Update READMEs and documentation to reflect new publications

[jdaymude]

This PR updates documentation related to the now-published Seet et al. (2025) paper and our own JOSS publication.

• Updates all documentation previously referring to the arXiv version of the Seet et al. paper to now point to the published and paginated JCIM version.
• Updates dataset generation scripts and documentation to refer to the Seet et al. code as assemblycpp-v5 instead of assembly_cpp.
• Fixed the Zenodo shield in our README to always refer to the latest release instead of the first one specifically.
• Adds a CITATION.cff file to the repository reflecting our own JOSS submission.
• Completes the Citation sections in our READMEs to reflect our JOSS submission.

[jdaymude]

@AgentElement I'm getting a Clippy failure here on GitHub that isn't happening locally. Fixing it would be out of scope for this PR. Please advise on how you'd like this handled.

[AgentElement]

Best to fix the clippy lint in a separate PR and rebase.

[AgentElement]

I fixed the lint errors in #137. If you rebase, the PR should be mergeable.

[AgentElement]

LGTM, congratulations all!