[Internal] [Feature] Add more bakta parameters to standard_params.config

[mikeyweigand]

What is the Feature Related To? Please Provide a Description. Add access to additional bakta parameters at runtime: --complete
--compliant
--gram
--keep-contig-headers
--skip-gap
--skip-ori
--skip-plot

Place an :x: in a Box that Best Matches the Feature's Importance:

• [] 1 - Most important (absolutely integral and will not use codebase at all without it)
• [x] 2-4 - Moderate (still using codebase for other functions but is serving as a blocker for future use-cases)
• [] 5 - Least important (would like to see but there are no stringent expectations nor urgency for current/future use-cases) 

Any Additional Context or Information? Has There Been Any Progress Made So Far Towards this Request? Any Helpful Resources to Reference? Screenshots or Links?

Full-feature annotation of bacterial genomes may also require option for user to define --replicons for granular description of contigs and/or known plasmids in multi-fasta inputs. Implementation is a little more complex because requires separate file input for each fasta. Maybe this is simplified with some logic to check if a ${basename}.replicons.tsv matching the fasta is provided in the input directory?

[kyleoconnell]

Updated these as optional params.