Items cannot be permanently removed from project

[deceze]

Steps to reproduce:

• open any project file
• remove items from the sidebar (right-click, Remove Selected Files..., Delete Reference)
• add some files in related parent folders through the Finder or close and reopen the project, i.e. do anything that causes Project+ to refresh the directory contents
• result: the removed items reappear in the sidebar

This is quite annoying behavior. I have a project that deals with a lot of temporary files which it stores in a subfolder. If this subfolder is in the file list, switching to TextMate takes several seconds while every file in that folder is re-examined. I need to exclude that folder from that project, but Project+ keeps reviving it at odd times.