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Stabilize CLI, modularize commands, migrate packaging to uv + pyproject.toml#25

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Stabilize CLI, modularize commands, migrate packaging to uv + pyproject.toml#25
Copilot wants to merge 2 commits into
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copilot/explore-codebase-improvement-plan

chore: migrate to uv + pyproject.toml, remove requirements.txt and se…

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