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Basically I have done 5 types of refactoring to the code to improve the overall design and code quality.
SET-1
Extract Method-> readingJavaFile(configuration) new method in java2c#mojo
RenameVariable->conversionConfigurations->conversionConfig
charsetEntry->charset
sourcePathEntry->sourcePath
customFileASTRequestor-> FileAstRequestor, same with CustomASTResolver-> AstResolver
SET-2
Extract class refactoring-> CSharpFileWriter was also printing which was out of scope for the writer so introduced new class called CSharpFilePrinter. moved 3 methods, removed unused object O from CsharpPrinter from csharp folder.
pull-up variable/method-> CSCastExpression and CSConditionalExpression both were using the same _expression variable of type CSExpression, so instead of making it redundunt, i moved that to the super class and created a getter method.
move-method -> 2 methods moved from CompilationUnitExtended.java to CSharpFileWriter, because of 2 reasons, 1st as they are getter and setter for the filke n ame, it makes more sense to keep them into the fileWriter class and the 2nd reason is that tghe methods been used there more likely then into the CompilationUnitExtended.java as getting and setting file name is more appropriate in that class.
The reason why i did that is because I wanted to contribute to any opensource and I liked your project. For academic purposes I selected this one.
In future I am looking forward to reduce code Smells in your program without affecting the actual code.