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Installing two patches that use the mw3 file



What exactly do you mean? .mw3 is just a data file for palettes, similar to .bin for graphics. It's automatically included by the patch rather than being any sort of separate thing.

If you want to edit the mw3 file, you can import/export a palette as one in Lunar Magic's palette editor using the standard #lm{imppal}#lm{exppal} buttons. When exporting the palette, just change the "save as type" dropdown to .mw3.

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I mean if two patches that use the mw3 file that we actually already know what it's for, the palettes will collide.

Yes?
The only time both would ever conflict with each other is when the palette files have the same name (which isn't the case, there are easy workarounds anyway) or both palettes are used at the same time on the exact same part of the (which also isn't the case; one patch only affects levels and the overworld, the other the nintendo presents screen).

The palettes in question are also inserted as you patch them into the ROM, you don't insert it into the level with Lunar Magic. In fact, the standard for custom palettes you insert with Lunar Magic is PAL for while MW3 is only used for patches since it contains the raw colours instead of a 24-bit RBG representation like in PAL.