I have posted about several tools to create PDF files, so today here is a tool to help you manipulate them. PDF Split and Merge is an open source program which does exactly as its name says:
- split your pdf documents (into chapters, single pages, etc.).
- merge many pdf documents or subsections of them.
- extract sections of your document into a single pdf document.
- mix alternate pages taken from two pdf documents in straight or reverse order into a single document.
- rotate pages of the selected pdf documents.
- visually reorder pages of a selected pdf document.
- visually compose a document dragging pages from selected pdf documents.
The program comes in both a basic and enhanced version. This tool in combination with a PDF creator for the most part should accommodate virtually all of your PDF needs.

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For a command-line tool which can do much the same, see PDFTK, e.g.:
http://en.wikipedia.org/wiki/Pdftk
Your program is frustrating. Very useful, but the source code is exceltionally poorly structured and basically uncommented. Terrible code to analyze.
I was also wondering why you chose to code the it in Java. Most of the classes have basically no invariant, which makes them haphazard collecions of function. It seems that a structured language such as C would have been a better choice: you could have done the same job in about half the lines, without all the incomprehensible overstructured that Java forces you to use.