Command Line Functionality#11

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AHumricho wants to merge 7 commits intoeridanirojas:mainfrom

Commits on Oct 15, 2025

Commits on Oct 29, 2025

Commits on Nov 5, 2025

Command line adapted to new parameters; still needs to change file output location but all functional
AHumricho
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updated clustering analysis files to match current
AHumricho
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