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The Win version of IDA only support debugging Windows Executable File. I don't have Linux and IDA for Linux, but I think the console version of IDA for Linux can debug the Linux ELF file. For remote debugging Linux ELF, DataRescue said: "REMOTE DEBUGGING between Linux and Windows systems. (only singlethreaded linux applications are supported by the debugger). Source code will also be available". For more informations, I suggest you read the tutorial at: hxxp://www.datarescue.com/idabase/remotedebugging/index.htm.
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