Has anyone ever looked at the linker script for Hexen or Heretic? They are linked as OS/2 Linear Executables, and I'm pretty sure the same must have been done for DOOM and Strife. But the question is, why would iD do that?

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Because the DOS Extender they used probably needed this format.

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They used DOS/4GW, and WatcomC, both had a seperate format for 32 bit DOS programs (I've tried it myself)

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The Watcom 32-bit extenders use the LE file format attached to a DOS stub. Just because it was developed for OS/2 first doesn't mean it isn't used elsewhere.

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Yup. When you want to load any of the EXEs into IDA Pro, you gotta tear off the DOS extender first in a hex editor because IDA, despite containing a large amount of DOS-relevant knowledge including what all the interrupt functions and IO ports do, doesn't know about the concept of extenders. Just gotta snip-snip at the second MZ header inside the file :)

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