exclude_tl_dirs drops same-named directories at every depth, not only at the top level #3408

What happens

MetaflowPackage documents exclude_tl_dirs as directories that are "only excluded at the top-level". In practice they are excluded at every depth. With data excluded, a nested package directory such as mypkg/data/ is also dropped from the code package, so mypkg/data/loader.py is silently missing at runtime.

Reproduction

import os, tempfile
from metaflow.packaging_sys.utils import walk

with tempfile.TemporaryDirectory() as root:
    for p in ["data/big.csv", "mypkg/data/loader.py", "mypkg/__init__.py"]:
        os.makedirs(os.path.join(root, os.path.dirname(p)), exist_ok=True)
        open(os.path.join(root, p), "w").close()
    print(sorted(a.split("/", 1)[1] for _, a in walk(root, exclude_tl_dirs=["data"])))

Output on master: ['mypkg/__init__.py']. Expected: ['mypkg/__init__.py', 'mypkg/data/loader.py'].

Root cause

In metaflow/util.py, walk_without_cycles resets skip_dirs = default_skip_dirs after the top level. But the reset changes a variable in the outer loop that the running os.walk iteration no longer reads, so the top-level exclusions keep applying below the top level.

Proposed fix

Reset the skip set inside the walk once the top-level directory has been processed. This is a two-line change plus a regression test in test/unit/test_packaging_utils.py that fails before and passes after. I have it ready and can open a PR if this approach is OK.