Current version of itextpdf (5.2.0) sometimes gets a nullPointerException with large pdfs. Version 5.5.0 is fixed. For someone with the same issue just replace itextpdf-5.2.0.jar with the latest.
The bug, which is no longer relevant, was here:
$ java -jar ./briss-0.9.jar -s source.pdf -d dest.pdf
Clustering PDF: aho-compilers-principles-techniques-and-tools-2e.pdf
Exception in thread "main" java.lang.NullPointerException
at com.itextpdf.text.pdf.PdfReader$PageRefs.iteratePages(PdfReader.java:3531)
at com.itextpdf.text.pdf.PdfReader$PageRefs.iteratePages(PdfReader.java:3559)
at com.itextpdf.text.pdf.PdfReader$PageRefs.iteratePages(PdfReader.java:3559)
at com.itextpdf.text.pdf.PdfReader$PageRefs.iteratePages(PdfReader.java:3559)
at com.itextpdf.text.pdf.PdfReader$PageRefs.iteratePages(PdfReader.java:3559)
at com.itextpdf.text.pdf.PdfReader$PageRefs.readPages(PdfReader.java:3366)
at com.itextpdf.text.pdf.PdfReader$PageRefs.<init>(PdfReader.java:3336)
at com.itextpdf.text.pdf.PdfReader$PageRefs.<init>(PdfReader.java:3314)
at com.itextpdf.text.pdf.PdfReader.readPages(PdfReader.java:1000)
at com.itextpdf.text.pdf.PdfReader.readPdf(PdfReader.java:528)
at com.itextpdf.text.pdf.PdfReader.<init>(PdfReader.java:169)
at com.itextpdf.text.pdf.PdfReader.<init>(PdfReader.java:158)
at at.laborg.briss.utils.ClusterCreator.clusterPages(ClusterCreator.java:38)
at at.laborg.briss.BrissCMD.autoCrop(BrissCMD.java:52)
at at.laborg.briss.Briss.main(Briss.java:32)</init></init></init></init>