I have come across several people trying to do this in a convoluted way. Here is the simple way of adding PDT to your Flash Builder IDE.
Since current Flash Builder is basically built on Eclipse Galileo, you just have to add the update site for Galileo
In Flash Builder, go to
Help > Install New Software
Click on “Available Software Sites” link, which should open up “Available Software Sites” window. If you don’t have the Galileo update site already configured, add a new Software site. Call it “Eclipse 3.5 updates” and add the URL: http://download.eclipse.org/releases/galileo/
Back in the “Available Software” screen, select “All available sites” for the “Work with” section. In the search input below that, type in PDT and you should see PDT as an item on the search result. Select it and click the next button. Eclipse will now prompt you with a review screen of the packages which are going to be installed. Click next and complete the installation. You may have to restart the IDE for the changed to take affect.
Shown below is the review screen of PDT installation.