Introduces the PathwayMonitor, an abstraction which refactor the reaction recursion depth monitor, and fixes bugs for the monitors.
Adds PathwayMonitor and test.
Adds the layout file namer.
Adds pathway classes.
Changes in exec and new classes to accommodate use of pathways for layouts.
Merge branch 'feature/pathwayBasedLay' into develop
Moves to 1.0.4-SNAPSHOTS, the first one with pathway support for PAMELA.