v1.1.0 Menu revamp, additional features and QOL improvements.

v1.1.0 introduces a number of improvements to the menu system for PyamilySeq and Seq-Combiner making both tools easier to tune to user needs. Below is a highlights list

• Users can now specific input gff and fasta file affixes
• Numerous additional checks to ensure we don't overwrite existing files & more error handling
• Refined menu parameter names
• Ability to output sequences and alignments for specific groups
• Fixed more issues with gene_presence_absence files

Specifically these changes have now resolved 3 previously raised githut bugs and/or feature requests.

• [Multiple alignment options with -w]
• [Options to specify input file extensions in separate input mode]
• [Seq-Combiner will read in and overwrite the output file.]

Thanks to @ecampbell50 for the requests.