Hi Zad,
It is not necessary to use a JAVA program to request the flash erasing.
Here's a batch for Windows to send erase flash request and upload program :
@mode com5:1200,n,8,1
@sleep 1
@C:\arduino-1.5.1r2\hardware\tools\bossac.exe %*
Copy this MS-DOS program in the "upload.bat" file and replace bossac.exe by upload.bat in your Eclipse External Tools.
(Here, it is the com5 is used, change the value and the bossac path if necessary)
You can find the equivalent for OSX / Linux.
Nassa.