Storf-reporter

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.

Fixed output format of StORF-Extractor to be more consistent with StORF-Reporter/Finder.

Thanks to pthieringer for reporting a bug with ('-aa True') outputting the amino acid sequences of the StORFs identified via StORF-Reporter under certain conditions.

Bug link: https://github.com/NickJD/StORF-Reporter/issues/3#issue-2015619725

Thanks to lobrien20 for identifying the change made by the [pyrodigal](https://github.com/althonos/pyrodigal) team to their API call (OrfFinder to GeneFinder).