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I realize you've kind of already covered this territory, but I've read through the entire tree of comments here and I feel really uncertain about which files I should include for an "optimal" combination.  I have at least some version of all the IWADs in question (there are multiple versions of almost all of them) but I'm not sure exactly which version of each IWAD is most desirable to create the best version of the output.

Would it be possible to create an "ideal IWAD list", based on the checksum information from these sites?

To minimize the work required on your end (which I certainly want to do), it seems like the most logical process would be for you to collect the ideal IWAD collection in a folder on your own system and then just run sha1sum (or md5sum, etc.) against them and post the checksums.  Then I can easily figure out exactly which version of each IWAD those checksums correlate to (I've already written a tool to do this, as preparation for writing this comment).

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Here are the sha1sums of my source wads. I'm 99% sure these are all just the totally stock last-known-good DOS versions you'd find on Steam or GoG before the Unity port overhaul:

7ec7652fcfce8ddc6e801839291f0e28ef1d5ae7  doom2.wad
9b07b02ab3c275a6a7570c3f73cc20d63a0e3833  doom.wad
3451288383fb16e196f273d9f85d58c1fda97bf4  nerve.wad
90361e2a538d2388506657252ae41aceeb1ba360  plutonia.wad
e2efdf379e1383c4e15c03de89063361897cd459  sigil.wad
9fbc66aedef7fe3bae0986cdb9323d2b8db4c9d3  tnt.wad

as for the Master Levels my sha256sums match the ones on this page:

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Yikes, I'm really sorry it took so long to reply to this after asking you to do kind of got in the way.  blech

Anyway, these are the IWADs you're using, based on those checksums:

Your filename
iwad-patches filename
doom2_1.9.wadDoom 2 1.9
doom.waddoom_ud.wadUltimate Doom (1995)
nerve.wadnerve_bfg.wadBFG Edition
plutonia.wadplutonia_1.9.wadOriginal retail box
sigil.wadn/a (not an IWAD)
Sigil 1.21
tnt.wadtnt_1.9.wadOriginal retail box

That's not the whole story, though.  For example, I have SEWERS.WAD and BETRAY.WAD which WadSmoosh does detect and use.  There's also some stuff about widescreen assets; I'm not sure if I personally care about that stuff since I'm just here for what happens after the menu, but if we're going to be pedantic about it (and I certainly have a pedantic streak :P) then I suppose it's worth bringing up.

There's a comment further down that seems to be a full list of everything, that I somehow missed before; would you mind taking a quick look and confirming that this is the list of all the WAD files you need to "max out" the final output file?

The Master Levels WADs only have one version so I won't clutter up this table with them, but thanks for confirming the checksums.  :)