v0.3.3

1. Multiple bug fixes for "reconstruction of untouched shredded contigs" module
   1.1 fix "KeyError" for reading scaffolds that have no shreds and therefore have no index appending to its name;
   1.2 fix a bug that incorrectly merges two different gene models during original path reconstruction. Now gene names, instead of their indices on shredded contigs, are used for correct connections;
2. This new release supports to view all inconsistencies identified between original and AGOUTI scaffolding in CytoScape; a style file is also provided in the package
3. Fix a bug that causes shredding annotation fails: semicolon at the end of attributes filed in GFF, or any attribute have no {}={} format.
4. Use a new way to check AGOUTI local version without requirement for git version 1.8+. (Thanks to @YourePrettyGood)
5. Improvements on Documentation/README