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Update docs: bring the command-line reference in sync with the CLI - #1934

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Split out of initial version of #1933

dandi validate gained many options that its page never documented: --grouping now takes seven repeatable keys, --min-severity five levels, and --format, --output, --summary, --max-per-group, --missing-file-content, and --load were missing altogether, as was the automatically saved JSON Lines companion file. Also document download --zarr, organize --jobs, and upload --zarr-mode, and add a page for the deprecated validate-bids pointing to validate.

Claude-Session: https://claude.ai/code/session_01HFhMPs6vF5zyeHDvPTvRcA

`dandi validate` gained many options that its page never documented:
`--grouping` now takes seven repeatable keys, `--min-severity` five levels,
and `--format`, `--output`, `--summary`, `--max-per-group`,
`--missing-file-content`, and `--load` were missing altogether, as was the
automatically saved JSON Lines companion file.  Also document
`download --zarr`, `organize --jobs`, and `upload --zarr-mode`, and add a
page for the deprecated `validate-bids` pointing to `validate`.

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01HFhMPs6vF5zyeHDvPTvRcA
@CodyCBakerPhD CodyCBakerPhD self-assigned this Sep 27, 2026
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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.30%. Comparing base (c3931cc) to head (b294fc9).

Additional details and impacted files
@@           Coverage Diff           @@
##           master    #1934   +/-   ##
=======================================
  Coverage   78.30%   78.30%           
=======================================
  Files          92       92           
  Lines       14068    14068           
=======================================
  Hits        11016    11016           
  Misses       3052     3052           
Flag Coverage Δ
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@CodyCBakerPhD CodyCBakerPhD added the documentation Changes only affect the documentation label Sep 27, 2026
@CodyCBakerPhD
CodyCBakerPhD added this pull request to stack #1935 September 27, 2026 17:53
@CodyCBakerPhD
CodyCBakerPhD removed this pull request from stack #1935 September 27, 2026 18:04
@CodyCBakerPhD
CodyCBakerPhD added this pull request to stack #1938 September 27, 2026 18:05
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CodyCBakerPhD removed this pull request from stack #1938 September 27, 2026 19:28
@CodyCBakerPhD
CodyCBakerPhD added this pull request to stack #1940 September 27, 2026 19:29
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CodyCBakerPhD removed this pull request from stack #1940 September 27, 2026 20:17
@CodyCBakerPhD
CodyCBakerPhD added this pull request to stack #1942 September 27, 2026 20:17
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