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compiling and linking mechanics


With the current set of gcc and loader, does there still exist the diffence that makes porting GNU Linux programs a challenge sometimes.  I haven't build for a while, but I recall that the order of libraries in a ? linking process on the command line wouldn't work as they do in on GNU Linux systems.  

Is this still the case?   Is there a document somewhere that describes the situation well and how to modify arguments to enable a clean link on cygwin?

Regards

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