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Multipath tcp application-level performance measurement

I am working on a project related to Multipath tcp and I want to measure the goodput and the RTT at the application level. I don't want to use a traditional tool(netperf, iperf, ...) and I want to ...
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MTU, RWIN, and MSS

I have been doing some reading into TCP Receive Window (RWIN), Maximum Segment Size (MSS) and Maximum Transmission Unit (MTU). Right off the bat I have some questions and I need a power user's help! ...