Support filtering functions for analysis creation and attaching

# Conflicts:
#	src/main/java/ai/reveng/toolkit/ghidra/binarysimilarity/ui/analysiscreation/RevEngAIAnalysisOptionsDialog.java
#	src/test/java/ai/reveng/AnalysisOptionsDialogTest.java

Author: fmagin

src/main/java/ai/reveng/toolkit/ghidra/Utils.java

@@ -55,6 +55,43 @@ public static <ROW_TYPE, COLUMN_TYPE> void addRowToDescriptor(
         addRowToDescriptor(descriptor, columnName, true, columnTypeClass, rowObjectAccessor);
     }
 
+    /**
+     * Helper method to add a column with sort ordinal specification.
+     * @param sortOrdinal 1-based sort priority (1 = primary sort), or -1 for no default sort
+     * @param ascending true for ascending sort, false for descending
+     */
+    public static <ROW_TYPE, COLUMN_TYPE> void addRowToDescriptor(
+            TableColumnDescriptor<ROW_TYPE> descriptor,
+            String columnName,
+            Class<COLUMN_TYPE> columnTypeClass,
+            RowObjectAccessor<ROW_TYPE, COLUMN_TYPE> rowObjectAccessor,
+            int sortOrdinal,
+            boolean ascending) {
+
+        var column = new AbstractDynamicTableColumn<ROW_TYPE, COLUMN_TYPE, Object>() {
+            @Override
+            public String getColumnName() {
+                return columnName;
+            }
+
+            @Override
+            public COLUMN_TYPE getValue(ROW_TYPE rowObject, Settings settings, Object data, ServiceProvider serviceProvider) throws IllegalArgumentException {
+                return rowObjectAccessor.access(rowObject);
+            }
+
+            @Override
+            public Class<COLUMN_TYPE> getColumnClass() {
+                return columnTypeClass;
+            }
+
+            @Override
+            public Class<ROW_TYPE> getSupportedRowType() {
+                return null;
+            }
+        };
+        descriptor.addVisibleColumn(column, sortOrdinal, ascending);
+    }
+
 
 
     @FunctionalInterface

src/main/java/ai/reveng/toolkit/ghidra/binarysimilarity/cmds/ApplyMatchCmd.java

@@ -48,9 +48,7 @@ private boolean shouldApplyMatch() {
         return func != null &&
                 // Do not override user-defined function names
                 func.getSymbol().getSource() != SourceType.USER_DEFINED &&
-                // Exclude thunks and external functions
-                !func.isThunk() &&
-                !func.isExternal() &&
+                GhidraRevengService.isRelevantForAnalysis(func) &&
                 // Only accept valid names (no spaces)
                 !match.functionMatch().nearest_neighbor_mangled_function_name().contains(" ") &&
                 !match.functionMatch().nearest_neighbor_function_name().contains(" ")

src/main/java/ai/reveng/toolkit/ghidra/binarysimilarity/ui/analysiscreation/RevEngAIAnalysisOptionsDialog.java

@@ -2,10 +2,12 @@
 
 import ai.reveng.model.ConfigResponse;
 import ai.reveng.toolkit.ghidra.binarysimilarity.ui.dialog.RevEngDialogComponentProvider;
+import ai.reveng.toolkit.ghidra.binarysimilarity.ui.functionselection.FunctionSelectionPanel;
 import ai.reveng.toolkit.ghidra.core.services.api.AnalysisOptionsBuilder;
 import ai.reveng.toolkit.ghidra.core.services.api.GhidraRevengService;
 import ai.reveng.toolkit.ghidra.core.services.api.types.AnalysisScope;
 import ai.reveng.toolkit.ghidra.plugins.ReaiPluginPackage;
+import ghidra.framework.plugintool.PluginTool;
 import ghidra.program.model.listing.Program;
 import ghidra.util.Msg;
 import ghidra.util.Swing;
@@ -25,6 +27,7 @@ public class RevEngAIAnalysisOptionsDialog extends RevEngDialogComponentProvider
     private JCheckBox dynamicExecutionCheckBox;
     private final Program program;
     private final GhidraRevengService service;
+    private final PluginTool tool;
     private JRadioButton privateScope;
     private JRadioButton publicScope;
     private JTextField tagsTextBox;
@@ -33,22 +36,25 @@ public class RevEngAIAnalysisOptionsDialog extends RevEngDialogComponentProvider
     private JCheckBox identifyCVECheckBox;
     private JCheckBox generateSBOMCheckBox;
     private JComboBox<String> architectureComboBox;
+    private FunctionSelectionPanel functionSelectionPanel;
     private boolean okPressed = false;
+    private boolean configCheckPassed = false;
 
