Create actual merge conflicts on template sync

[grst]

Currently, if there are merge conflicts, cruft either creates .rej files or some inline merge markers (>>>>>>>).

Both are hard to overlook, in particular if pre-commit CI is not activated in one of the repos.

It would be better if the conflicts showed up as actual conflicts in GitHub, such that they can be resolved directly in the web interface.

[grst]

It doesn't seem easy. Cruft already merges the files and I don't think it's possible to trick git into believing there are conflicts.
Only now I appreciate how genious the nf-core solution is to have the TEMPLATE branch from the beginning on.

When simply regenerating the template onto a new --orphan branch, github refuses to merge them because they have unrelated histories (using command-line git this actually works by using `--allow-unrelated-histories). Maybe a branch derived from the initial commit of the repo would work 🤔

[grst]

@flying-sheep fyi