Keep custom code during regeneration

Commit changes you want to retain to the configured base branch, usually main. The generation PR compares those changes with the next generated output. Review that diff before merging; resolve overlapping edits on the base branch and rebuild.

Use custom.keep for files your team owns completely. An ownership rule is different from preserving selected lines inside a generated file. Keep paths specific and review their effect on the next PR.

For edits inside generated files, commit the change to the base branch and inspect the next regeneration. A conflict needs a resolution; regeneration is not evidence that every custom edit applied successfully. Do not resolve the conflict by editing only the rolling doctorine-next branch and assuming the next run will retain it.

Doctorine-managed workflow and metadata files are regenerated by design. Avoid using them as the only copy of a custom integration. Keep independent automation in separately owned files and review the linking dialog's managed-file inventory.

Tracked customization history, per-patch states and Forget are not promised by this guide. Use those features only when they are explicitly available in your project; they require a separate rollout and verification.

Generated source already in your repository remains yours when you stop using Doctorine. Keep your normal Git history and review practices; see Plans and offboarding.