Fix reindex script to exclude __DELETE files

[fawad24051]

What this fixes
Previously, the reindex script counted and indexed files marked with
__DELETE in their filename, even though these are meant to be excluded
(treated as deleted/removed entries).
Change
Updated scripts/bonsai-reindex.sh so that files with __DELETE in the
name are skipped during reindexing — both in the file count and in the
generated _index.md output.
Testing
Manually tested with a test-workspace containing:
real-note.md (should be indexed)
old-note__DELETE.md (should be excluded)

Confirmed the resulting _index.md only lists real-note.md, and the
reindex count correctly shows 1 file instead of 2.