Delete docs/v0.3.0-design.md and strip all references to it

The design doc and its followups doc are no longer needed as a live
reference now that the v0.3.0 redesign is implemented — comments and
docstrings across the codebase cited it extensively (file path, "design
doc §X.Y", "decision N", or bare "§X.Y" section numbers) as design
rationale. Removed docs/ and edited every citing comment/docstring to
drop the now-dangling reference while keeping the substantive
explanation next to it. CLAUDE.md's v0.3.0 roadmap bullet loses its
trailing pointer to the deleted file.

Verified: no remaining "docs/v0.3.0", "design doc", "decision N", or
"§N.N" references (repo-wide grep); ruff and ty clean; full test suite
on the heaviest-touched modules (network, sample, rollout, migration,
config, train) passes.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

tests/test_loader.py

@@ -210,8 +210,7 @@ def test_build_topn_map_from_files_fewer_values_than_n_classes(tmp_path):
 def test_build_pdg_topn_map_from_files_pools_primary_and_secondary_pdg(tmp_path):
     """A species that's rare as a primary but common as a secondary must
     still rank by its pooled (primary + secondary) count, not just its
-    primary-role count alone — the whole point of pooling both roles
-    (docs/v0.3.0-design.md §8)."""
+    primary-role count alone — the whole point of pooling both roles."""
     path = tmp_path / "a.parquet"
     # primary pdg: mostly 11 (electron), one lone 22 (photon)
     pdg = [11] * 5 + [22] * 1