Added functionality to check if all requested processes are operational.
Added some basic sphinx doucumentation and used assembler to create a linux script to run rampart
Overhauled project structure and build lifecycle.  Now the build cycle looks roughly like this:

clean - target, dist, build
compile
test - only unit tests
package - creates scripts and copies resources to "build"
integration-test - got this working again
install - creates javadoc jar, source jar and places in build dir.  Also creates a distributable package and puts it in "dist".
deploy - puts rampart jar into TGAC maven repo.
Cleaned up the front end.  Now we have system default configuration files, and user configuration files, which if present override the system configs.
Changed front end so that each tool has it's own entry point.
Updating the manual
More updates to the manual
Made some changes.
Optimised imports, cleaned up the cli and updated the manual.
Updated the README, and added a text version of the manual when building.  This might be useful if the users have no graphical interface for opening pdfs or viewing HTML.
More updates to readme and manual
Somehow the end of the introduction got lost in the last commit.  Reverted to previous introduction.rst.
Modified RAMPART structure to separate out assembly analysis into a separate module.  The user can also explicitly select a specific assembly to run from the AMP stage onwards if they don't want to trust the automatically selected one.
Added ability for the user to select a custom assembly for the second half of the pipeline.
Updated documentation to reflect recent changes.

Optimized imports.

Tidied front end.

Removed generation of shaded jar.
Added Nizar and David to author list in the manual.  Added creation of man pages for RAMPART.
A few tweaks to the documentation
Fixed a bug where MASS was failing to stop before running onto the analysis.  Also modified the analysis xmls elements to contain underscores rather than dashes.
Some minor updates to documentation.
Updated some of the documentation.

Fixed some minor bugs.

Added better control of parallel processing in MASS.