cleanup

You don't have any comments in this code.

Why you using boolean class rather than boolean primitive?  You have 'Boolean go = false;' rather than 'boolean go = false;'  Do you know the difference?

You got the packaging right -- org.basilthebeagles.tools -- but you did it wrong.  You need to make dir name org, then in it, one named basilthebeagles, and then in it, a tools dir, and in this, you put the java file Collatz.java (remove the directory collatzClass... that is not right). That is how it is done in bigger java projects.  

Change your IDE so that it uses spaces for tabs rather than tabs themselves.  When tabs it depends on the settings folks have on their computer and it varies so your code looks different to other fellows.... It is a setting in your IDE.  Set 'spaces for tabs'.  Do 4 spaces for a tab or 2.

What is with the weird do/while formatting.  It is important that they layout is clean.  It makes stuff easier to read.  You have it up against the left hand margin.  Should be in line with the rest of the code.

I want you to do it as a command line tool... so it prints on the terminal rather than in the option box.  That is how folks normally write 'tools' in java.