fix: auto-resolve spurious index.html conflict on pull/merge

With index.html now sync-tracked, two peers curating between syncs each
produce a divergent index.html locally. The merger would treat the diff
as a conflict — but the index is derived from the topic set, so any
divergence is spurious.

- FileContextTreeMerger (used by /space switch): skip index.html in the
  per-file loop; the caller regenerates from the merged topic set.
- vc-handler merge / pull (used by `brv vc merge` / `brv vc pull` via
  isomorphic-git): when index.html shows up in the conflict set, run
  regenerateContextTreeIndex, stage the result, and — if it was the only
  conflict — finalize the merge commit so the user sees a clean success.
  Any other conflicts surface as before.
- After a successful merge or pull (not already-up-to-date), refresh
  index.html so it reflects the merged topic set.