Remove PhosphoScoring.py, runPhosphoScoring.py and GUI_*.py files from examples (#490)

* Initial plan

* chore: remove PhosphoScoring.py and GUI_*.py files from examples

Co-authored-by: timosachsenberg <5803621+timosachsenberg@users.noreply.github.com>

* chore: remove runPhosphoScoring.py and update README.md

Co-authored-by: timosachsenberg <5803621+timosachsenberg@users.noreply.github.com>

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Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: timosachsenberg <5803621+timosachsenberg@users.noreply.github.com>
Co-authored-by: Timo Sachsenberg <timo.sachsenberg@uni-tuebingen.de>

Author: Copilot