There are three parts to your question.
First, automatically generating a document number. To do that, consider writing a "service" class that is responsible for handing out document numbers. It's up to you whether you store the number in a database or somewhere in the repository. Many people prefer to just write a little JSON document in the Data Dictionary that tracks document numbers.
Next, you want to insert the number into the content of a file. This is tricky because if you are dealing with a variety of binary file formats, you'll potentially need an API for each one. You also need a way to specify where in the file the document number will be placed.
If you could simplify your requirement to a specific file type that would help. For example, if you were to only need to insert the doc number into Word documents, you could use docx4j. I like docx4j because it is easy to do simple things like create a document template that has a placeholder, then send key-values to the API to replace the placeholders with the values. You can place this logic in a general "doc generation" service class.
Last, how you actually trigger the generation and insertion. As Jose mentioned, a rule is probably the best approach here. The rule should probably invoke a Java-based rule action class that leverages the autonumber service and the "doc generation" service mentioned above.
