Merge pull request #157 from stevenweaver/master

Ubuntu Qt CMake Fix
Removed the bloated xcode directory which was in the distro for no good reason
Merge branch 'master' of github.com:veg/hyphy
Restoring error reporting for WarnError in GUI versions
Auto-rename conflicting internal node names by default now
Allow to override tree rebalancing options in qndhelper1
Require QT 4.7
Fixed BranchLengthFitters.bf
Renormalize LCAP
Fixed up MPITools.ibf and added the option to skip jobs
Fixed 0^0 issue; removed bumping up lower bound in Bracket; added some verbose debugging infrastrure
Demote ConjugateGradient error to a warning
Merge pull request #167 from stevenweaver/master

Adding check for cURL in CMake
Merge pull request #168 from stevenweaver/master

Defining __HYPHYCURL__ in CMake as opposed to in the codebase.
Added a fix to seq aligners where there would be gaps relative to the reference on the 3' end
Merge branch 'master' of github.com:veg/hyphy
Added missing GUI includes into bayesgraph.cpp
Fixed always setting SEQ_ALIGN_NO_TP to 0 in SeqAlignCodonShared
Linux GCC does not search include paths recursively, explicitly adding the sqlite path to include path