Initial Wo and Ho matrices must be non-negative

This explains the issue being resolved with a positive filter prior to
return - as any negative initials were corrected on the first iteration.

Properly document this and remove filter.
Be a little more intelligent in doing work
Failed to retain reallocation
Optional allocation for Apply and Clone
Documentation improvements
Almost all inter-type operations supported
Remove/remodel relict vector code

A long time ago vectors in either axis were representable with single
rows (actually columns then), to improve performance. The sparse code
deleted here is a relict of that. A minor modification of this is still
valid for the dense representation.

Also, make c safe when c == the receiver.
Remove unnecessary use of unsafe
Provide direct access to matrix representation

This allows engineering of lower level operations using e.g. blas, and
easy conversion between biogo dense matrices and go.matrix dense
matrices.
Make UnsafeDense binary compatible with go.matrix

I like this layout less, but this makes interconversion easier.
Missed in previous commit
Revisions due to github issue report 2

https://github.com/kortschak/biogo/issues/2

Looking at the code because of this report showed a fair amount of work
to be done.
Get and Set columns and rows
More type interoperation
Add migration warning

Development has moved to code.google.com/p/biogo.matrix so that users do
not need to pull all of biogo when they are only interested in linalg.
Make package deprecation automatic
Revision of bed handler - use new feat types

I'm not completely sure of the formatting approach, but it works and
changes to the implementation should leave the API untouched.

An alternative approach to the structure of the collection of Bed* types
was to use embedding resulting in nesting up to 4 levels deep. I felt
that this would be cumbersome for the user, so we have code duplication
here instead.
Revision of gff handler - use new feat types
Documentation improvements
Use new feat type