Hi there. My bibliography files were named with a .bib extention (i.e. \bibliography{MyStuff.bib}) with the result that BibTeX produces log messages referring to MyStuff.bib.bib. This crashes TeXlipse, but otherwise would work, so I propose adding:

        if (fileName.endsWith(".bib.bib"))
        fileName = fileName.replace(".bib.bib", ".bib");

at line 264 of BibtexRunner.java.

By the way I can't seem to clone the git repository for this project. Every time I try I get "fatal: The remote end hung up unexpectedly."