In a couple of old projects we have an Ant target setup to run a deploy with a destructiveChanges.xml file specified.
AFAIK the Force.com IDE "Deploy to Server..." takes no notice of this - Ant has to be used. Am I correct?
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I believe you can use the Developer Workbench to deploy destructive changes - as you said, the Force.com IDE cannot be used for these.
Got the answer "no" here https://github.com/forcedotcom/idecore/issues/19 (where the Force.com IDE is open sourced).