Fix: registered algorithms silently produced no graph via the CLI

[fesanghary]

Summary

causal-ts discover --algorithm <plugin> silently produced nothing. discover's
if/elif chain covers only the built-ins and had no else, so a registered third-party
algorithm passed validation, printed "Results saved to…", exited 0, and wrote a
summary.json with no graph at all.

• cli.py — added the else branch: runs run_algorithm(...) and saves
  estimated_graph.npy like every other branch. The edge-list/diagnostics code after the
  chain already reloads the graph from disk, so it picks this up for free.
• algorithms/__init__.py — added causalts.algorithms entry-point discovery, so an
  installed distribution reaches the causal-ts command without the caller importing
  anything. Scans once, lazily; a broken plugin warns and is skipped; a plugin can never
  shadow a built-in name.
• cli.py — --validate is now rejected for plugins. Its bootstrap re-discovery
  closure only special-cases cdnots/cdnots+ and otherwise re-runs CEDAR — dead code
  for grace/grace-ss (rejected earlier in the same file), but the new else branch
  makes it reachable for plugins, where it would have silently annotated the plugin's
  edges with CEDAR's persistence values.
• custom_algorithm.ipynb — Step 6 claimed "once your module is imported, the CLI
  picks up your algorithm automatically." That can't work: the CLI is a separate process
  that never imports the caller's code. Replaced with the entry-point workflow that
  actually works, plus two smaller instances of the same overclaim in cells 0 and 13.

Only df/ci_test/max_lag reach a plugin from the CLI. Forwarding CDNOTS/CEDAR-specific
flags like --alpha or --include-c has no defined meaning for an arbitrary plugin, so
that limit is documented rather than guessed at.

Test plan

• Fresh venv, real pip-installed plugin package, real causal-ts console script
  (not python -m / PYTHONPATH): before install --algorithm granger is rejected;
  after install it appears in --algorithm's choices and produces a real 7-edge graph
• --validate + plugin → clean BadParameter, exit 2, nothing written
• Built-in --validate still works (persistence.npy written); GRACE's existing
  --validate guard still fires; unknown algorithm still rejected
• 13 new tests, self-contained (pass with zero plugins installed)
• 328/328 full suite; custom_algorithm.ipynb executes 0 errors
• black(24 pin)/isort/flake8/codespell clean

[github-actions]

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Dependency Review

✅ No vulnerabilities or license issues or OpenSSF Scorecard issues found.

Scanned Files

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