[Feat]: Use three way merge

### Describe the feature

Consider using a three way merge to update derived projects from a template.

### Use Case

Context: A derived project that has modified files imported from a template. PRs opened to sync the template will suggest reverting changes back to the template's version.

This is particularly annoying if you are using the template to dictate flow (build, GitHub workflows) with derived projects making changes to suit their needs.
A sync with ANY change to the template will identify common files changed in the derived child as needing to be reverted.

### Proposed Solution

Use a three way merge to identify whether the change was done in the derived project (Thus shouldn't be part of a PR) or in the template (Should be part of a PR).

### Acknowledgements

- [ ] I may be able to implement this feature request