Make plotting part of the base package

[iskandr]

Summary

• make matplotlib, adjustText, and matplotlib-venn standard oncoref dependencies
• remove the plots extra and its optional-install documentation
• make plotting tests fail rather than skip when the installation is incomplete
• verify the clean base-install CI environment includes every plotting dependency

Rationale

Oncoref ships plotting modules and plot CLI commands as supported package features. Requiring a separate extra made a normal installation behaviorally incomplete and allowed missing plotting dependencies to suppress test coverage.

Validation

• ./test.sh: 1042 passed, zero skipped
• Ruff check and format checks pass
• wheel build succeeds and declares all three plotting libraries as unconditional Requires-Dist entries