Building a docker image with the following repo results in file merge conflict

Debug with docker-compose

docker-compose run --rm debug
git clone https://github.com/dimitar-petrov/pants_merge_debug.git
cd pants_merge_debug
./pants package py/apps/pyapp/docker:docker_src

Debug without docker-compose

Command

./pants package py/apps/pyapp/docker:docker_src

Output

12:40:26.87 [WARN] The target py/libs/pybind/setup.py:pybind0 imports `pytest`, but Pants cannot safely infer a dependency because more than one target owns this module, so it is ambiguous which to use: ['py/libs/nufft#pytest', 'py/libs/pybind#pytest'].

Please explicitly include the dependency you want in the `dependencies` field of py/libs/pybind/setup.py:pybind0, or ignore the ones you do not want by prefixing with `!` or `!!` so that one or no targets are left.

Alternatively, you can remove the ambiguity by deleting/changing some of the targets so that only 1 target owns this module. Refer to https://www.pantsbuild.org/v2.12/docs/troubleshooting#import-errors-and-missing-dependencies.
12:40:27.09 [ERROR] 1 Exception encountered:

  Exception: Can only merge Directories with no duplicates, but found 2 duplicate entries in :

`MANIFEST.in`: 1.) file digest=993ef9cb52c13947733519a4c8eb3a2bf49a38cfdfa922a385f648d3dfa68402 size=179:

include README.rst LICENSE VERSION 
include pybind/cnufft/cnufft.c
include pybind/cnufft/cnufft.h
include pybind/cnufft/libcnufft.so
include pybind/cnufft/libfnufft.so
prune *.pyc

`MANIFEST.in`: 2.) file digest=892591bf1e4c7e1337cfd470096a467805fa2cb6f46b792fe6e3a6a8b0a72e0a size=366:

include README.rst
include setup.py
include nufft/__init__.py
include nufft/nufft.py
include nufft/nufft.pyf
include src/nufft/dfftpack.f
include src/nufft/dirft1d.f
include src/nufft/dirft2d.f
include src/nufft/dirft3d.f
include src/nufft/next235.f
include src/nufft/nufft1df90.f
include src/nufft/nufft2df90.f
include src/nufft/nufft3df90.f
include pyproject.toml