YourePrettyGood/PIBv1_manuscript: PIBv1 manuscript 1.0.0

Release for second resubmission (2026/01/12) of PIBv1 manuscript titled "Long-term isolation and archaic introgression shape functional genetic variation in Near Oceania". This release contains all relevant Nextflow pipelines including those used for both rounds of reviewer responses, and includes submodules for the analysis code and plotting scripts of sections performed by co-authors Daniela Tejada Martinez (@GenomeGaia), Stephen Rong (@stephenrong), Audrey Tjahjadi (@teriyakiaud), and Chang Liu (@Chg-Liu). See the README.md, PROCESSING.md, ANALYSIS.md, and PLOTS.md documents for a detailed description of all contained data processing, analyses, and plots.