Prevent deprecated tools from rendering as broken links (#1693)

This fixes the remaining link checker failures by ensuring deprecated tools
render as bold text instead of clickable links.

Changes:
- Modified README template to conditionally render deprecated tools as **Tool Name**
  instead of [Tool Name](url) to prevent broken link errors
- Fixed backfill logic to preserve manually set deprecated flags instead of
  overwriting them with values from old JSON data
- Removed broken sponsor links from template footer
- All deprecated tools now show ⚠️ icon without clickable URLs

This ensures the link checker will pass while maintaining clear visual
indication that tools are deprecated and no longer maintained.

Author: mre