Complete phase 1: fix hardcoded elements

1. Remove Hardcoded Scheme Names

- WindowsPlatform: Now queries LinkService for schemes
- LinuxPlatform: Now queries LinkService for schemes
- Both platforms now:
  - Inject LinkService as a parameter
  - Implement collectSchemes() helper method
  - Check/install/uninstall ALL schemes dynamically

2. Add getSchemeInstaller method

- New method: DesktopIntegrationProvider#getSchemeInstaller
- Allows platforms to provide SchemeInstaller instances
- All three platforms now implement this method:
  - WindowsPlatform: Returns WindowsSchemeInstaller
  - LinuxPlatform: Returns LinuxSchemeInstaller
  - MacOSPlatform: Returns null (Info.plist only)

3. Refactor DefaultLinkService#createInstaller()

- Removed: Hardcoded OS name string checks
- Added: Uses PlatformService.getTargetPlatforms() to find platform
- Result: Plugin-based architecture, no OS-specific code in LinkService

Co-authored-by: Claude Sonnet 4.5 <noreply@anthropic.com>

Author: ctrueden

NEXT.md

@@ -29,7 +29,19 @@ The component uses a plugin system where Platform implementations (LinuxPlatform
 - File extension registration
 - Windows Start Menu icon generation
 - First launch dialog for desktop integration opt-in
-- SchemeInstallerProvider interface for platforms
+
+## Implementation Phases
+
+### Phase 1: Fix Hardcoded Elements (High Priority)
+These fixes are required for scijava-desktop to work for applications other than Fiji.
+
+### Phase 2: File Extension Registration (High Priority)
+Core functionality for Fiji and other scientific applications.
+
+### Phase 3: Polish (Medium Priority)
+First launch dialog, Windows desktop icon, etc.
+
+---
 
 ## Priority Work Items
 
@@ -89,36 +101,16 @@ private Set<String> collectSchemes() {
 
 Similar changes needed for LinuxPlatform.
 
-### 2. Add SchemeInstallerProvider Interface
+### 2. Add getSchemeInstaller method
 
 **Goal**: Allow platforms to provide SchemeInstaller instances without hardcoding in DefaultLinkService.
 
-**New file**: `src/main/java/org/scijava/desktop/links/SchemeInstallerProvider.java`
-
-```java
-package org.scijava.desktop.links;
-
-/**
- * Interface for platforms that provide {@link SchemeInstaller} functionality.
- * <p>
- * Platform implementations can implement this interface to provide
- * platform-specific URI scheme installation capabilities.
- * </p>
- */
-public interface SchemeInstallerProvider {
-    /**
-     * Creates a SchemeInstaller for this platform.
-     *
-     * @return a SchemeInstaller, or null if not supported
-     */
-    SchemeInstaller getSchemeInstaller();
-}
-```
+**New method**: `DesktopIntegrationProvider#getSchemeInstaller()`
 
 **Files to modify**:
-- WindowsPlatform.java - implement SchemeInstallerProvider
-- LinuxPlatform.java - implement SchemeInstallerProvider
-- MacOSPlatform.java - implement SchemeInstallerProvider (return null)
+- WindowsPlatform.java - implement getSchemeInstaller
+- LinuxPlatform.java - implement getSchemeInstaller
+- MacOSPlatform.java - implement getSchemeInstaller (return null)
 
 ### 3. Refactor DefaultLinkService#createInstaller()
 
@@ -151,8 +143,8 @@ private SchemeInstaller createInstaller() {
     if (platformService == null) return null;
 
     final Platform platform = platformService.platform();
-    if (platform instanceof SchemeInstallerProvider) {
-        return ((SchemeInstallerProvider) platform).getSchemeInstaller();
+    if (platform instanceof DesktopIntegrationProvider) {
+        return ((DesktopIntegrationProvider) platform).getSchemeInstaller();
     }
 
     return null;
@@ -189,7 +181,7 @@ Either way: "To change these settings in the future, use Edit > Options > Deskto
 - If user selects "No", do nothing
 - Store user preference by writing to a local configuration file -- avoids showing dialog again
 
-### 5. File Extension Registration (Future)
+### 5. File Extension Registration (High Priority)
 
