Storf-reporter

- Fixed - UR-Extractor now conforms better to 'standard' FASTA and GFF formats.
- Added - 'Multi_Contig_Genome' test directory for testing against fragmented genomes.

* Fixed - Con-StORFs were incorrectly being reported with middle '*' when 'remove_stop' was set to True (default)
* Fixed - In some instances, when using -odir with 'Multiple_Genomes', 'Multiple_Combined_GFFs' or 'Multiple_GFFs', the input directory name was being applied to the output filename.

The hashing of StORF IDs may have been different between GFF/DNA and the AA outputs. Now the hashing takes the GFF input filename or in the case of a Pyrodigal run, will take the input FASTA filename.

Fixes for issues raised in issue: https://github.com/NickJD/StORF-Reporter/issues/1

Small but important release.
StORF-Reporter can now be run on a directory containing multiple Prokka/Bakta output directories.

Example:
`StORF-Reporter -anno Prokka Multiple_Out_Dirs -p ../Test_Datasets/Multi_Prokka_Outs
`

Thanks to elchaarn (https://github.com/NickJD/StORF-Reporter/issues/1#issue-1927093894) for the suggestion.

- Finalised overhaul of user IO to accommodate user requests and become OS independent for StORF-Reporter.
- Fixed some issues with StORF-Reporter running on a directory of matched Prokka/Bakta gff/fna files.
- Added option "-af" to allow Prokka/Bakta directory names to differ from internal filename prefixes.
- Minor changes to parameter handling to ensure "-sout" is called when "-aa" is selected.
- Feature_Types parameter "-gene_ident Prokka" will select features present in Prokka annotations.

Thanks to [Dx-wmc](https://github.com/Dx-wmc) ([#2 (comment)](https://github.com/NickJD/StORF-Reporter/issues/2#issue-1967329610)) for suggesting some changes to how StORF-Reporter handles IO.