feat(ls): add 'dt list' and a tracked-object tree with md/html export (0.26.0)

[johnyaku]

Summary

Adds dt list (an alias for dt ls) and a --tree mode that renders the repository as a nested tree in three formats — plain text, Markdown, and a self-contained interactive HTML page.

Tree scope — the tracked-object view

By default the tree shows the git-tracked + DVC-tracked objects and nothing else:

• untracked files are excluded (add them with --all);
• git-ignored and dvc-ignored files are never shown (.snakemake/, __pycache__/, …);
• DVC / VCS bookkeeping is hidden — *.dvc pointers, dvc.lock, .gitignore, .dvcignore, and the .dvc/ and .dt/ directories. The tracked object is shown, not the file that points at or configures it.

DVC-tracked data is always shown even though DVC keeps it under .gitignore (matched via isout). dvc list already honours .dvcignore, so dvc-ignored paths never appear.

Flag	Effect
--tree	Render as a tree (plain text)
-o {text,md,html}	Render format (md/html imply --tree)
--all	Also include untracked files (still never ignored ones)
--dvc-only	Restrict to DVC outputs
-L, --level N	Cap depth; deeper contents collapse to … (N files)

A remote URL or a committed --rev is treated as an already-tracked tree (only bookkeeping is stripped).

Rendering

• Text / Markdown print the repository name and the revision — short SHA, any tags on that commit, and its date.
• HTML titles the repository (linked to its web page), shows the revision subtitle, and reuses the collapsible fold-up from dt diff -o html (per-directory <details>, Expand/Collapse all).
  • Git-tracked files link straight to GitHub — each git-tracked file (e.g. a README) is a direct link to its blob on the repo's web page, pinned to the listed revision's SHA. Browse docs straight from the tree.
  • DVC objects get a command popup — their data isn't on the git host, so the dvc button opens copy-pastable dvc get / dvc import commands with HTTPS / SSH tabs (default HTTPS, remembered across popups). Both clone URLs are derived from the repo, so SSH works for private repos. (Directories offer the same popup.)

myrepo
b802a00 · v1.2.0 · 2026-08-31
├── data/
│   └── samples.h5ad        ← DVC object: dvc get/import popup
└── README.md               ← git-tracked: links to GitHub

Performance

dt ls / dt list no longer ask dvc list for --size / --show-hash unless a flag or filter needs them, keeping dvc off its heavy, mmap-intensive resolution path on large (100k+ file) trees. Subtree counts are memoized so HTML rendering is linear in the number of nodes.

Docs

• docs/ls.md — new Tree view section (scope, options, formats, HTML features incl. GitHub links) + alias note.
• docs/commands.md — updated dt ls entry.

Tests

• Unit (tests/unit/test_ls.py): tree build/render (text/md/html), depth collapse, the tracked/--all/--dvc-only filtering model, bookkeeping/.dvc/.dt suppression, repo-URL parsing (HTTPS/SSH), popup contents, the revision subtitle, and git-file-to-GitHub linking (+ no-web-URL fallback).
• Integration (tests/integration/test_ls_cmd.py): dt list alias parity, tree formats against a real DVC repo, default excludes untracked/ignored/bookkeeping, --all re-includes untracked, HTML repo-link + popup, git-tracked files link to GitHub while DVC objects keep the popup, and the revision/tag subtitle.

All unit tests pass locally (90) and the full ls integration suite passes on an NCI compute node (25).

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