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Currently, there is no way to define an External Tool as a builder on a project to only run on specific types of build (full, incremental or auto). We provide a variable, but its not very practicle (see bug 20336). Nick suggestion: "The right solution is to add 3 checkboxes, with defaults as follows: Run on: [X] Full build [ ] Manual incremental build [ ] Auto-build These would only appear on the new/edit external tool builder dialog, not the regular new/edit external tool dialog."
To be fixed in 2.0.1
Release code changes into R2_0_1 stream.