Fix changelog fragment PR check

[anth-volk]

Fixes #698

Summary

• Replace the recursive changelog.d file count with Towncrier diff-aware checking against origin/main.
• Remove stale nested changelog fragments that made PRs without new fragments pass the old check.
• Add a top-level changelog fragment for this fix.

Test plan

• git diff --check
• Parsed .github/workflows/pr.yaml as YAML
• uv run --no-sync towncrier check --compare-with origin/main

[anth-volk]

@baogorek would love review on this following merge of #697. This should prevent the versioning skip we had on #684.

[baogorek]

Looks good — the core fix is correct and towncrier check --compare-with origin/main is the right replacement for the naive file count.

Two minor notes (not blocking):

1. 553.md and 589.md are unconsumed — their text never made it into CHANGELOG.md despite multiple version bumps since they were added. Deleting them won't break anything, but those changelog entries will be lost permanently. They also don't need to be deleted for the fix to work, since towncrier check --compare-with origin/main only looks at the diff.

2. uv sync --dev is heavy for this job — it installs the full dev dependency tree just to run towncrier. Something like pip install towncrier>=24.8.0 or uvx towncrier check would be faster.