This is the second time I got the terminal crashing on me as soon as it was opened.
login(506, 0x7fff7644b000) malloc: *** error for object 0x7ff402715e70: pointer being free was not allocated
*** set a breakpoint in malloc_error_break to debug
So I tried every solutions found on the net, delete com.apple.Terminal.plist, First Aid with Diskutility13, patched diskutility10 and none worked.
One solution that worked was booting with Recovery HD, select terminal and these commands to fix my El_Capitan Volume. It took about 3 minutes to run the repair.
ls /Volumes (to get the correct name of the Volume to repair)
/Volumes/El_Capitan/usr/libexec/repair_packages --repair --standard-pkgs --volume /Volumes/El_Capitan/
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