feat: Reuse indices for plasmids based on md5sum

[berntpopp]

Description:
Implement a mechanism to reuse existing indices for plasmids by saving them with an md5sum hash of the input file. If the plasmid input file hasn't changed (based on its md5sum), the corresponding index should be reused, avoiding unnecessary recomputation.

Tasks:

• Generate an md5sum hash for each plasmid input file.
• Save indices with a name or directory structure incorporating the md5sum.
• Check if an index exists for a plasmid input by comparing the md5sum before generating a new index.
• Update documentation to explain the md5sum-based indexing system.
• Add tests to ensure that indices are correctly reused when input files are unchanged.

Benefits:

• Significantly reduces computational time by avoiding redundant index creation.
• Makes the pipeline more efficient, especially when working with large datasets.