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UpdateMD5 not considering all files #237

Description

@mojontwins

Describe the bug
I've created a custom modloader for merged a1.1.2_01. The "BUILD" task correctly outputs working ZIPs for client/server with all my changes and additions.

Now I rebuild the md5 hashes so I can start making mods. I have made a single mod that adds 4 new classes. When I click "BUILD" such classes are exported, but there's also more files in the zips that shouldn't be there as they haven't been modified after md5 hashes were rebuilt.

The extre files are two pngs (gui/items.png and terrain.png, modified in the original mod BEFORE hashes were rebuilt) and two subclasses, also untouched (ItemArmor$EnumArmorMaterial.class & TileEnitityFurnace$1.class).

I guess those files weren't considered to calculate the new md5 hashes so they are "new" again after rebuilding the hashes.

Expected behavior
After rebuilding the md5 hashes, no "untouched" files should be included in the builds.

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RetroMCP Version
v1.2

Minecraft version
a1.1.2_01 merged

Additional context
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