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 96.40288% with 5 lines in your changes missing coverage. Please review.
✅ Project coverage is 77.53%. Comparing base (d91a041) to head (1a7fe98).

Files with missing lines	Patch %	Lines
dandi/files/__init__.py	93.75%	3 Missing ⚠️
dandi/tests/test_files.py	95.55%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1915      +/-   ##
==========================================
+ Coverage   77.35%   77.53%   +0.18%     
==========================================
  Files          89       89              
  Lines       13325    13463     +138     
==========================================
+ Hits        10307    10439     +132     
- Misses       3018     3024       +6     

Flag	Coverage Δ
unittests	77.53% <96.40%> (+0.18%)	⬆️

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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.

[AtomicGlance]

Added focused coverage for the upload omission discovery helper in 414df4e. The new tests cover missing paths, hidden/metadata entries, and rejecting paths outside the Dandiset root. The helper tests pass locally; this is test-only and leaves the warning behavior unchanged. CI can rerun when convenient.

[AtomicGlance]

The new run on 414df4e completed. Lint, typing, docs, CodeQL, and the Windows/macOS matrix are green except the existing macOS Intel 3.13 and several Ubuntu test jobs; those jobs fail in their generic test step, while the new omission-helper tests pass locally. GitHub does not expose the runner log details in this environment, so I have not changed application code based on guesswork. The remaining check_labels failure is maintainer-only; I also confirmed this fork cannot add the required label. Could a maintainer inspect the failed job logs and apply the label when convenient?

[AtomicGlance]

Also marked the four upload-warning regression tests with the repository-required ai_generated marker. Ruff and the focused discovery tests still pass; no behavior changed.

[AtomicGlance]

I corrected the omission warning so singular messages use “it was” and plural messages use “they were,” while preserving the original upload error. The diff is limited to dandi/upload.py; compileall and git diff --check pass locally. The focused Docker-backed test is skipped here because Docker is unavailable, so I’m relying on the pushed CI run for the full fixture coverage.

[AtomicGlance]

The new run reached the test jobs, but the Ubuntu matrix is blocked before collection by the shared Docker setup: docker compose pull cannot pull minio/minio (pull access denied ... repository does not exist or may require docker login). The warning-specific test therefore has not executed in this run; the failure is infrastructure/setup, not a traceback from the changed formatter. The one code change remains the singular/plural pronoun fix in dandi/upload.py.

[AtomicGlance]

The full matrix now passes after switching the test stack's MinIO image from Docker Hub to quay.io/minio/minio:latest in 1a7fe98. The previous image could not be pulled, which prevented the integration fixtures from starting.

All test environments, both Codecov checks, lint, typing, and documentation are green. The API suite includes the four upload-omission regressions (291 passed, 2 xfailed in the completed EMBER-DANDI job).

Only check_labels remains. Could a maintainer @yarikoptic apply the appropriate release label and review this when convenient? Thanks!