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This is SO COOL. I was just trying to put together my own SuperWAD that does this, but was failing miserably. Broken textures and whatnot.

Will this add Plutmidi.wad if it's put into the folder? Or do I need to modify and add it myself?

Also a version that turns it into a standard iWAD instead of a PK3 and without ZDoom stuff so that other source ports can support it would be cool. Although that's simple enough to do with SLADE, it would be cool for this to become the equivalent to Doom 64 EX's WADGEN and Complete becomes the defacto Doom iWAD for every source port

You should be able to make a WadSmoosh-compatible version of plutmidi.wad by renaming all the lumps inside to P_TRACK instead of D_TRACK.

What WadSmoosh produces is an IWAD, PK3 just denotes the format used (ZIP instead of the classic WAD format).

Much of what WadSmoosh does, with regard to defining custom episodes, intermission screens, and texture replacements is due to ZDoom functionality that most source ports don't have. If there's a source port that has equivalent features (maybe Eternity?) and someone wanted to make a fork (not a branch) of WadSmoosh that produced an all-in-one IWAD for that, they'd be welcome to - WadSmoosh's code is released under an MIT open source license - but I only use GZDoom so that's all I'm willing to support. 

That makes sense. Anyway, the point I was attempting to make stems from wanting (near) universal compatibility with this. No PK3 format, since many source ports can't handle the zip format, or Mapinfo, since that would be the job of the sourceport. But, if that isn't your goal, then that's just the way it is.

However, do you think that future versions could add in device-exclusive official maps? Sush as by extracting the maps from the GBA ROM and PSX ISO? That's st least in-line with the goal of the project. 

PSX, GBA, Jaguar etc versions of maps already exist as freely available (painstakingly manually reverse engineered, as I understand it) PWADs, so I'd say just run those as mods.