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fgprof produces the same pprof-formatted data as the Go's embedded profiler. profefe should support that out of the box. You might need to specify type=other when sending the profiles to the collector. Let me know if you can test that.
I don't think adding fgprof to the agent is a good idea (at least, not yet). As its author had mentioned in the thread, there are still some issues with the implementation but there are also chances it could be moved to the upstream in future versions of Go.
https://github.com/felixge/fgprof
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