 **Scope**: Extend DesktopIntegrationProvider to support file type associations.
 
@@ -201,9 +193,52 @@ void setFileExtensionsEnabled(boolean enable) throws IOException;
 ```
 
 **Platform implementations**:
-- **Linux**: Add MIME types to .desktop file (e.g., `image/tiff`, `application/x-imagej-macro`)
-- **Windows**: Register file associations in Registry under `HKCU\Software\Classes\.<ext>`
-- **macOS**: Declared in Info.plist (build-time, read-only)
+
+#### Linux (Complex - Custom MIME Types Required)
+
+**Problem**: Microscopy formats (.sdt, .czi, .nd2, .lif, etc.) lack standard MIME types.
+
+**Solution**: Register custom MIME types in `~/.local/share/mime/packages/fiji.xml`
+
+**Steps**:
+1. Create extension → MIME type mapping
+   - Standard formats: use existing types (`image/tiff`, `image/png`)
+   - Microscopy formats: define custom types (`application/x-zeiss-czi`, `application/x-nikon-nd2`)
+2. Generate `fiji.xml` with MIME type definitions
+3. Install to `~/.local/share/mime/packages/`
+4. Run `update-mime-database ~/.local/share/mime`
+5. Add MIME types to .desktop file's `MimeType=` field
+
+**MIME type naming convention**:
+- Use vendor-specific: `application/x-{vendor}-{format}`
+- Examples: `application/x-zeiss-czi`, `application/x-becker-hickl-sdt`
+
+**Unregistration**:
+- Remove MIME types from .desktop file (preserve URI schemes)
+- Optionally delete `~/.local/share/mime/packages/fiji.xml`
+- Run `update-mime-database` again
+
+#### Windows (Simple - SupportedTypes Only)
+
+**Solution**: Use `Applications\fiji.exe\SupportedTypes` registry approach
+
+**Steps**:
+1. Create `HKCU\Software\Classes\Applications\fiji.exe\SupportedTypes`
+2. Add each extension as a value: `.tif = ""`
+3. All ~150-200 extensions in one registry location
+
+**Safety**: Deletion is safe - only removes our own `Applications\fiji.exe` tree
+
+**Unregistration**:
+- Delete entire `HKCU\Software\Classes\Applications\fiji.exe` key
+
+#### macOS (Build-Time Only)
+
+**Solution**: Declare all extensions in Info.plist at build time
+
+**Format**: `CFBundleDocumentTypes` array with extension lists
+
+**No runtime action needed** - this is a packaging/build concern
 
 ### 6. Windows Start Menu Icon
 
@@ -216,6 +251,7 @@ void setFileExtensionsEnabled(boolean enable) throws IOException;
 
 ## Testing Checklist
 
+### Phase 1 (Hardcoded Elements)
 - [ ] Test URI scheme registration on Windows (registry manipulation)
 - [ ] Test URI scheme registration on Linux (.desktop file updates)
 - [ ] Test desktop icon installation on Linux
@@ -225,6 +261,16 @@ void setFileExtensionsEnabled(boolean enable) throws IOException;
 - [ ] Test toggling features on/off via UI
 - [ ] Verify no hardcoded "fiji" references remain
 
+### Phase 2 (File Extensions)
+- [ ] Test Linux MIME type generation and installation
+- [ ] Verify `update-mime-database` runs successfully
+- [ ] Test file extension associations appear in file managers (Nautilus, Dolphin)
+- [ ] Test Windows SupportedTypes registration
+- [ ] Verify Fiji appears in "Open With" for all extensions
+- [ ] Test unregistration (verify complete cleanup)
+- [ ] Test with ~150-200 actual file extensions
+- [ ] Verify no `application/octet-stream` claims
+
 ## System Properties Reference
 
 - `scijava.app.executable` - Path to application executable (required for all platforms)
@@ -243,7 +289,6 @@ void setFileExtensionsEnabled(boolean enable) throws IOException;
 
 ## Questions to Resolve
 
-1. Should SchemeInstallerProvider be a separate interface or extend Platform?
-2. How to handle partial scheme installation failures?
-3. Should first launch dialog be mandatory or optional?
-4. What file extensions should be supported by default?
+1. How to handle partial scheme installation failures?
