Add collate config file with timeout params per command

Rather than passing in cli flags, let's enable users to set up a config file to specify args on a global or per-command basis. 

For example, the user might want to specify a very long timeout command for all commands. 

Or a very long timeout command for just coach check. 

Allow the running of `tsu collate` using `with-config` as a param

Follow modern best practices for use of config files. 