The tab autocompletion of AFNI programs is a different beast. Run:

apsearch -update_all

and when it is done running (shouldn't take very long), check the terminal-- there may likely be a message for you to copy+paste something into your current shell's ~/.*rc file. If not, just open a new terminal, and put an AFNI command followed by a space and a hyphen '-', and then hit tab (probably a few times, since you will have several options to complete). Does that work?

Re. the beeping-- are you on a Mac? To turn that annoyance off, go to the Terminal's menu bar, select Terminal -> Preferences -> Profiles -> Advanced, and then deselect "Audible bell" and "Visual bell" items.

On Ubuntu, at least, I don't think there are bells by default.

Note that the "set file ..." and other "set ..." commands are *only* for your ~/.cshrc file, not for ~/.bashrc (as noted in the instructions here: [afni.nimh.nih.gov]). The syntax is wrong for ~/.bashrc-- that might even cause an error when reading the ~/.bashrc file, so you should remove those from it.

To find out what shell you are using in a terminal, you can type:

echo $0

--pt