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Is there any way of disabling FDT's error check for a particular source folder?
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Yes. Right click on the project and select "Properties". Select the entry "FDT Build Path". The list contains all your source folders and SWCs. Select the one you don't want errors for and deselect the checkbox "Generate Problems/Tasks". FDT will not generate errors for the source folder anymore (only if you open a file from the folder with an editor you will see the errors inside the editor).