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On Linux, Amaya appears to open: fonts.gl.deb fonts.gl.deb1 fonts.gl.rd It does not open fonts.gl. Changing the contents of these configuration files (as well as that of fonts.gl) does not produce any effect on the fonts used by running Amaya (after the change).
Adding a fonts.gl to the user's home .amaya directory makes Amaya use small serif fonts, which are even worse than the default ones. P.S. in the fonts.gl file that is present in the Amaya distro, fonts that do not exist in Ubuntu filesystem are referenced. It is likely then that Amaya chooses some default font. The goal should to be able to see in Amaya fonts that are as clear as the ones used, e.g. by Firefox when displaying the same html page. The fonts used currently by Amaya are much less clear; they are so blurred that produce a very high strain to the eyes, similar to that of old CRT displays even when using a LDC one.