I think I found the solution by myself on Nios Wiki --> Login HOWTO :
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Busybox -->
Login/Password Management Utilities -->
[*] Use internal DES and MD5 crypt functions
[*] getty
[*] login
[*] passwd
Core Applications --->
[*] init
[ ] enable console shell <== unselect this
[ ] execute firewall rules
[ ] process init.conf
(Sash) Shell Program
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Then :
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Method 2, for Fedora, and others that don't have mkpasswd to encrypt password.
Change passwd file, remove the 'x' for root entry
root::0:0:root:/:/bin/sh
ftp:x:14:50:FTP User:/home/ftp
Boot nios2 uClinux, login as root without password needed. Then run "passwd", enter your new password. Now you can save the content of /etc/passwd on your nios2 uClinux.
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