I want to specify multiple quartus.ini files. Is there a way to use both $HOME/quaruts.ini and /quartus/bin/quartus.ini?

Only one quartus.ini is loaded, so you cannot use more than one.

The order of precedence is as follows
(1) quartus.ini in the Quartus Project folder
(2) quartus.ini in $HOME
(3) quartus.ini in the Quartus Install folder /bin64 or /linux64

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Category: Quartus® Prime
Tools: Quartus® Prime
Devices: -