[Biopython-dev] Modules to be removed from Biopython

[Peter]

As part of the general Martel/Mindy clean up, I've added a deprecation
warning to Mindy and several other closely related modules, but have
only made a docstring change to Martel.  I'm not sure if we should add
a deprecation warning to Martel directly - it would be triggered by
running the Biopython setup.py file which is nasty.  Perhaps for this
special case, documentation is enough?

Summary:

* Martel - labelled as deprecated for 1.49, but no explicit warning (see above)
* Bio.Mindy - deprecated for 1.49
* Bio.Std - deprecated for 1.49
* Bio.StdHandler - deprecated for 1.49
* Bio.builders - deprecated for 1.49
* Bio.Decode - deprecated for 1.49
* Bio.Writer (and Bio.writers.*) deprecated in 1.48
* Bio.expressions - deprecated in 1.44, removed for 1.49
* Bio.config - effectively deprecated in 1.44, explicitly in 1.48,
removed for 1.49
* Bio.dbdefs - effectively deprecated in 1.44, explicitly in 1.48,
removed for 1.49
* Bio.formatdefs - effectively deprecated in 1.44, explicitly in 1.48,
removed for 1.49

Open questions:
* Bio.DBXRef - does anyone known what this is for?
* Bio.SGMLExtractor - deprecated in 1.46, ready for removal?

As a bonus once we've moved from CVS to SVN, we should be able to
remove some of the now empty directories in CVS :)

Peter