Traditionally, AFNI GUI menus have given first priority to dataset type, with alphabetization in second place. But this can make it challenging to find a desired dataset, as most people are used to searching based on just alphabetical considerations.
There is a new environment variable from AFNI ver=25.2.13 which users can use to control the menu file listing, called AFNI_SESSION_SORT (e.g., in your ~/.afnirc settings file). The default AFNI GUI behavior (env var value = ALPHA) will now be to prioritize alphabetical order---or, more precisely, ascending numbers, then ascending caseless letters, then underscores. Users can set the environment variable REVALPHA to reverse the ordering, or MRITYPE to go back to the original hierarchy of ordering by dataset type first and alphabetization second.
The description is:
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Variable: AFNI_SESSION_SORT
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This is a string to set the sort order within the dataset choosers
in the afni GUI. The allowed values are
ALPHA = alphabetical, case insensitive (A=a) (numeric,alpha Aa-Zz,underscore)
REVALPHA = reverse alphabetical (reverse of ALPHA:underscore,zZ-aA,numeric)
MRITYPE = dataset type - anatomical, functional
NONE = no sorting at all, but order of filling is AFNI then NIFTI
Note that when multiple directories have been loaded (e.g., when starting AFNI with afni -R -all_dsets or if the AFNI_GLOBAL_SESSION variable has been set), the primary ordering will still be to list files within one given directory, then all those in another, etc. That is, this ordering will not "splash" datasets across directories. But now, by default, the ordering within a given directory list will be alphabetical.
When a new dataset is created in a directory in which afni has already been run, that new dataset will appear at the bottom of the file.
Thanks for sorting this out go to @dglen --- or, as you will henceforth be known, aDeiln eGln (*unless a different value of AFNI_SESSION_SORT is set, of course).