Updated version number to V0.9.1.

Fixed javadoc errors and warnings when using JDK8.  JDK8 is much stricter than V7 and forces valid java doc annotations.  All RAMPART javadoc annotations in this commit are now consistent and don't create any warnings.

Also made some small tweaks to the documentation to make it clear where the distributable tarball can be downloaded from.
Added Kmer genie and reapr support.

Updated documentation
Updated version to V0.10.0.

Updated documentation and README to include section about common installation problems and how to fix them.

Added additional validation on XML parsing.

Changed acknowledgements

Updated example config files.
Updated assembly analysis section so that it includes the number of genes found in each assembly.
Modified the way we calculate feature scaling for each metric.
Added description of "uniform" library attribute to documentation.
Additional input validation for MECQ and MASS tools.  We also check the input libraries are present before starting the pipeline.
Added additional space to the jellyfish buffer foir counting reads.
Large update, to V0.10.0.

Using new conan lib: 3.1.0 and TgacConanProcs 0.9.1.

Processes now return ExecutionResult objects that contain Resource usage information for each process.

Changed pipeline structure so that selection of MASS assemblies is a separate stage.

Kmer calculation (kmer genie) is a separate stage.

Renamed output directory for each stage so it is indexed.  Also each stage (except for MASS selection) produces a summary file containing resource usage from each sub process.
Updated citation document.  Just request that the github URL is used for now.
- Fixed a bug where the scaffolds file was used instead of the longest assembly file.

- Removed unnecessary second call for assembler setup.

- Changed logic behind running assemblies in parallel slightly so that mass parallel automatically sets each mass job to run in parallel too.
Fixed a bug in analyse_mass where we did not make use of kmer genie derived kmer values where available.

Removed extra check for kmer genie in MASS stage, which is no longer necessary.
Fixed a bug in the job cleaner script, which was not cleaning some of the rampart stage directories.

Added a new check to ensure user has requested read kmer analysis if they are doing a asm kmer analysis.
Add check to ensure user has right data for driving ALLPATHS
Fixed a bug in the dependency downloader so that files are downloaded into the working directory if no directory was specified.  Also updated URLS for some dependencies.
Extra validation for AMP stages to ensure that the user picks only valid libraries for input to each AMP stage.
Fixed a bug with cegma so that results are now properly extracted.
Added a "potential runtime problems" section to the documentation.  Includes details on how to fix those problems.
Updates to the documentation to include an ecoli example to test that their configuration is working correctly.
Using TGAC conan process wrappers 0.10.2