The skill deduplication mechanism has changed from inode-based comparison (which relied on filesystem-level identity via inodes, symlinks, or hard links) to file-based comparison. Debug messages now say "same file" instead of "same inode". This likely improves compatibility across different filesystem types and platforms.
Evidence
Skill dedup logging (search for "skills (same file)")
Strings lifted out of the shipped bundle, so the claim above can be checked against them.