Improve 'help' command POD documentation has been modified to list available shell commands using =head2 instead of =item. This, combined with run_help() modified to accept arguments, allows one to use 'help <command name>' to get help for a specific command, similar/equal to getting help for shell builtins in regular shells. E.g.: help cat help list

Fix precedence of command line arguments Previously, when autogenerating the config file, the name of config itself was included in the YAML contents. This in turn caused the config file to be re-parsed again and any command line arguments were overwritten with values from the config file. Now the name of config file is not dumped if it is equal to the file being written, and the config file is not reparsed if it is the same file.