[Bioperl-l] documentation changes

[Allen Day]

Okay, I've made some major changes to the core bioperl documentation 
generation process.  The documentation itself remains the same, except 
that I've slightly modified "bioperl.pod".

However, there are no longer .pod files distributed with bioperl.  They've 
all been converted over to .PL files, and in Makefile.PL, there is a 
directive to generate .pod files from .PL files.  This is useful in that 
it allows us to alter the content of the documentation based 
on a configuration file.  It works like this:

- Makefile.PL has a section that writes a file called "bioperl.conf".  
  bioperl.conf is simple, currently containing only a version number and
  a reference to where the bioperl author info can be found.

- when the user runs 'make all', the .PL files are processed into .pod 
  files by doing variable substitution using the bioperl.conf file, and 
  a module called LocalConfig.pm (included in the bioperl distribution).

- when the user runs 'make install', the .pod files are installed to the 
  man section 3, as before.

So I've added links to the currently existing pod documentation to 
bioperl.pod, and would like to add more links to other existing 
documentation, so let me know what is available!

I'd also like to move bptutorial into a .PL file for autogeneration as
well, and would like to be able to have it installed into man section 3 as
well.  Can we do this Peter?

-Allen