- Navigate to Eclipse's installation folder
- Open eclipse.ini and find the '-product' flag. Mine was something like this: -product org.eclipse.epp.package.jee.product
- Open the plugins folder and look for your product folder. It looks similar to your product flag (mine was org.eclipse.epp.package.jee_184.108.40.20640612-0500)
- All you need to do now is to replace the png files (javaee-ide_x32.png, javaee-ide_x64.png, ...) with the icons that you want.
- (Optional) In case you want to use the brand new "flatty" icon, just navigate to plugins\org.eclipse.platform_4.4.0.v20140606-1215, copy the flat png icons and repeat the step 4.
I just tried to do the same and got in the same issue than @imanzal and it is true that as @ilkeraksoy mention I'm using the installer. Now I'm not going to stop using it but there must be a way to do this in the installer version too. Should someone would find a way to do it on the installer version it would be nice to share. Should I find a way I'll put it here.