[keshav55]

Problem and change

atris init, update --yes, and sync --yes could overwrite customized project and global skill files with packaged copies. Preserve existing differing files and links, report preserved paths, and create missing packaged files exclusively. Refuse symlinked skill roots, skip linked skill subtrees, and remove the legacy writer that could follow a user-owned link. Clarify skill counts in update output.

Validation

• 43 focused offline tests passed, including real init, update, sync, and dry-run commands in disposable projects and homes, existing empty/custom files and symlinks, and business-template coverage.
• Independent review passed 25 focused tests on this exact head and found no new blocking issue.
• git diff --check passed.

Tradeoffs and limits

• Existing packaged copies do not automatically upgrade: there is no ownership baseline that proves an older file is unmodified. Users must compare and update existing copies intentionally.
• Symlinked skill roots are refused; linked skill subtrees are skipped. There is no copy fallback when symlink creation fails.
• Checks and writes are not fenced against concurrent path or ancestor swaps. Broader workspace-template sync is not transactional and can have made earlier writes before an error.
• Offline fixtures do not establish live rollout behavior. This remains a draft for review; no production rollout has been performed.