I took a look at the Linux install guide there, just glanced over it and didn't notice this listed. You are supposed to remove a couple files (unless this has changed), though I doubt it would cause issues logging in. The files to remove, I think, are as follows:
arena.eqg
arena_EnvironmentEmitters.txt
lavastorm.eqg
nektulos.eqg
Nektulos_EnvironmentEmitters.txt
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