Starting work on RAMPART 0.9.  Added ability to select libraries from each AMP stage.
Refactored most of the RAMPART codebase to use the latest Conan classes and data structures.  This involved removing most of the executor classes, and modifying mocks in tests as appropriate.  Also the params and args classes were merged into the process classes where approprate.
Implementation AMP analysis.  Untested however.
Updated documentation.

Moved location of where we handle kmer ranges.
Updated documentation related to anlaysing AMP assemblies.
Fixing a few issues with pipeline.  Problem dealing with conan execution service.  Still an outstanding issue with execution contexts in assembly analyser.
Bug fixes for mass analysis, amp and amp analysis stages.
Fixes to AMP pipeline.

Introduced some problems with MASS, which still need to be sorted.
Updated the documentation around setting kmer values.  Modified the way we execute mass jobs.
Using updated interface
Records any bubble files produced during the MASS stage and passes them onto AMP for use as required.
A number of bug fixes and improvements throughout the RAMPART pipeline.  Have brought back ability to run end-to-end for most tools again.
Added functionality for checked and unchecked arguments.
Altered package structure.

Added jellyswarm to rampart.

Cleaned CLI help messages for both tools.

Refactored some code to make it cleaner.
Updated jellyswarm.  Added ability to alter mem limit and hash size.  Added extra documentation, related to multi-sample projectes.
Fixed some jellyswarm tests, and removed logging.

Fixed a bug with MASS selector where bubble path was not being output properly if no bubble file exists.  Output "NA" in this case now.
Added ability to vary any assembly parameter with MASS.
Added ability for finaliser to compress output

User can get current version number at runtime, also version will be output at the top of the log.
Using new code for handling ReadEnhancers in MECQ.
Added checked and unchecked arg handling to MECQ.

Using new Conan command line handling interface.