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I can not map subdirectories in project into other directories/files in midlet suite (eg. project file /res/icon.png -> /icon.png in midlet suite). This mapping should be depended on current configuration to make posible to use different resources with different configurations.
Of course you can. You can add whatever folder as root of your resources to any project configuration. This can be done from Project Properties / Libraries & Resources panel / Add Folder button. The folder (or jar or zip) you select is the root and its content is taken as is. If you add for example your /res folder the /res/icon.png will be mapped to /icon.png in your application jar.