Trump
I'm sure I use the Arduino IDE makefile. As far as I know I have no other makefiles or toolchain stuff on my systems (2 to be precise). I just tested it this way: Renamed "makefile.exe" to "weg makefile.exe" and ran the clean command
The result is:
**** Clean-only build of configuration Release for project blink2 ****
make clean
Cannot run program "make": Launching failed
Error: Program "make" is not found in PATHPATH=[C:\arduino-0022\arduino-0022\hardware\tools\avr\bin;C:\arduino-0022\arduino-0022\hardware\tools\avr\utils\bin; .....]
**** Build Finished ****
It is another error than you get.
You see that the path has been extended by the tool to contain the folders provided with the settings.
You can try the same rename trick to find out which makefile is being used and how it is called.
Have you both avreclipse and Arduino eclipse installed? I ask because this setup is not supported/tested. avreclipse is included in the arduino eclipse but in a modified version using different names/locations/.... It is very likely there will be conflicts
Can you also open the error view and look for clues what is going wrong? (windows-> show view->other ->general->error log)
If all of this doesn't work would you be so kind to install the latest version of eclipse indigo + the Arduino eclipse to test whether you have the same problems?
About compiling the plugin warning "an API baseline has not been set for the current workspace"
Note that the managed builder is avr eclipse code. The warning itself is not a great deal (it is checking of the eclipse baseline) This article explains on how to get rid of it https://teambruegge.in.tum.de/groups/unicase/wiki/5b324/Remove_API_baseline_warning.html
Best regards
Jantje