Handle removed replisomes in superhelical density calculations

[thalassemia]

If a replisome is unexpectedly removed from the simulation, the superhelical density calculation will fail (see gh-268). While our simulation does not allow this to happen, it can happen in real cells (see https://doi.org/10.1016/S0968-0004(00)01565-6), so I figured I might as well try to tackle the issue.

My solution was to always assume that the now bare replication fork is located at the last recorded location for a removed replisome. For now, I also assume that the bare fork acts like a regular one, treating it as a stationary boundary for superhelical density calculations. In the future, we could introduce more dynamic models of replication fork collapse that include things like dsDNA breaks and replication restart. At that time, we could replace the placeholder indices for removed replisomes with designated indices for each possibility. We could then calculate superhelical density differently for segments bounded by molecules with those indices.

Other minor things:

• Update dependency versions
• Require full experiment ID for runscripts/workflow.py --resume
• Change analysis publish mode to copy to allow caching (no need to rerun when resuming)
• Sanity check that unique molecule indices are unique upon creation
• Add pre-commit instructions to set up ruff linting and formatting for every commit

[github-actions]

Package	Line Rate	Complexity	Health
.	30%	0	❌
analysis	100%	0	✔
analysis.antibiotics_colony	11%	0	❌
analysis.antibiotics_colony.subgen_gene_plots	20%	0	❌
analysis.causality_network	18%	0	❌
analysis.colony	11%	0	❌
analysis.multidaughter	100%	0	✔
analysis.multiexperiment	100%	0	✔
analysis.multigeneration	23%	0	❌
analysis.multiseed	17%	0	❌
analysis.multivariant	17%	0	❌
analysis.single	15%	0	❌
composites	35%	0	❌
composites.ecoli_configs	90%	0	✔
composites.environment	26%	0	❌
debug	17%	0	❌
ecoli	9%	0	❌
ecoli.compendium	18%	0	❌
ecoli.dataclasses	31%	0	❌
ecoli.dataclasses.process	22%	0	❌
ecoli.dataclasses.state	32%	0	❌
ecoli.scripts	43%	0	❌
ecoli.scripts.fold_changes	15%	0	❌
ecoli.scripts.metabolism_kinetics	36%	0	❌
ecoli.scripts.metabolite_concentrations	26%	0	❌
ecoli.scripts.nca	10%	0	❌
ecoli.scripts.protein_half_lives	29%	0	❌
ecoli.scripts.rna_half_lives	21%	0	❌
experiments	35%	0	❌
io	52%	0	➖
library	48%	0	❌
library.cell_wall	14%	0	❌
processes	42%	0	❌
processes.antibiotics	27%	0	❌
processes.chemotaxis	14%	0	❌
processes.environment	29%	0	❌
processes.listeners	78%	0	✔
processes.membrane	27%	0	❌
processes.spatiality	19%	0	❌
processes.stubs	45%	0	❌
tests	22%	0	❌
tests.io	24%	0	❌
tests.utils	25%	0	❌
utils	28%	0	❌
utils._netflow	45%	0	❌
variants	36%	0	❌
Summary	28% (8461 / 30175)	0	❌