I'll post what I had to do to get things going, using a fresh eclipse install (in case I need to do it again) :
1. Create a folder somewhere to let Eclipse use as a workspace folder.
2. Extract the content of the Stencyl SDK somewhere, and copy the Sample Project folder in the eclipse workspace folder you created in step 1.
3. Open Eclipse, point it to use the folder you created in step1 as the workspace folder.
4. Go to File -> New ->Java Project, and for the name type
Sample Project and press Next. (
http://i.imgur.com/fSwOS2G.png)
5. Go to the Libraries tab, and select Add External JARs, locate the Stencyl install dir and add sw.jar from it then Click Finish. (
http://i.imgur.com/T0oJctM.png)
6. Open build.xml in eclipse and edit accordingly. (
http://i.imgur.com/6JI7s1D.png)
7. Go to Project -> Properties ->Java Compiler and click on Configure Workspace Settings (upper right corner)
8. Under Compiler Compliance level select 1.6 and after that click on Configure (
http://i.imgur.com/1aL3KWc.png)
9.Click on Add in the window that appears, select Standard VM, and in the next window select Directory and navigate to your Jdk1.6 install dir (
http://i.imgur.com/KrhiMYE.png)
10. Click Finish. You will be returned to the Preferences window where you must select the new jdk instead of the default one (
http://i.imgur.com/q8irQPr.png)
11. Click all the OK and Finish buttons that may come up in the process, right click build.xml, select RunAs Ant Build and things should work (if you can actually stand those 42 warning messages)
12. Go to Run -> External Tools ->External Tools Configurations, select the JREs tab and make sure you have Separate JRE selected and that it points to jdk1.6 (
http://i.imgur.com/556bHnU.png)
13. Click Apply then Run and eclipse should recompile the extension (Without 42 warnings this time)