Is there a way to make Git mark a file as conflicted?

If the index is already in a conflict state, simply check out the file with the --conflict=merge flag:

git checkout --conflict=merge file

If the index is clean because the unresolved file has been [erroneously] added, just reset it before checking it out:

git reset file
git checkout --conflict=merge file

This will allow you to resume conflict resolution normally (e.g., git mergetool).

NOTE: Promoting a comment to @jakub-narębski’s answer into its own answer by request from @fourpastmidnight. 🙂

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