Warn when uploads omit unrecognized paths

[AtomicGlance]

Fixes #1493

dandi upload discovers only recognized assets. Before this change, a requested directory could finish with files omitted from the upload without telling the user.

This adds a discovery helper that reports omitted files individually when a requested tree contains recognized assets, or collapses a wholly unrecognized directory to one entry. It keeps Dandiset metadata, dot/VCS paths, common OS metadata, empty directories, Zarr contents, and directory symlinks out of the warning. Partial uploads stay scoped to the requested paths, and --allow-any-path remains an explicit opt-out.

The warning is registered after the progress table is created, so it is emitted after the table closes and still appears when another asset upload fails.

Tests added:

• mixed recognized and unrecognized trees, unknown directories, ignored paths, Zarr directories, empty directories, and directory symlinks
• whole-Dandiset warning, partial-upload suppression, --allow-any-path suppression, and warning-on-upload-error behavior

Local validation:

• focused discovery tests: 3 passed, 1 symlink test skipped because the platform does not permit the fixture
• upload tests collected successfully; they require the repository's Docker-backed API fixture, and Docker is not installed in this environment
• ruff check and python -m py_compile passed

[codecov]

Codecov Report

❌ Patch coverage is 62.18487% with 45 lines in your changes missing coverage. Please review.
✅ Project coverage is 54.30%. Comparing base (d91a041) to head (95ac3d3).

Files with missing lines	Patch %	Lines
dandi/tests/test_upload.py	12.12%	29 Missing ⚠️
dandi/upload.py	0.00%	8 Missing ⚠️
dandi/files/__init__.py	87.50%	6 Missing ⚠️
dandi/tests/test_files.py	93.33%	2 Missing ⚠️

❗ There is a different number of reports uploaded between BASE (d91a041) and HEAD (95ac3d3). Click for more details.

HEAD has 109 uploads less than BASE

Flag	BASE (d91a041)	HEAD (95ac3d3)
unittests	124	15

Additional details and impacted files

@@             Coverage Diff             @@
##           master    #1915       +/-   ##
===========================================
- Coverage   77.35%   54.30%   -23.05%     
===========================================
  Files          89       89               
  Lines       13325    13443      +118     
===========================================
- Hits        10307     7300     -3007     
- Misses       3018     6143     +3125     

Flag	Coverage Δ
unittests	54.30% <62.18%> (-23.05%)	⬇️

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[AtomicGlance]

Fixed the three Linux upload-test failures by placing the NWB fixture under a valid sub-01/ subject directory. The implementation was not changed. The helper test passes locally; the Docker-backed upload tests are covered by CI. Please rerun the checks when convenient.

[AtomicGlance]

The rerun found one remaining assertion: the singular warning used “1 path were”. I fixed that in 95ac3d3 so one path reads “was” while plural counts keep “were”. Ruff checks pass; CI is running again.

[AtomicGlance]

One macOS 3.13 job in the new matrix failed while cloning the external dandi-datasets/nwb_test_data repository (14 setup errors; 749 tests passed). That failure is unrelated to this PR. The upload-warning integration job is still running.