Fix Linux desktop integration: holistic sync, wildcard MIME resolution

Three interconnected fixes:

1. Wildcard MIME sentinel resolution (image/* -> image/x-m71 etc.)
   LinuxPlatform now resolves wildcard sentinels from DesktopService at
   write time: checks /usr/share/mime/globs2 for a system-known type
   matching the prefix, otherwise synthesizes prefix/x-sanitized-ext.
   Fixes StringIndexOutOfBoundsException in generateMimeTypeComment for
   extensions that produce empty parts after sanitization.

2. Holistic desktop file synthesis
   Add syncDesktopIntegration(webLinks, desktopIcon, fileTypes) to
   DesktopIntegrationProvider (default delegates to individual setters).
   LinuxPlatform overrides it to build the .desktop file from scratch in
   one pass: all-false deletes the file; otherwise Exec is always written,
   icon fields / scheme handlers / MIME types are added conditionally.
   Individual setters now read current state and delegate, staying correct
   when called in isolation.

3. Fix isDesktopIconPresent() and OptionsDesktop.run()
   isDesktopIconPresent() now checks Name+Exec in the loaded file rather
   than bare file existence, so a file present only for web links or MIME
   types is not mistaken for an icon entry.
   OptionsDesktop.run() gathers all three desired states then calls
   syncDesktopIntegration once, eliminating order-dependent stomping.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: ctrueden

src/main/java/org/scijava/desktop/DesktopIntegrationProvider.java

@@ -101,6 +101,32 @@ public interface DesktopIntegrationProvider {
 	 */
 	void setFileExtensionsEnabled(final boolean enable) throws IOException;
 
+	/**
+	 * Atomically applies all three desktop integration settings at once.
+	 * <p>
+	 * Implementations that store all three settings in a single artifact
+	 * (e.g. a Linux {@code .desktop} file) should override this method to
+	 * synthesize that artifact in one pass rather than via three independent
+	 * read-modify-write cycles.
+	 * </p>
+	 * <p>
+	 * The default implementation calls the three individual setters in order,
+	 * guarded by the corresponding {@code isXxxToggleable()} checks.
+	 * </p>
+	 *
+	 * @param webLinks     whether URI scheme handlers should be registered
+	 * @param desktopIcon  whether the application launcher entry should be present
+	 * @param fileTypes    whether file-extension associations should be registered
+	 * @throws IOException if any part of the update fails
+	 */
+	default void syncDesktopIntegration(final boolean webLinks,
+		final boolean desktopIcon, final boolean fileTypes) throws IOException
+	{
+		if (isWebLinksToggleable()) setWebLinksEnabled(webLinks);
+		if (isDesktopIconToggleable()) setDesktopIconPresent(desktopIcon);
+		if (isFileExtensionsToggleable()) setFileExtensionsEnabled(fileTypes);
+	}
+
 	/**
 	 * Creates a SchemeInstaller for this platform.
 	 *

src/main/java/org/scijava/desktop/options/OptionsDesktop.java

@@ -29,7 +29,7 @@
 
 package org.scijava.desktop.options;
 
-import java.util.concurrent.Callable;
+import java.io.IOException;
 import java.util.stream.Stream;
 
 import org.scijava.ItemVisibility;
@@ -99,21 +99,22 @@ public void initialize() {
 	@Override
 	public void run() {
 		desktopPlatforms().forEach(p -> {
-			if (p.isWebLinksToggleable()) {
-				final Boolean enabled = getInputValue(webLinksItem);
-				toggle(() -> { p.setWebLinksEnabled(enabled); return null; },
-					enabled ? "enabling web links" : "disabling web links");
+			// Resolve each feature's desired state: use the checkbox value
+			// if toggleable, otherwise preserve the current platform state.
+			final boolean webLinks = p.isWebLinksToggleable()
+				? Boolean.TRUE.equals(getInputValue(webLinksItem))
+				: p.isWebLinksEnabled();
+			final boolean desktopIcon = p.isDesktopIconToggleable()
+				? Boolean.TRUE.equals(getInputValue(desktopIconItem))
+				: p.isDesktopIconPresent();
+			final boolean fileTypes = p.isFileExtensionsToggleable()
+				? Boolean.TRUE.equals(getInputValue(fileTypesItem))
+				: p.isFileExtensionsEnabled();
+			try {
+				p.syncDesktopIntegration(webLinks, desktopIcon, fileTypes);
 			}
-			if (p.isDesktopIconToggleable()) {
-				final Boolean enabled = getInputValue(desktopIconItem);
-				toggle(() -> { p.setDesktopIconPresent(enabled); return null; },
-					enabled ? "adding desktop icon" : "removing desktop icon");
-			}
-			if (p.isFileExtensionsToggleable()) {
-				final Boolean enabled = getInputValue(fileTypesItem);
-				toggle(() -> { p.setFileExtensionsEnabled(enabled); return null; },
-					enabled ? "enabling file type associations" :
-						"removing file type associations");
+			catch (final IOException e) {
+				if (log != null) log.error("Error performing desktop integration", e);
 			}
 		});
 		super.run();
@@ -154,15 +155,6 @@ private Boolean getInputValue(final ModuleItem<?> item) {
 		return (Boolean) getInput(item.getName());
 	}
 
-	private void toggle(final Callable<?> toggleAction, final String errorMessage) {
-		try {
-			toggleAction.call();
-		}
-		catch (final Exception e) {
-			if (log != null) log.error("Error " + errorMessage, e);
-		}
-	}
-
 	private boolean isDesktopIconToggleable() {
 		return desktopPlatforms().anyMatch(p -> p.isDesktopIconToggleable());
 	}