Hi Chris.
This topic is often quite confusing for new pentaho users. By default Pentaho Server uses an hsqldb database as a repository, unless you configure it to create the repository in another sql database engine (like postgresql, mysql, sql server, oracle, etc.)
I guess you have left the standard configuration, so if it's that the case, the pentaho repository will be in an hsqldb database.
So, the entire directory structure you see in the pentaho console is stored in tables in the database, not in a file system and the file you uploaded in /home/pat is in that database, not in a file system.
One more thing: since the file is a transformation, you can not edit it from the pentaho console, but from Pentaho Data Integration (PDI or Spoon, as you prefer to call it), connecting to the standard Pentaho repository (you have the Connect button in the upper right corner of Pentaho Data Integration).
Best regards