Remove PhosphoScoring.py, runPhosphoScoring.py and GUI_*.py files from examples

[Copilot]

Removes legacy example files from src/examples/ as requested.

Removed files

• PhosphoScoring.py
• runPhosphoScoring.py
• GUI_EXAMPLE_BASE.py
• GUI_ErrorWidget.py
• GUI_MS1MapWidget.py
• GUI_ScanBrowserWidget.py
• GUI_ScanTableWidget.py
• GUI_SequenceIonsWidget.py
• GUI_SpectrumWidget.py
• GUI_TICWidget.py

Updated files

• README.md - removed runPhosphoScoring.py documentation entry

Original prompt

remove PhosphoScoring.py and all files with GUI_*.py in the examples folder

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[timosachsenberg]

@copilot check if these files are anywhere referenced or used

[Copilot]

@copilot check if these files are anywhere referenced or used

I checked for references to the removed files:

PhosphoScoring.py is referenced in:

• src/examples/runPhosphoScoring.py (line 4) - imports PhosphoScorerSimple, PhosphoScorerAScore from it
• src/examples/README.md (line 23) - documents runPhosphoScoring.py

GUI_*.py files - No external references found. They only imported from each other internally.

The runPhosphoScoring.py script is now broken since it imports from the removed PhosphoScoring.py. Would you like me to also remove runPhosphoScoring.py and update the README.md to remove its documentation entry?

[timosachsenberg]

@copilot remove runPhosphoScoring.py and update readme

[Copilot]

@copilot remove runPhosphoScoring.py and update readme

Done in b4f16d4. Removed runPhosphoScoring.py and updated README.md to remove its documentation entry.