I created a workspace with XWiki Manager 4.5 and then upgraded to 5.0RC1. I didn't modify any of the workspace pages. During the upgrade I got a merge conflict on the workspace home page title, Main.WebHome:
The issue is that the Workspace Template is overwriting the home page, changing the title. The Extension Manager sees this as a change made by the user and so it tries to do an automatic 3-way merge, which fails with a conflict.