Fixing flow property resolution

The shared properties use to override the embedded flow parameters. Not only was this inconsistent, but it was very intuitive.

The current property precedence is the following ascending order. (i.e. 1 has least precedence, and 8 has the most)
 1. Global props (set in the FlowRunner)
 2. Shared job props (depends on job directory)
 3. Flow Override properties
 4. Previous job outputs to the embedded flow (Only if contained in embedded flow)
 5. Embedded flow properties (Only if contained in embedded flow)
 6. Previous job outputs (if exists)
 7. Specific plugin properties (plugin.properties)
 8. Job Props (*.job)