I wanted to sync a folder (services) to the services folder in my project. My project was already added to the project view.

I then went to the file view and selected the services folder (not the one in the project) that I wanted to sync to, right-clicked it and chose "Create new sync connection..."

I then chose to "Add new project shortcut" and selected the services folder inside my project. Then hit the cancel button. If you then look in your Sync Manager pane, and click the dropdown arrow and select "Show Local Sync Targets" you will see your new addition. However, you cannot use it yet.

Restart Aptana.

Now go back to the file view, right-click the services folder you want to sync (not the one in your project) and this time select the project's shortcut that you previously made.

I didn't mess around with it too much after getting it working, but if you have any questions feel free to contact me (or leave a comment here).

I create 2 project shortcuts, 1 from the project I'm working on and 1 (dummy project) to the filesystem I want to sync to. Then I restart aptana <- I wish it would refresh in the sync menu automatically. After restarting I can select the project in the shortcust to synchronise and then in the drop down list (ftp) there are all the other project shortcuts, so I select the dummy one.

Would be a great feature request to be able to do this in some easier way.