+2. Should first launch dialog be mandatory or optional?
+3. What file extensions should be supported by default?

spec/DESKTOP_INTEGRATION_PLAN.md

@@ -172,7 +172,7 @@ Applications configure desktop integration via system properties:
 
 2. **OS Checks**: DefaultLinkService:119-132 hardcodes OS name checks
    - Should use PlatformService to get active platform
-   - Should add SchemeInstallerProvider interface
+   - Should add getSchemeInstaller method
    - See NEXT.md Work Items #2 and #3
 
 ### Missing Features
@@ -256,7 +256,7 @@ java -Dscijava.app.executable="/path/to/myapp" \
 
 - Remove hardcoded "fiji" scheme references
 - Remove hardcoded OS checks in DefaultLinkService
-- Add SchemeInstallerProvider interface
+- Add getSchemeInstaller method
 
 ### ❌ Not Implemented
 

spec/IMPLEMENTATION_SUMMARY.md

@@ -108,8 +108,8 @@ The component uses SciJava's plugin architecture to avoid hardcoded OS checks:
 **Impact**: Violates plugin architecture; makes adding new platforms difficult.
 
 **Fix Required**:
-1. Add SchemeInstallerProvider interface
-2. Platforms implement SchemeInstallerProvider
+1. Add getSchemeInstaller method
+2. Platforms implement getSchemeInstaller
 3. DefaultLinkService queries PlatformService.platform() instead of checking OS name
 
 ### ❌ Not Yet Implemented
@@ -345,7 +345,7 @@ Linux .desktop files are used by both LinuxPlatform (for desktop icon) and Linux
 See NEXT.md for detailed implementation plan, including:
 
 1. Remove hardcoded scheme names (Priority 1)
-2. Add SchemeInstallerProvider interface (Priority 2)
+2. Add getSchemeInstaller method (Priority 2)
 3. Refactor DefaultLinkService#createInstaller() (Priority 3)
 4. Implement first launch dialog (Optional)
 5. Add file extension registration (Future)

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

@@ -31,6 +31,8 @@
 
 import java.io.IOException;
 
+import org.scijava.desktop.links.SchemeInstaller;
+
 /**
  * Marker interface for platform implementations that provide desktop
  * integration features.
@@ -79,4 +81,11 @@ public interface DesktopIntegrationProvider {
 	 * @throws UnsupportedOperationException if not supported on this platform
 	 */
 	void setDesktopIconPresent(final boolean install) throws IOException;
+
+	/**
+	 * Creates a SchemeInstaller for this platform.
+	 *
+	 * @return a SchemeInstaller, or null if not supported on this platform
+	 */
+	SchemeInstaller getSchemeInstaller();
 }

src/main/java/org/scijava/desktop/links/DefaultLinkService.java

@@ -30,10 +30,11 @@
 
 import org.scijava.event.ContextCreatedEvent;
 import org.scijava.event.EventHandler;
+import org.scijava.desktop.DesktopIntegrationProvider;
 import org.scijava.desktop.links.SchemeInstaller;
-import org.scijava.desktop.platform.linux.LinuxSchemeInstaller;
-import org.scijava.desktop.platform.windows.WindowsSchemeInstaller;
 import org.scijava.log.LogService;
+import org.scijava.platform.Platform;
+import org.scijava.platform.PlatformService;
 import org.scijava.plugin.AbstractHandlerService;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
@@ -55,6 +56,9 @@ public class DefaultLinkService extends AbstractHandlerService<URI, LinkHandler>
 	@Parameter(required = false)
 	private LogService log;
 
+	@Parameter(required = false)
+	private PlatformService platformService;
+
 	@EventHandler
 	private void onEvent(final ContextCreatedEvent evt) {
 		// Register URI handler with the desktop system, if possible.
@@ -112,23 +116,23 @@ private void installSchemes() {
 	/**
 	 * Creates the appropriate {@link SchemeInstaller} for the current platform.
 	 * <p>
-	 * Windows and Linux are supported via runtime registration. macOS uses Info.plist
-	 * in the .app bundle (configured at build time, not at runtime).
