Hey there Antoine,
Thank you very much for your patience - I’ve been pretty backed up with other work the last couple days due to internal conferences.
So I’ve tried at great length to reproduce this with the AdditionalPluginDirectories, and I have yet to reproduce this as such (I’ve migrated over 100+ plugins to various external folders - mapped via uproject AdditionalPluginDirectories). After reviewing the breadth of the divergence, I can only assume that this issue is likely emanating from such changes. UBT and UBA do have some coupling together. That being said, I would still expect a raw UBACli.exe command to work here. Would it be possible for you to run your command above:
UbaCli.exe -workdir=C:\dne\monorepo-preview\UE\Engine\Source -cache="192.168.3.127" local "C:\Program Files (x86)\Microsoft Visual Studio\2022\BuildTools\VC\Tools\MSVC\14.38.33130\bin\Hostx64\x64\link.exe" @C:\dne\monorepo-preview\DNE\Plugins\Core\DNEAnimationCore\Intermediate\Build\Win64\x64\UnrealEditor\Development\DNEAnimationCoreRuntime\UnrealEditor-DNEAnimationCoreRuntime.dll.rsp
… with debug UBA binaries (as described here). This should at least help with verbosity. This could be somewhat related to the files being pulled in from out of sync root - but again I’d expect detours to help with that (unless we are missing some type of virtualization/map update [mention removed] ).