Can I instrument Eclipse plugins with pdebuilder (the command-line tool that builds Eclipse plugins)? I see the Clover plugin that allows builds inside the Eclipse IDE to be instrumented, but I have a product that includes actual Eclipse plugins that need to be instrumented.
In general yes, but it's more tricky than building it from Eclipse IDE.
Please get familiar with http://www.eclipse.org/articles/Article-PDE-Automation/automation.html headless build process first.
As the process is quite complex and involves multiple ant build files - called one from another - you would have to "hack" into master build files from org.eclipse.pde.build_<version>/scripts plugin and add Clover tasks there (the <clover-setup> would be preferred over <clover-instr>).
Note: as Ant scripts might be called without the "inheritrefs" option, it can be necessary to add Clover tasks in more than one build file.
There is also a second approach possible. Instead of "hacking" org.eclipse.pde.build/scripts you can
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