venv create no longer includes --sources-directory contents when all files are nested

[huonw]

It seems like there was a regression from 2.1.148 -> 2.1.149 with the behaviour of venv create with a --pex-repository that was created with --sources-directory: those sources aren't included in the final venv.

Reproducer:

cd $(mktemp -d)

# create our dummy file
mkdir -p source_files/foo
touch source_files/foo/bar.py # NB.1
# touch source_files/qux.py # NB.2

for version in v2.1.148 v2.1.149; do
    curl -s -L https://github.com/pantsbuild/pex/releases/download/$version/pex > pex-$version
    chmod +x pex-$version

    # NB.3
    ./pex-$version --output-file=repository-$version.pex --sources-directory=source_files

    # NB.4
    PEX_SCRIPT=pex3 ./pex-$version venv create --dest-dir=dest-$version --pex-repository=repository-$version.pex --layout=flat

    # what was included?
    tree dest-$version
done

Running that shows that the contents of the dest-... directory depends on the version, without the bar.py file when using v2.1.149, but should be the same:

dest-v2.1.148
└── foo
    └── bar.py

1 directory, 1 file
dest-v2.1.149

0 directories, 0 files

Ablative studies:

• uncommenting NB.2 line (to have two files) passes ✅ (both versions have both foo/bar.py and qux.py)
• replacing the NB.1 with NB.2 (to just qux.py at the top level) passes ✅
• always using v2.1.148 on line NB.3 (create the pex) and v2.1.149 on line NB.4 (create the venv) passes ✅
• v2.1.149 for NB.3 and v2.1.148 for NB.4 fails ❌
• I think third-party dependencies work okay, but haven't confirmed in this reduced setting
• This reproduces without --layout, but the output is simpler with --layout=flat

(First observed in pantsbuild/pants#20149.)

[huonw]

Bisecting narrows it down to f9a9d94

mkdir -p source_files/foo
touch source_files/foo/bar.py

python -m pex --output-file=repository.pex --sources-directory=source_files
python -m pex.cli venv create --dest-dir=dest --pex-repository=repository.pex --layout=flat
tree dest