this seems to be pointing to an issue with dex transforms, I can see there is only 1 .class file in lib/a but 2 dex files.

./lib/build/intermediates/runtime_library_classes_dir/debug/com/example/lib/a/BuildConfig.class ./lib/build/intermediates/javac/debug/classes/com/example/lib/a/BuildConfig.class ./lib/build/generated/source/buildConfig/debug/com/example/lib/a/BuildConfig.java ./lib/build/.transforms/adfcd297971eeda5a95b2b2e7fff7506/transformed/debug/com/example/lib/BuildConfig.dex ./lib/build/.transforms/adfcd297971eeda5a95b2b2e7fff7506/transformed/debug/com/example/lib/a/BuildConfig.dex ./app/build/intermediates/project_dex_archive/debug/out/com/example/app/BuildConfig.dex ./app/build/intermediates/javac/debug/classes/com/example/app/BuildConfig.class ./app/build/generated/source/buildConfig/debug/com/example/app/BuildConfig.java

ok root of the issue is the SerializedChange is incorrect : SerializableChange(file=/usr/local/google/home/jedo/bugs/223365583/DuplicateClassBug/lib/build/intermediates/runtime_library_classes_dir/debug/com/example/lib/BuildConfig.class, fileStatus=REMOVED, normalizedPath=BuildConfig.class)

normalizedPath seems like it needs to contain the package name + class name to function properly.

Yes this is a regression in AGP 7.1+ introduced by https://android.googlesource.com/platform/tools/base/+/9f3b509b589d309818e527e786b06f5662d35e25.

In DexingTranform.kt, we have this code (edited to show key ideas) to remove stale dex files in the transform outputs:

inputChanges.removedFiles.forEach { removedClassFile: org.gradle.work.FileChange -> 
    val staleDexFileRelativePath = removedClassFile.normalizedPath + ".dex"
    FileUtils.deleteRecursivelyIfExists(dexOutputDir.resolve(staleDexFileRelativePath))
}

Note that the call to removedClassFile.normalizedPath is meant to get a relative path, which means the dexing transform's input needs to be annotated with PathSensitivity.RELATIVE or @Classpath.

Previously, the input was annotated as @Classpath, but in AGP 7.1+ it was changed to PathSensitivity.NAME_ONLY (the commit above) to fix https://issuetracker.google.com/205968564.

I guess we will need to find another way to get the relative path (or find a different way to fix the other bug?)

yes, I have made a change that uses RELATIVE path sensitivity

Change-Id: If04c848a174fb2a981f402a855c5132433f6a0fd

Any chance we could get this back-ported to the 7.1 series? This is incredibly painful for us.

yes, I am planning to have this backported to 7.1.3, I will confirm

Excellent. Being able to convey this to our folks should help appease them a bit in the mean time. Thanks.

Fixed, will be available in 7.1.3 and up.

How can I download the soure code for AGP plugin 7.1.3 ?

It's here: https://maven.google.com/web/index.html?q=gradle#com.android.tools.build:gradle

If you wanted to see the fix at comment #5, then it's here: https://android.googlesource.com/platform/tools/base/+/f9155596787198b33a6386c4238825ae0aea88ac

Re #15: You are almost certainly hitting https://issuetracker.google.com/248576022.