Looking at  it some more, there is a simpler question, I can see a good 
chunk of the js file it is SDL, code that that is not there if MAIN_MOULE=1 
is omitted

The following environment variables are set.

EMCC_FORCE_STDLIBS=libc
EMCC_ONLY_FORCED_STDLIBS=1

Should SDL still be there? I suspect I'm just missing a setting.

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