balanceFruit.cfg

or whether to put the sniper in it's place instead?

The sniper is already "in it's place"

so it becomes more like a shockrifle primary but you can do headshots with it too.

Xonotic != UT
Besides rifle already does everything you described, why do people want to remove the nex?

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So far i'm really happy with

laser
mg
electro (god damn this is awesome, good job frutiex!)
crylink
RL
mortar

To that list I'd add:
shotgun
nex
Maybe even:
crifle (with 4 bullet mag)

What still needs work is the hagar as you say, and what about the HLAC, seeker and the fireball?

Not sure we have to completely revamp the hagar though, just making it useful (and then also balanced) should be enough. It does have it's unique (albeit spammy) uses.