External output folder in eclipse

Is there a way in eclipse to make the project's output folder an external folder, instead of a folder located under the project root?

Yes, you can define it as a linked folder.

This this SO answer for more (or this one)

To create a new linked folder select New->Folder, input bin in the folder name: field then click Advanced>>

Click Link to folder in the file system
Click on Variables... to bring up the Select Path Variable dialog.

If this is your first time, or you are linking to a new location select New... and give the variable a sensible name and path.

More precisely, you define your output directory (say 'bin') as a linked folder, then you set that directory as the official output one of your project.