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For situations when some CVS servers need to be accessed via one proxy server, and some by another (or by direct connection), it would be nice to be able to set Proxy per connection, instead of as a global setting.
We don't have plans to address the issue. However bug 246068 would allow a solution to be provided by third party.
Moreover it think is OS responsibility to support a setting like this. There is such a possibility with Proxy auto-config (PAC) script. You could even set the script locally and specify it using file:// scheme. Eclipse supports PAC handling although some problems with it are tracked by bug 257443 and bug 257420.
Since it's not an Eclipse responsibility to provide such a functionality I'm marking the bug as WONTFIX. However, when bug 257443 is resolved one could use a third party plug-in that adds this kind of support.