Sources/Models
    resources:
      - path: Resources
    settings:
      base:
        PRODUCT_BUNDLE_IDENTIFIER: com.example.demo
        GENERATE_INFOPLIST_FILE: YES

Run xcodegen generate, then:

grep -c "config.plist" Demo.xcodeproj/project.pbxproj
# => 0

config.plist does not appear anywhere in the generated project.pbxproj — no file reference, no build file, no resources build phase entry. No error or warning is printed during generation.

Workaround

Removing the resources: key and instead adding the resources folder as one more entry in the sources: array makes it work correctly (XcodeGen auto-classifies non-compilable extensions like .plist into the Resources build phase):

    sources:
      - path: Sources/App
      - path: Sources/Models
      - path: Resources

grep -c "config.plist" Demo.xcodeproj/project.pbxproj
# => 4  (file reference + build file + 2 group listings)

Notes on what does/doesn't trigger it, from bisecting:

• resources: + a single, flat sources: entry (no subdirectories) → works fine.
• resources: + a single sources: entry whose directory contains subdirectories → broken (0 matches).
• resources: + two or more sources: entries (even flat, sibling directories) → broken (0 matches).
• Moving the resources path into sources: instead of resources: → always works, regardless of how many other sources: entries exist.

This doesn't seem related to defaultSourceDirectoryType: syncedFolder (not used here, plain group-type sources) so I don't think it's the same as #1586 — that one was specific to synced folders and was fixed by #1587, but this reproduces with plain path-based sources on a fresh 2.46.0 install.

Impact

Since this fails silently (no error, no warning, successful build), it's easy to ship an app missing critical bundled resources without noticing until a runtime crash or missing-asset bug shows up. Given how common it is to have more than one sources: path in a real project, this seems worth flagging even though there's a simple workaround once you know about it.

Happy to provide more detail or test a fix if useful.

Reproduce the issue with the shown project.yml by running xcodegen generate, then inspect Demo.xcodeproj/project.pbxproj and confirm config.plist is absent. Trace resource handling for multiple or nested sources; done means the resource has file-reference, PBXBuildFile, and PBXResourcesBuildPhase entries, with regression coverage for the listed triggering cases.