add `summary` concept to `CTree` and `CProject`

[petermr]

At present the summary/analysis routines create files like

/ami2/target/tutorial/zika10old/PMC3113902/search.tropicalVirus.snippets.xml
/ami2/target/tutorial/zika10old/PMC3113902/sequence.dnaprimer.count.xml

This is messy, non semantic and visually difficult.
I intend to change to a directory structure under CTree and CProject, e.g.

/ami2/target/tutorial/
zika10old/
    PMC3113902/
        summary/
            search/
                tropicalVirus/
                    snippets.xml
            sequence/
                dnaprimer/
                    count.xml                    

this will mirror the results structure

Also we can create the same structure for the cproject

/ami2/target/tutorial/zika10old/
            summary/
            search/
                tropicalVirus/
                    snippets.xml
            sequence/
                dnaprimer/
                    count.xml      

[petermr]

Now added in latest commit. Works and is available for comment, then will close