[Bioperl-l] IO code, tempfile, File::Spec etc

[Hilmar Lapp]

Meanwhile not only the -fh/-file object initialization code
started to be duplicated all over the place, but also some code
about central and cross-platform tempfile creation accumulated in
Bio::Root::RootI, where it doesn't naturally belong to.

I thought this situation was calling for trouble sooner or later
and went ahead creating Bio::Root::IO as the new central hub for
file/stream-related IO as well as tempfile/tempdir creation and
cross-platform safe path construction. I mostly gathered the code
from various places, after clean-ups and partial rewrites.

The way to use this module is either by inheriting directly from
it, inheriting by multiple inheritance, or instantiating an object
to use for delegation.

I removed the respective code from Bio::Root::RootI and changed
various modules accordingly. The new IO module is already used by
all IO/parsing modules I was immediately aware of. 

While tests pass so far on my machine, please test on other
platforms, especially on one which has all the Bio::Tools::Run::*
programs available. At the same time some cross-platform should
have gone away, or should be easier to fix.

	Hilmar
--  
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Hilmar Lapp                              email: hlapp@gmx.net
GNF, San Diego, Ca. 92122                phone: +1 858 812 1757
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