diff --git a/src/main/java/org/scijava/Disposable.java b/src/main/java/org/scijava/Disposable.java
index ac72c90b4..0d9ee8735 100644
--- a/src/main/java/org/scijava/Disposable.java
+++ b/src/main/java/org/scijava/Disposable.java
@@ -33,7 +33,11 @@
  * An object that knows how to clean up after itself.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.spi.Disposable} (scijava-spi) instead,
+ *             whose {@code dispose()} is abstract rather than a no-op default.
  */
+@Deprecated
 public interface Disposable {
 
 	/**
diff --git a/src/main/java/org/scijava/Identifiable.java b/src/main/java/org/scijava/Identifiable.java
index 53db16039..7168bdf5e 100644
--- a/src/main/java/org/scijava/Identifiable.java
+++ b/src/main/java/org/scijava/Identifiable.java
@@ -51,7 +51,11 @@
  * </p>
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.spi.Identifiable} (scijava-spi) instead,
+ *             whose {@code getIdentifier} is named {@code id()}.
  */
+@Deprecated
 public interface Identifiable {
 
 	/** Gets a string intended to function as an identifier for the object. */
diff --git a/src/main/java/org/scijava/ItemIO.java b/src/main/java/org/scijava/ItemIO.java
index fa8b68684..5b2908465 100644
--- a/src/main/java/org/scijava/ItemIO.java
+++ b/src/main/java/org/scijava/ItemIO.java
@@ -42,7 +42,10 @@
  * </ul>
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.struct.ItemIO} (scijava-struct) instead.
  */
+@Deprecated
 public enum ItemIO {
 	INPUT, OUTPUT, BOTH
 }
diff --git a/src/main/java/org/scijava/Named.java b/src/main/java/org/scijava/Named.java
index 9a381ee3a..f495189d1 100644
--- a/src/main/java/org/scijava/Named.java
+++ b/src/main/java/org/scijava/Named.java
@@ -33,7 +33,12 @@
  * Interface for things that have names.
  * 
  * @author Lee Kamentsky
+ *
+ * @deprecated Use {@code org.scijava.spi.Named} (scijava-spi) instead, whose
+ *             method is {@code name()}. It has no setter: naming an object is
+ *             a separate contract from knowing its name.
  */
+@Deprecated
 public interface Named {
 
 	/** Gets the name of the object. */
diff --git a/src/main/java/org/scijava/Prioritized.java b/src/main/java/org/scijava/Prioritized.java
index 86bd0691a..2232ecafc 100644
--- a/src/main/java/org/scijava/Prioritized.java
+++ b/src/main/java/org/scijava/Prioritized.java
@@ -35,7 +35,11 @@
  * An object that can be sorted according to priority.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.priority.Prioritized} (scijava-priority)
+ *             instead.
  */
+@Deprecated
 public interface Prioritized extends Comparable<Prioritized> {
 
 	/**
diff --git a/src/main/java/org/scijava/Priority.java b/src/main/java/org/scijava/Priority.java
index 69da7767e..d62e48f73 100644
--- a/src/main/java/org/scijava/Priority.java
+++ b/src/main/java/org/scijava/Priority.java
@@ -36,7 +36,11 @@
  * @author Curtis Rueden
  * @see org.scijava.Prioritized#getPriority()
  * @see org.scijava.plugin.Plugin#priority()
+ *
+ * @deprecated Use {@code org.scijava.priority.Priority} (scijava-priority)
+ *             instead.
  */
+@Deprecated
 public final class Priority {
 
 	private Priority() {
diff --git a/src/main/java/org/scijava/Versioned.java b/src/main/java/org/scijava/Versioned.java
index 6e746dad4..29e481b50 100644
--- a/src/main/java/org/scijava/Versioned.java
+++ b/src/main/java/org/scijava/Versioned.java
@@ -35,7 +35,11 @@
  * An object that knows its version.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.spi.Versioned} (scijava-spi) instead,
+ *             whose method is {@code version()}.
  */
+@Deprecated
 public interface Versioned {
 
