I had good luck integrating BC4 with Eclipse by using the Beyond CVS plug-in, as described in http://www.scootersoftware.com/support.php?zz=kb_vcs. The only issue I had was specifying the location of the BC executable. /usr/local/bin/bcompare worked for me; /usr/local/bin/bcomp did not.
Essentially, install the BC4 command line tools from the Beyond Compare menu. Then within Eclipse add the following as an update site
http://beyondcvs.sourceforge.net/update/0.8.x/.
I selected all options from that site (though I supposed you could not select Subversive or Subclipse if you don't need). Once the install completed and Eclipse restarted, I visited the External Tools section of the Preferences, and specified the 'bcompare' executable in /usr/local/bin. I was then able to use BC in eclipse. BC did not come to the foreground; it is obscured by Eclipse.
Essentially, install the BC4 command line tools from the Beyond Compare menu. Then within Eclipse add the following as an update site
http://beyondcvs.sourceforge.net/update/0.8.x/.
I selected all options from that site (though I supposed you could not select Subversive or Subclipse if you don't need). Once the install completed and Eclipse restarted, I visited the External Tools section of the Preferences, and specified the 'bcompare' executable in /usr/local/bin. I was then able to use BC in eclipse. BC did not come to the foreground; it is obscured by Eclipse.