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Previoiusly because of the lack of VCF4 format definition, the user upload of VCF
type data (stored in text) could not be validated. This change is intended to add
this missing information so that those VCF records could be validated and parsed.

Also add space as a valid delimiter in addition to tab. I know this is violating
the VCF4.x spece. But I could not get tab delimited VCF record to work. I don't
know why.

Related to ENSEMBL-5050.

get_raw_samples_info() was returning a ":"-delimited string where
the first element was the sample name. This broke downstream methods
when the sample name contained ":", so the method has been changed
to return a listref instead.

It seems we have others within the team that would like to use
ensembl-io but will not because of the core dependency. This commit
attempts to

1. Remove any use of Utils::Exception and replace it with Carp

2. Remove any use of Utils::IO work_with_file and replace it with an
open

3. Remove any un-used import (there were a lot)

Also this commit pulls up that simple_list.t is no longer a valid test
because its dependencies are broken.

In a number of places the Apache2 license was not applied, the older
Apache-like license was applied or dates were wrong. A header LICENSE
file was not present. It has now been added to all files.

If an array then key by contents of array not the ref which we might be
unlucky and have cached before and it been reused.

For the duplicated methods replace individual by sample to match
the new sample schema in the variation API.

add some extra methods and gymnastics to make fetching genotypes for a subset of individuals much much faster

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