Small fixes and documentation.

I’ve spent the last two days fixing small things that’s been bothering me for awhile, and a few nasty bugs (especially one where files opened using a File constructor would not set xormode properly, resulting in all data being read to be corrupt.

Also, I’ve made some improvements to the wiki page on the tools, however it’s far from complete yet. The changes there will then be merged into the README. Still missing are details on the tools, and the formatting could certainly be improved.

Also, the recent changes in trunk has been merged again, so all functionality added during GSOC should now be present in the branch.