I understand bonita uses documents to store files uploaded by users however they are stored in the bonita database and for me this is unnacceptable. Is there a way to change this so it’s stored as a file in a place I wish or is there a way to upload a file via groovy script?
Apologies for the short answer: 
I understand bonita uses documents to store files uploaded by users however they are stored in the bonita database and for me this is unnacceptable.
Sort of correct. When designing in Studio you define, and can load templates, documents which are saved as part of the process (used at start-up).
Files loaded by users are saved as part of the execution of the Process, yes they are saved to the database, but not as the originating process documents. For example, start process A will use template X, user loads document (File3) and ends process. File3 is saved with that execution of the process. Start another process A and it will again start with template X. Not File3 which is what you are probably hoping for.
Is there a way to change this so it’s stored as a file in a place I wish or is there a way to upload a file via groovy script?
OK then Short answer is Yes,
Longer answer you can use connectors such as Alfresco (4.x - you need to check first, OpenKM v6.x are examples) or write your own connectors that save documents to PostgreSQL or MySQL or Nuxeo.
We do this with PostgreSQL very successfully and when a user starts process A, he will always get the latest version of the file loaded by the user.
see the documentation and search for Documents for more information
Hope that helps, regards
Seán
I’m trying to use OpenKM v6.2 Community but their .war seems to be incomplete when deploying it on tomcat… What about FTP uploading via groovy script or connector? Is that even possible?
Never tried FTP - and I think that could be an issue for security reasons, port opening etc. You could also write your own connectors (groovy or java) to REST your documents to OpenKM. Not done this but I know it has a REST connector.