Documentation update

[Willem Ferguson]

Herewith another update. Two changes:

1) Correction of references to external literature as previously 
discussed. Only URLs to web in manual now.
2) Section on the subsurface Preferences added.

Please look at at last two paragraphs on the preferences section, as 
well as the problematic parts with external references.

Two things to keep in mind:
a) I personally prefer the asciidoc translation with a toclevels=3 
option. default toclevels=2 shortens contents list so as to loose a lot 
of functionality for a person seeking specific information.

b) The links to web outside that I added actually do not work well if 
the documentation is invoked from Help->User manual. One cannot get back 
from the external source to the user manual. Any ideas?

External sources of information a big headache. Immersed magazine does 
not exist anymore. Baker's articles all in third-level repositories that 
may have a doubtful long term existence. In my work I deal with 
copyright issues every day. I am looking at possibilities.

Kind regards,
willmf

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