New phenotype msa output

Goal of this merge request is to update the phenotype output of the msa function. It was only generated for one phenotype that had to be included wit

Most important changes

• Removed the old output files
• A phenotype file is generated for every phenotype property. The output holds shared/specific/exclusive SNPs or substitutions. Does not create output for phenotypes with numerical values, because the majority of variable positions will be specific.
• Generation of phenotype output is optional. Output is only created when --phenotype argument is included.
• A new gene tree is created for every phenotype property in the pangenome. Phenotype values are included in the label
• Resolved issue in add_phenotype where all phenotypes values were recognized as a 'String'.
• Resolved issue where the ITOL tree templates in msa —method=multiple-groups did not match the gene trees.
• The MLSA function no longer finds phenotype specific positions.

To do:

• Resolve merge conflicts
• Document the Java functions
• Update the read the docs manual
• Use --phenotype-thresold to adjust thresholds
• Update changelog