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Sorry for the late reply 
Actually, the easiest way is to start from the MAngband code and then add anything you want from your preferred variant. That's what I did with PWMAngband: took the MAngband code from the 1.0.0 era, added features I liked from PernMAngband, then ported anything I could from Vanilla to stay close to the original Angband feel.
I wouldn't really recommend starting from a variant and then add multiplayer code, unless you're really familiar with such coding.
After that, it's up to you to choose the starting point for your variant: MAngband 1.1.4 branch is probably the cleanest point, with features mainly from the Angband 2.8 era + some from 3.0; MAngband trunk has a completely rewritten network code, but it's probably in a beta (or even alpha) state; TomeNET code is heavily maintained, but it's already using a lot of stuff from multiple other variants (Z, Cth...) and it's still based off the old 2.7-2.8 Angband code. And finally PWMAngband code: based off latest Angband + MAngband 1.1.4 (so without the new networking code) + new content. Just you know: since I only own a Windows PC, I've removed all OS compatilibity code from PWMAngband, so it's assumed to run under Windows. If you want to use Linux, you'll have to run it with WinE.
Actually, the easiest way is to start from the MAngband code and then add anything you want from your preferred variant. That's what I did with PWMAngband: took the MAngband code from the 1.0.0 era, added features I liked from PernMAngband, then ported anything I could from Vanilla to stay close to the original Angband feel.
I wouldn't really recommend starting from a variant and then add multiplayer code, unless you're really familiar with such coding.
After that, it's up to you to choose the starting point for your variant: MAngband 1.1.4 branch is probably the cleanest point, with features mainly from the Angband 2.8 era + some from 3.0; MAngband trunk has a completely rewritten network code, but it's probably in a beta (or even alpha) state; TomeNET code is heavily maintained, but it's already using a lot of stuff from multiple other variants (Z, Cth...) and it's still based off the old 2.7-2.8 Angband code. And finally PWMAngband code: based off latest Angband + MAngband 1.1.4 (so without the new networking code) + new content. Just you know: since I only own a Windows PC, I've removed all OS compatilibity code from PWMAngband, so it's assumed to run under Windows. If you want to use Linux, you'll have to run it with WinE.