Attempt to reinstate javadoc generation

Author: tferr

pom.xml

@@ -182,15 +182,16 @@
 			<!--
 				WORKAROUND: jzy3d-native-jogl-awt has an invalid automatic module
 				name ('native' is a Java keyword), causing javadoc generation to fail
-				with "Unable to derive module descriptor". failOnError=false allows
-				the release to proceed. Remove once jzy3d publishes a fixed jar with
-				a valid Automatic-Module-Name in its manifest. See also:
-				https://github.com/jzy3d/jzy3d-api/issues
+				with "Unable to derive module descriptor". legacyMode bypasses JPMS
+				module-path resolution entirely, using classpath instead. Remove once
+				jzy3d publishes a fixed jar with a valid Automatic-Module-Name in
+				its manifest. See also: https://github.com/jzy3d/jzy3d-api/issues
 			-->
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-javadoc-plugin</artifactId>
 				<configuration>
+					<legacyMode>true</legacyMode>
 					<failOnError>false</failOnError>
 				</configuration>
 			</plugin>

src/main/java/sc/fiji/snt/PathFitter.java

@@ -60,10 +60,10 @@
  * List<PathFitter> fitters = paths.stream()
  *     .map(p -> new PathFitter(img, p))
  *     .collect(Collectors.toList());
- *
+ * <p>
  * // Parallel fitting
  * fitters.parallelStream().forEach(PathFitter::call);
- *
+ * <p>
  * // Sequential application
  * fitters.forEach(PathFitter::applyFit);
  * }

src/main/java/sc/fiji/snt/SearchProgressCallback.java

@@ -24,6 +24,10 @@
 
 import sc.fiji.snt.tracing.SearchInterface;
 
+/**
+ * Callback interface for monitoring progress of a search operation during path tracing.
+ * Provides updates on points evaluated, completion status, and thread state changes.
+ */
 public interface SearchProgressCallback {
 
 	/* How many points have we considered? */

src/main/java/sc/fiji/snt/analysis/PersistenceAnalyzer.java

@@ -456,7 +456,7 @@ public List<Double> getBarcode(final String descriptor) throws UnknownMetricExce
      * <strong>Correspondence:</strong> The order of node pairs matches the order of birth-death pairs 
      * returned by {@link #getDiagram(String)}, allowing direct correlation between topological 
      * features and their spatial locations.
-     * 
+     * <p>
      * <strong>Example Usage:</strong>
      * <pre>{@code
      * List<List<Double>> diagram = analyzer.getDiagram("geodesic");

src/main/java/sc/fiji/snt/analysis/UnknownMetricException.java

@@ -22,6 +22,9 @@
 
 package sc.fiji.snt.analysis;
 
+/**
+ * Exception thrown when a requested metric is not available or recognized.
+ */
 public class UnknownMetricException extends IllegalArgumentException {
 	private static final long serialVersionUID = 1L;
 

src/main/java/sc/fiji/snt/event/SNTEvent.java

@@ -22,6 +22,10 @@
 
 package sc.fiji.snt.event;
 
+/**
+ * Base event class for SNT events. Represents various application-level events
+ * such as quit, exit, and data transfer operations.
+ */
 public class SNTEvent {
 
 	/** Event type indicating no specific event */

src/main/java/sc/fiji/snt/event/SNTListener.java

@@ -22,6 +22,10 @@
 
 package sc.fiji.snt.event;
 
+/**
+ * Listener interface for SNT events. Implementers are notified when
+ * SNT events occur.
+ */
 public interface SNTListener {
 
 	/**

src/main/java/sc/fiji/snt/gui/CheckboxSpinner.java

@@ -25,6 +25,10 @@
 import javax.swing.*;
 import java.awt.*;
 
+/**
+ * A custom GUI component combining a checkbox and spinner control in a single panel.
+ * Useful for options where a numeric parameter can be enabled or disabled with a checkbox.
+ */
 public class CheckboxSpinner extends JPanel {
 
 	private static final long serialVersionUID = 937359242995500492L;

src/main/java/sc/fiji/snt/gui/ColorChooserButton.java

@@ -27,7 +27,7 @@
 
 /**
  * Creates a JButton holding a color chooser. It is based on
- * https://stackoverflow.com/a/30433662 released under cc-by-sa
+ * <a href="https://stackoverflow.com/a/30433662">...</a> released under cc-by-sa
  */
 public class ColorChooserButton extends JButton {
 

src/main/java/sc/fiji/snt/gui/ComponentMover.java

@@ -32,13 +32,13 @@
  *  moved can be a high level Window (ie. Window, Frame, Dialog) in which case
  *  the Window is moved within the desktop. Or the Component can belong to a
  *  Container in which case the Component is moved within the Container.
- *
+ * <p>
  *  When moving a Window, the listener can be added to a child Component of
  *  the Window. In this case attempting to move the child will result in the
  *  Window moving. For example, you might create a custom "Title Bar" for an
  *  undecorated Window and moving of the Window is accomplished by moving the
  *  title bar only. Multiple components can be registered as "window movers".
- *
+ * <p>
  *  Components can be registered when the class is created. Additional
  *  components can be added at any time using the registerComponent() method.
  */
@@ -237,7 +237,7 @@ public void setSnapSize(Dimension snapSize)
 
     /**
      *  Setup the variables used to control the moving of the component:
-     *
+     * <p>
      *  source - the source component of the mouse event
      *  destination - the component that will ultimately be moved
      *  pressed - the Point where the mouse was pressed in the destination