 	/** Gets the version of the object. */
diff --git a/src/main/java/org/scijava/annotations/AbstractIndexWriter.java b/src/main/java/org/scijava/annotations/AbstractIndexWriter.java
index 28fe310a5..a42988b31 100644
--- a/src/main/java/org/scijava/annotations/AbstractIndexWriter.java
+++ b/src/main/java/org/scijava/annotations/AbstractIndexWriter.java
@@ -55,7 +55,12 @@
  * </p>
  * 
  * @author Johannes Schindelin
+ *
+ * @deprecated Use {@code org.scijava.index.AbstractIndexWriter}
+ *             (scijava-index) instead. The index format is unchanged, so
+ *             indexes written by either are readable by both.
  */
+@Deprecated
 public abstract class AbstractIndexWriter {
 
 	private final Map<String, Map<String, Object>> map =
diff --git a/src/main/java/org/scijava/annotations/AnnotationCombiner.java b/src/main/java/org/scijava/annotations/AnnotationCombiner.java
index 9b152b924..5f5894baf 100644
--- a/src/main/java/org/scijava/annotations/AnnotationCombiner.java
+++ b/src/main/java/org/scijava/annotations/AnnotationCombiner.java
@@ -48,7 +48,11 @@
  * Combines annotation indexes from all JAR files on the classpath.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated No replacement here: merging indexes for shaded JARs is build
+ *             tooling, and belongs in scijava-maven-plugin.
  */
+@Deprecated
 public class AnnotationCombiner extends AbstractIndexWriter implements Combiner
 {
 
diff --git a/src/main/java/org/scijava/annotations/AnnotationProcessor.java b/src/main/java/org/scijava/annotations/AnnotationProcessor.java
index e17d707a9..e9cae43d0 100644
--- a/src/main/java/org/scijava/annotations/AnnotationProcessor.java
+++ b/src/main/java/org/scijava/annotations/AnnotationProcessor.java
@@ -89,8 +89,13 @@
  * </p>
  * 
  * @author Johannes Schindelin
+ *
+ * @deprecated Use {@code org.scijava.index.AnnotationProcessor}
+ *             (scijava-index) instead. The index format is unchanged, so
+ *             indexes written by either are readable by both.
  */
 @SupportedAnnotationTypes("*")
+@Deprecated
 public class AnnotationProcessor extends AbstractProcessor {
 
 	private RoundEnvironment roundEnv;
diff --git a/src/main/java/org/scijava/annotations/DirectoryIndexer.java b/src/main/java/org/scijava/annotations/DirectoryIndexer.java
index ac6be8fcd..2bced1047 100644
--- a/src/main/java/org/scijava/annotations/DirectoryIndexer.java
+++ b/src/main/java/org/scijava/annotations/DirectoryIndexer.java
@@ -50,7 +50,12 @@
  * </p>
  * 
  * @author Johannes Schindelin
+ *
+ * @deprecated Use {@code org.scijava.index.DirectoryIndexer} (scijava-index)
+ *             instead. The index format is unchanged, so indexes written by
+ *             either are readable by both.
  */
+@Deprecated
 public class DirectoryIndexer extends AbstractIndexWriter {
 
 	public void index(final File directory) throws IOException {
diff --git a/src/main/java/org/scijava/annotations/EclipseHelper.java b/src/main/java/org/scijava/annotations/EclipseHelper.java
index 67f17ff7d..25d17c327 100644
--- a/src/main/java/org/scijava/annotations/EclipseHelper.java
+++ b/src/main/java/org/scijava/annotations/EclipseHelper.java
@@ -93,7 +93,12 @@
  * </p>
  * 
  * @author Johannes Schindelin
+ *
+ * @deprecated No replacement. Modern m2e generates the annotation processor
+ *             path itself; for indexing a directory, use
+ *             {@code org.scijava.index.DirectoryIndexer} (scijava-index).
  */
+@Deprecated
 public class EclipseHelper extends DirectoryIndexer {
 
 	private static final String FORCE_ANNOTATION_INDEX_PROPERTY = "force.annotation.index";
diff --git a/src/main/java/org/scijava/annotations/Index.java b/src/main/java/org/scijava/annotations/Index.java
index 244b00d37..19b6ccfe9 100644
--- a/src/main/java/org/scijava/annotations/Index.java
+++ b/src/main/java/org/scijava/annotations/Index.java
@@ -53,7 +53,12 @@
  * </pre>
  * 
  * @author Johannes Schindelin
+ *
+ * @deprecated Use {@code org.scijava.index.Index} (scijava-index) instead. The
+ *             index format is unchanged, so indexes written by either are
+ *             readable by both.
  */
+@Deprecated
 public class Index<A extends Annotation> implements Iterable<IndexItem<A>> {
 
