@defragster The latest quick series of changes in Arduino required had considerable impact on both Teensyduino and the ArduinoEclipse plugin, so the 2.2.0 branch won't run with Arduino 1.6.5.
You should install one of the nightly builds (see
http://eclipse.baeyens.it/nightly-win.html). You also can try to install an update from the nightly update site (Eclipse Help/Install new Software, then type
http://eclipse.baeyens.it/nightly in the "Work with" box). After that, the configuration screen still gives a message about Arduino 1.6.5, but - at least here - it works.
Oh, and there's another configuration you might have to do. Eclipse doesn't recognize .ino and .pde files as C/C++ source files. You'll have to configure this in Windows/Preferences/C/C++/File Types.
On Windows, there can be another issue with the missing "make" program, see the "Make" screen on
http://eclipse.baeyens.it/getting-started.shtml.
If you want, we can set up a session on Skype or Teamviewer and I'll walk you through the setup.
Now for the good news. After the Teensy 3.2 came out, I was able to spend some more time on the software debugger stack (
https://forum.pjrc.com/threads/26358-Software-Debugger-Stack). While it still needs some work, I'm happy to say that last weekend I was able to use Eclipse to single step myself through the first program running on the Teensy. So, breakpoints already work. I'll check memory and hardware register access this weekend and let you know.