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Created attachment 166653 [details] Error log Using Eclipse I20100429-1549, I installed the Helios EMF and Data Tools and clicked Apply Changes when the install completed. I got an endless string of error prompting. I have attached the error log. Restarting Eclipse fixed the problem.
The basic problem here is we don't know (programmatically) which plug-ins are safe to apply vs. install. This is why you get the big disclaimer about apply potentially causing errors... We've talked in the past about removing the ability to apply, but this has been unpopular because some tools (like releng tools) which we install frequently are known to be safe to apply.
There are things you can do to avoid the error barrage. For instance, you can keep track of the errors you have logged and not report/log that particular error more than once.
The "apply now" button is now removed by default.