Allow console colors to be disabled globally.

Also adds support for forcing the use of colors, even if the destination
is not a terminal. This allows colors when using e.g. 'less' or piping to
a file.
Missing .fai file in example project.
Fix for setup script for phylo example project.
Move ExtractReference node / add sanity checks.
Allow multiple ref. sequences in phylo_pipeline.

The name of the sample is now used to locate the
FASTA file in the prefix folder; thus to include the
prefix, the name of the prefix is used for a sample with
the "Reference Sequence" genotyping method.
Cleanup.
Option to add prefix to output contig names.
Minor improvements of BED check messages.
Reworking sequence nodes, and related phylo parts.

Reworking / cleanup of 'sequences' nodes; add extra checks to
ensure that sequences are correctly collected; index genotyped
sequences to simplify merging.

Reference sequences included in the phylo pipeline are now expected
to be located in the 'refseqs' folder; thus if sample X is a
"Reference Sequence", the default location is expected to be
./data/refseqs/{Prefix}.{X}.fasta. This is to allow mutliple
reference sequences and/or different prefixes.
Minor cleanup.
Require that Paired pre-trimmed reads are in fact paired.
Include qualities to avoid false positives for optical duplicates.