When I type program A in the terminal, I end up getting program B. Where are the aliases or other file that controls which commands trigger program opening?
Aliases to commands are stored in ~/.bashrc and /.bash_aliases. However, these may not always be the cause of the redirect. If the alias is not, then you can find out what path the terminal is following by typing type <command>. The type command will tell you where the file is that the terminal is executing and whether it is hashed to another executable elsewhere on the filesystem. In order to find out what file the link is to in that case, cd into that directory and type ls -l <file>.