     private JLabel fileSizeWarningLabel;
     private JLabel loadingLabel;
 
-    public static RevEngAIAnalysisOptionsDialog withModelsFromServer(Program program, GhidraRevengService reService) {
-        return new RevEngAIAnalysisOptionsDialog(program, reService);
+    public static RevEngAIAnalysisOptionsDialog withModelsFromServer(Program program, GhidraRevengService reService, PluginTool tool) {
+        return new RevEngAIAnalysisOptionsDialog(program, tool, reService);
     }
 
-    public RevEngAIAnalysisOptionsDialog(Program program, GhidraRevengService service) {
+    public RevEngAIAnalysisOptionsDialog(Program program, PluginTool tool, GhidraRevengService service) {
         super(ReaiPluginPackage.WINDOW_PREFIX + "Configure Analysis for %s".formatted(program.getName()), true);
         this.program = program;
         this.service = service;
+        this.tool = tool;
 
         buildInterface();
-        setPreferredSize(320, 420);
+        setPreferredSize(600, 550);
 
         fetchConfigAsync();
     }
@@ -176,18 +182,26 @@ private void buildInterface() {
         loadingLabel.setBorder(BorderFactory.createEmptyBorder(5, 5, 5, 5));
         workPanel.add(loadingLabel);
 
+        workPanel.add(new JSeparator(SwingConstants.HORIZONTAL));
+
+        // Add function selection panel
+        functionSelectionPanel = new FunctionSelectionPanel(tool);
+        functionSelectionPanel.initForProgram(program);
+        functionSelectionPanel.getTableModel().addTableModelListener(e -> updateStartButtonState());
+        workPanel.add(functionSelectionPanel);
+
+
         addCancelButton();
         addOKButton();
 
         okButton.setText("Start Analysis");
-        okButton.setEnabled(false); // Disabled until config check completes
+        okButton.setEnabled(false); // Disabled until config check completes and functions are selected
     }
 
-    public @Nullable AnalysisOptionsBuilder getOptionsFromUI() {
-        if (!okPressed) {
-            return null;
-        }
-        var options = AnalysisOptionsBuilder.forProgram(program);
+    public AnalysisOptionsBuilder getOptionsFromUI() {
+        // Use the selected functions from the function selection panel
+        var selectedFunctions = functionSelectionPanel.getSelectedFunctions();
+        var options = AnalysisOptionsBuilder.forProgramWithFunctions(program, selectedFunctions);
 
         options.skipScraping(!scrapeExternalTagsBox.isSelected());
         options.skipCapabilities(!identifyCapabilitiesCheckBox.isSelected());
@@ -216,6 +230,10 @@ protected void okCallback() {
         close();
     }
 
+    public boolean isOkPressed() {
+        return okPressed;
+    }
+
     @Override
     public JComponent getComponent() {
         return super.getComponent();
@@ -239,7 +257,8 @@ private void handleConfigResponse(@Nullable ConfigResponse config) {
 
         if (config == null) {
             // Config fetch failed, allow upload attempt (server will reject if too large)
-            okButton.setEnabled(true);
+            configCheckPassed = true;
+            updateStartButtonState();
             return;
         }
 
