Problem

CocoaPods/Xcodeproj#985 added support for Xcode 16's folder (new file system synchronized groups)

When I convert xcconfigs group which has App.debug.xcconfig into a folder, the related diff would be like this:

                D95B3A471F823EDA005F1F58 /* Debug */ = {
                        isa = XCBuildConfiguration;
-                       baseConfigurationReference = D9BCA5E41FD034D80016CEE2 /* App.debug.xcconfig */;
+                       baseConfigurationReferenceAnchor = 350FEC862DC066CB00D526AF /* xcconfigs */;
+                       baseConfigurationReferenceRelativePath = App.debug.xcconfig;
                        buildSettings = {
                                ASSETCATALOG_COMPILER_APPICON_NAME = AppIcon;

with this diff, i can still successfully build without any problem.

Then, if i run pod install, it automatically adds baseConfigurationReference like below:

		D95B3A471F823EDA005F1F58 /* Debug */ = {
			isa = XCBuildConfiguration;
+			baseConfigurationReference = 0B456502102A390A3C7ACE32 /* Pods-blabla-app-ios.debug.xcconfig */;
			baseConfigurationReferenceAnchor = 350FEC862DC066CB00D526AF /* xcconfigs */;
			baseConfigurationReferenceRelativePath = App.debug.xcconfig;

this behavior prevents me from using Environment Value that was set via my custom xcconfig App.debug.xcconfig in the build phase, resulting in Command PhaseScriptExecution failed with a nonzero exit code

App.debug.xcconfig

#include "../../Pods/Target Support Files/Pods-blabla-app-ios/Pods-blabla-app-ios.debug.xcconfig"
#include "../../xcconfigs/Environment.debug.xcconfig"

Environment.debug.xcconfig

// sets Environment values here

Environment

Xcode 16.2
cocoapods (1.16.2)
xcodeproj (>= 1.27.0, < 2.0)

Ideal Behaviour

I think when baseConfigurationReferenceAnchor and baseConfigurationReferenceRelativePath are set, 'pod install' should not add baseConfigurationReference.

Any opinion is welcome, thank you for looking over this issue ❤