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Support for evolutionary design approaches is not a very much investigated topic in the automation domain. Advanced facilities for semantic validation, refactoring and model transformations, which are necessary for rapid prototyping of control applications, are seldom found in design tools. Implementing such facilities is even more difficult when using the IEC 61499 standard, through some characteristics of the persistence model. This paper presents a specialized development environment for modelling and automatically generating applications for the industrial automation field, its unique facilities for supporting evolutionary design and the suggested improvements to the IEC 61499 model. This environment was developed inside a project for assessing the IEC 61499 principles and for verifying design approaches and execution models on a real plant.