Add clipping mode for GFF parser, add code to allow separate reading/getting of header, needed to support fileserver.

Fix up file server to cope with a default alignment/block, NOTE, this needs reworking to cope with multiple alignments/blocks.

Make all feature structs have unique_id + original_id and add an AnyFeatureStruct for general handling of features.

Interim check-in; most things now work, but the hash table is not kept in sync when you change item coordinates