Overhauled the way we use autotools.  Hopefully these changes should make the install procedure more robust than before.
Minor fix to seqan path setting.
If jellyfish is setup the normal way then just link against the shared library, otherwise if the user specified the path then use the static lib... it's just easier this way! :S
Removing files that can be automatically generated.  Updated readme to say that now if you clone the git repo (rather than download the tarball) you must first run ./autogen.sh to create the configure script.
Don't need the kat.pro.user file in the repo
Should have been in previous commit.