Hey David, we should keep communication on the geotools user list (if you would 
like to email questions to me privately, my employer LISAsoft can arrange a 
support contract). Plus this way you get a wide range of feedback, incase I am 
no the wrong track myself. 
> What happens when many polygons are digitised as one polygon.

That is called a MultiPolygon. You may want to look at the standards side of 
the street (rather than ESRI) in order to get a hold
of the functionality (and language) we use. 

The geometry support follows the "Simple Features for SQL" standard, if you 
download that document from the OGC you will be able to answer many of your 
questions.

Our feature comes from the OGC "General Feature Model", the specific project 
> ESRI's feature to polygon function can convert features into polygons.

If you would like to combine individual polygons (or multi-polygons) into a 
single multi-polygon you can use lookup how to do "union".
- http://docs.geotools.org/latest/userguide/library/jts/combine.html
> 
> Can Geotools do the same?
If it cannot, you as a developer can do the rest :-)

Cheers,
Jody
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