@@ -251,7 +270,8 @@ private void validateFileSize(long maxFileSizeBytes) {
         long fileSize = getProgramFileSize();
         if (fileSize < 0) {
             // Could not determine file size, allow upload attempt
-            okButton.setEnabled(true);
+            configCheckPassed = true;
+            updateStartButtonState();
             return;
         }
 
@@ -262,13 +282,19 @@ private void validateFileSize(long maxFileSizeBytes) {
                     "<html><center>File size (%s) exceeds<br>server limit (%s)</center></html>"
                             .formatted(fileSizeStr, maxSizeStr));
             fileSizeWarningLabel.setVisible(true);
-            okButton.setEnabled(false);
+            configCheckPassed = false;
+            updateStartButtonState();
         } else {
             fileSizeWarningLabel.setVisible(false);
-            okButton.setEnabled(true);
+            configCheckPassed = true;
+            updateStartButtonState();
         }
     }
 
+    private void updateStartButtonState() {
+        okButton.setEnabled(configCheckPassed && functionSelectionPanel.getSelectedCount() > 0);
+    }
+
     private long getProgramFileSize() {
         try {
             Path filePath;

src/main/java/ai/reveng/toolkit/ghidra/binarysimilarity/ui/functionselection/FunctionRowObject.java

@@ -0,0 +1,106 @@
+package ai.reveng.toolkit.ghidra.binarysimilarity.ui.functionselection;
+
+import ai.reveng.toolkit.ghidra.core.services.api.types.FunctionInfo;
+import ghidra.program.model.address.Address;
+import ghidra.program.model.listing.Function;
+
+import javax.annotation.Nullable;
+
+/**
+ * Wrapper around a Ghidra {@link Function} with a mutable selection flag.
+ * Used to display functions in a table where users can select which functions
+ * to include in analysis.
+ */
+public class FunctionRowObject {
+    private final Function function;
+    private boolean selected;
+    private boolean enabled = true;
+    @Nullable
+    private FunctionInfo remoteFunctionInfo;
+
+    public FunctionRowObject(Function function, boolean selected) {
+        this.function = function;
+        this.selected = selected;
+    }
+
+    public Function getFunction() {
+        return function;
+    }
+
+    public String getName() {
+        return function.getName();
+    }
+
+    public Address getAddress() {
+        return function.getEntryPoint();
+    }
+
+    /**
+     * Returns the size of the function based on address count.
+     */
+    public long getSize() {
+        return function.getBody().getNumAddresses();
+    }
+
+    public boolean isExternal() {
+        return function.isExternal();
+    }
+
+    public boolean isThunk() {
+        return function.isThunk();
+    }
+
+    /**
+     * Returns a human-readable type string for the function.
+     */
+    public String getType() {
+        if (isExternal()) {
+            return "External";
+        } else if (isThunk()) {
+            return "Thunk";
+        } else {
+            return "Normal";
+        }
+    }
+
+    public boolean isSelected() {
+        return selected;
+    }
+
+    public void setSelected(boolean selected) {
+        if (!enabled) {
+            return;
+        }
+        this.selected = selected;
+    }
+
+    public boolean isEnabled() {
+        return enabled;
+    }
+
+    public void setEnabled(boolean enabled) {
+        this.enabled = enabled;
+        if (!enabled) {
+            this.selected = false;
+        }
+    }
+
+    @Nullable
+    public FunctionInfo getRemoteFunctionInfo() {
+        return remoteFunctionInfo;
+    }
+
+    public void setRemoteFunctionInfo(@Nullable FunctionInfo remoteFunctionInfo) {
+        this.remoteFunctionInfo = remoteFunctionInfo;
+    }
+
+    @Nullable
+    public String getRemoteFunctionName() {
+        return remoteFunctionInfo != null ? remoteFunctionInfo.functionName() : null;
+    }
+
+    @Nullable
+    public Long getRemoteFunctionID() {
+        return remoteFunctionInfo != null ? remoteFunctionInfo.functionID().value() : null;
+    }
+}