I made the mistake of deleting my app in Windows Explorer. Instead, I should have did it from Aptana. The reason is because after I did that, Aptana’s file system/registry got confused because my workspace project was mapped to that directory. After that it got stuck and I couldn’t do anything.
Normally, if you wanted to delete a project, you’d go to Aptana’s App Expolorer, click on the settings icon, and then select to delete the project. However, if you delete it from Windows Explorer, this becomes greyed out.
It took me awhile, but I finally figured out that in the menu path, if you go to Edit, you can also delete the project.