Remove SpectralRecovery/MbrAnalysis feature (#2605)

* Remove SpectralRecovery/MbrAnalysis feature

This removes the unused SpectralRecovery feature which had failing tests.

Deleted:
- TaskLayer/MbrAnalysis folder (SpectralRecoveryPSM, SpectralRecoveryResults, SpectralRecoveryRunner)
- EngineLayer/ClassicSearch/MiniClassicSearchEngine.cs
- Test/SpectralRecoveryTest.cs and test data

Removed DoSpectralRecovery parameter and related UI from SearchTaskWindow,
MainWindow settings, GuiGlobalParams, and UpdateGUISettings.

Co-Authored-By: Claude Opus 4.5 <[email protected]>

* Remove SpectralRecovery/MbrAnalysis feature

This removes the unused SpectralRecovery feature which had failing tests.

Deleted:
- TaskLayer/MbrAnalysis folder (SpectralRecoveryPSM, SpectralRecoveryResults, SpectralRecoveryRunner)
- EngineLayer/ClassicSearch/MiniClassicSearchEngine.cs
- Test/SpectralRecoveryTest.cs and test data

Removed DoSpectralRecovery parameter and related UI from SearchTaskWindow,
MainWindow settings, GuiGlobalParams, and UpdateGUISettings.

Co-Authored-By: Claude Opus 4.5 <[email protected]>

---------

Co-authored-by: Claude Opus 4.5 <[email protected]>
Co-authored-by: trishorts <[email protected]>

Author: 3 people

MetaMorpheus/EngineLayer/ClassicSearch/MiniClassicSearchEngine.cs

@@ -5,15 +5,4 @@ internal class ScanWithIndexAndNotchInfo(int notch, int scanIndex)
         public readonly int Notch = notch;
         public readonly int ScanIndex = scanIndex;
     }
-
-    /// <summary>
-    /// For use in MiniClassicSearchEngine
-    /// </summary>
-    /// <param name="scan"></param>
-    /// <param name="notch"></param>
-    /// <param name="scanIndex"></param>
-    internal class ExtendedScanWithIndexAndNotchInfo(Ms2ScanWithSpecificMass scan, int notch, int scanIndex) : ScanWithIndexAndNotchInfo(notch, scanIndex)
-    {
-        public readonly Ms2ScanWithSpecificMass TheScan = scan;
-    }
 }

MetaMorpheus/EngineLayer/Util/ScanWithIndexAndNotchInfo.cs

@@ -1001,20 +1001,15 @@
                             <CheckBox Grid.Row="5" Grid.Column="1" Content="Ask" IsChecked="{Binding AskAboutArgCParams, Mode=TwoWay}" VerticalAlignment="Center"/>
                             <CheckBox Grid.Row="5" Grid.Column="2" Content="Use" IsChecked="{Binding UseArgCParams, Mode=TwoWay}" VerticalAlignment="Center"/>
 
-                            <TextBlock Grid.Row="6" Grid.Column="0" Text="Spectral Recovery Recommendations" 
-                                           VerticalAlignment="Center" Style="{StaticResource TextBlockStyle}"/>
-                            <CheckBox Grid.Row="6" Grid.Column="1" Content="Ask" IsChecked="{Binding AskAboutSpectralRecoveryParams, Mode=TwoWay}" VerticalAlignment="Center"/>
-                            <CheckBox Grid.Row="6" Grid.Column="2" Content="Use" IsChecked="{Binding UseSpectralRecoveryParams, Mode=TwoWay}" VerticalAlignment="Center"/>
-                            
-                            <TextBlock Grid.Row="7" Grid.Column="0" Text="Overwrite Output Directory" 
+                            <TextBlock Grid.Row="6" Grid.Column="0" Text="Overwrite Output Directory"
                                        VerticalAlignment="Center" Style="{StaticResource TextBlockStyle}"/>
-                            <CheckBox Grid.Row="7" Grid.Column="1" Content="Ask" IsChecked="{Binding AskAboutOverwritingOutputDirectory, Mode=TwoWay}" VerticalAlignment="Center"/>
-                            <CheckBox Grid.Row="7" Grid.Column="2" Content="Overwrite" IsChecked="{Binding OverwriteOutputDirectory, Mode=TwoWay}" VerticalAlignment="Center"/>
-                            
-                            <TextBlock Grid.Row="8" Grid.Column="0" Text="Protein/RNA Mode Switching Prompt" 
+                            <CheckBox Grid.Row="6" Grid.Column="1" Content="Ask" IsChecked="{Binding AskAboutOverwritingOutputDirectory, Mode=TwoWay}" VerticalAlignment="Center"/>
+                            <CheckBox Grid.Row="6" Grid.Column="2" Content="Overwrite" IsChecked="{Binding OverwriteOutputDirectory, Mode=TwoWay}" VerticalAlignment="Center"/>
+
+                            <TextBlock Grid.Row="7" Grid.Column="0" Text="Protein/RNA Mode Switching Prompt"
                                        VerticalAlignment="Center" Style="{StaticResource TextBlockStyle}"/>
-                            <CheckBox Grid.Row="8" Grid.Column="1" Content="Ask" IsChecked="{Binding AskAboutModeSwitch, Mode=TwoWay}" VerticalAlignment="Center"/>
-                            <ComboBox Grid.Row="8" Grid.Column="2" VerticalAlignment="Center" Width="154" HorizontalAlignment="Left"
+                            <CheckBox Grid.Row="7" Grid.Column="1" Content="Ask" IsChecked="{Binding AskAboutModeSwitch, Mode=TwoWay}" VerticalAlignment="Center"/>
+                            <ComboBox Grid.Row="7" Grid.Column="2" VerticalAlignment="Center" Width="154" HorizontalAlignment="Left"
                                       ItemsSource="{Binding AllModeSwitchValues}"
                                       SelectedItem="{Binding CachedModeSwitchResult, Mode=TwoWay}" />
                         </Grid>