+	 * Uses the platform plugin system to obtain the installer, avoiding
+	 * hardcoded OS checks. Windows and Linux platforms provide runtime registration.
+	 * macOS uses Info.plist in the .app bundle (configured at build time).
 	 * </p>
 	 */
 	private SchemeInstaller createInstaller() {
-		final String os = System.getProperty("os.name");
-		if (os == null) return null;
+		if (platformService == null) return null;
 
-		final String osLower = os.toLowerCase();
-		if (osLower.contains("linux")) {
-			return new LinuxSchemeInstaller(log);
-		}
-		else if (osLower.contains("win")) {
-			return new WindowsSchemeInstaller(log);
+		// Find a platform that provides a SchemeInstaller
+		for (final Platform platform : platformService.getTargetPlatforms()) {
+			if (platform instanceof DesktopIntegrationProvider) {
+				final SchemeInstaller installer = ((DesktopIntegrationProvider) platform).getSchemeInstaller();
+				if (installer != null) return installer;
+			}
 		}
 
-		return null; // macOS or other unsupported platforms
+		return null;
 	}
 
 	/**

src/main/java/org/scijava/desktop/platform/linux/LinuxPlatform.java

@@ -31,7 +31,9 @@
 
 import org.scijava.app.AppService;
 import org.scijava.desktop.DesktopIntegrationProvider;
+import org.scijava.desktop.links.LinkHandler;
 import org.scijava.desktop.links.LinkService;
+import org.scijava.desktop.links.SchemeInstaller;
 import org.scijava.log.LogService;
 import org.scijava.platform.AbstractPlatform;
 import org.scijava.platform.Platform;
@@ -44,6 +46,9 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
 
 /**
  * A platform implementation for handling Linux platform issues.
@@ -109,7 +114,14 @@ public void open(final URL url) throws IOException {
 	public boolean isWebLinksEnabled() {
 		try {
 			final DesktopFile df = getOrCreateDesktopFile();
-			return df.hasMimeType("x-scheme-handler/myapp");
+			final Set<String> schemes = collectSchemes();
+			if (schemes.isEmpty()) return false;
+
+			// Check if any scheme is registered
+			for (final String scheme : schemes) {
+				if (df.hasMimeType("x-scheme-handler/" + scheme)) return true;
+			}
+			return false;
 		} catch (final IOException e) {
 			if (log != null) {
 				log.debug("Failed to check web links status", e);
@@ -124,13 +136,17 @@ public boolean isWebLinksEnabled() {
 	@Override
 	public void setWebLinksEnabled(final boolean enable) throws IOException {
 		final DesktopFile df = getOrCreateDesktopFile();
-		
-		if (enable) {
-			df.addMimeType("x-scheme-handler/fiji");
-		} else {
-			df.removeMimeType("x-scheme-handler/fiji");
+
+		final Set<String> schemes = collectSchemes();
+		for (final String scheme : schemes) {
+			final String mimeType = "x-scheme-handler/" + scheme;
+			if (enable) {
+				df.addMimeType(mimeType);
+			} else {
+				df.removeMimeType(mimeType);
+			}
 		}
-		
+
 		df.save();
 	}
 
@@ -195,6 +211,11 @@ public void setDesktopIconPresent(final boolean install) throws IOException {
 		}
 	}
 
+	@Override
+	public SchemeInstaller getSchemeInstaller() {
+		return new LinuxSchemeInstaller(log);
+	}
+
 	// -- Helper methods --
 
 	/**
@@ -296,4 +317,22 @@ private boolean isDesktopFileUpToDate(final Path desktopFile) {
 	private String sanitizeFileName(final String name) {
 		return name.replaceAll("[^a-zA-Z0-9._-]", "-").toLowerCase();
 	}
+
+	// -- Helper methods --
+
+	/**
+	 * Collects all URI schemes from registered LinkHandler plugins.
+	 */
+	private Set<String> collectSchemes() {
+		final Set<String> schemes = new HashSet<>();
+		if (linkService == null) return schemes;
+
+		for (final LinkHandler handler : linkService.getInstances()) {
+			final List<String> handlerSchemes = handler.getSchemes();
+			if (handlerSchemes != null) {
+				schemes.addAll(handlerSchemes);
+			}
+		}
+		return schemes;
+	}
 }