The compare plugin only compares the open window. I want to compare more than 1000 procedure, triggers etc. agains my filesystem. So the plugin would take to much time.
I now compare exports but its time consuming due to differences in trailing spaces, lines etc.
Use the Export User Objects tool, use the "File per object" option, export the program units you want to compare, and run a script that performs a diff between the exported files and the VCS files.