 	/**
diff --git a/src/main/java/org/scijava/annotations/IndexItem.java b/src/main/java/org/scijava/annotations/IndexItem.java
index e5265fc21..c6308afaf 100644
--- a/src/main/java/org/scijava/annotations/IndexItem.java
+++ b/src/main/java/org/scijava/annotations/IndexItem.java
@@ -41,7 +41,12 @@
  * Allows access to individual annotations.
  * 
  * @author Johannes Schindelin
+ *
+ * @deprecated Use {@code org.scijava.index.IndexItem} (scijava-index) instead.
+ *             The index format is unchanged, so indexes written by either are
+ *             readable by both.
  */
+@Deprecated
 public class IndexItem<A extends Annotation> {
 
 	private final Class<A> annotation;
diff --git a/src/main/java/org/scijava/annotations/Indexable.java b/src/main/java/org/scijava/annotations/Indexable.java
index 325739efd..ed36365ff 100644
--- a/src/main/java/org/scijava/annotations/Indexable.java
+++ b/src/main/java/org/scijava/annotations/Indexable.java
@@ -42,7 +42,12 @@
  * </p>
  * 
  * @author Johannes Schindelin
+ *
+ * @deprecated Use {@code org.scijava.index.Indexable} (scijava-index) instead.
+ *             The index format is unchanged, so indexes written by either are
+ *             readable by both.
  */
 @Retention(RetentionPolicy.RUNTIME)
 @Target({ ElementType.TYPE, ElementType.ANNOTATION_TYPE })
+@Deprecated
 public @interface Indexable {}
diff --git a/src/main/java/org/scijava/event/DefaultEventHistory.java b/src/main/java/org/scijava/event/DefaultEventHistory.java
index 4b94b8bc3..e794be88d 100644
--- a/src/main/java/org/scijava/event/DefaultEventHistory.java
+++ b/src/main/java/org/scijava/event/DefaultEventHistory.java
@@ -41,8 +41,11 @@
  * Default service for keeping a history of SciJava events.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated No replacement; see {@link org.scijava.event.EventHistory}.
  */
 @Plugin(type = Service.class)
+@Deprecated
 public class DefaultEventHistory extends AbstractService implements
 	EventHistory
 {
diff --git a/src/main/java/org/scijava/event/DefaultEventService.java b/src/main/java/org/scijava/event/DefaultEventService.java
index 3eca42db0..5282b55b7 100644
--- a/src/main/java/org/scijava/event/DefaultEventService.java
+++ b/src/main/java/org/scijava/event/DefaultEventService.java
@@ -56,8 +56,12 @@
  * 
  * @author Curtis Rueden
  * @author Grant Harris
+ *
+ * @deprecated Use {@code org.scijava.events.DefaultEventBus} (scijava-events)
+ *             instead.
  */
 @Plugin(type = Service.class, priority = DefaultEventService.PRIORITY)
+@Deprecated
 public class DefaultEventService extends AbstractService implements
 	EventService
 {
diff --git a/src/main/java/org/scijava/event/EventDetails.java b/src/main/java/org/scijava/event/EventDetails.java
index 5e9344b24..41ef6fea3 100644
--- a/src/main/java/org/scijava/event/EventDetails.java
+++ b/src/main/java/org/scijava/event/EventDetails.java
@@ -38,7 +38,10 @@
  * itself (since doing so could leave dangling references).
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated No replacement; see {@link org.scijava.event.EventHistory}.
  */
+@Deprecated
 public class EventDetails {
 
 	private final Date timestamp;
diff --git a/src/main/java/org/scijava/event/EventHandler.java b/src/main/java/org/scijava/event/EventHandler.java
index fa59a2a50..b5a4e697b 100644
--- a/src/main/java/org/scijava/event/EventHandler.java
+++ b/src/main/java/org/scijava/event/EventHandler.java
@@ -53,9 +53,15 @@
  * 
  * @author Curtis Rueden
  * @see EventService
+ *
+ * @deprecated Use
+ *             {@code org.scijava.events.EventBus.subscribe(Class, Consumer)}
+ *             (scijava-events) instead, which needs no reflection into the
+ *             subscriber.
  */
 @Retention(RetentionPolicy.RUNTIME)
 @Target(ElementType.METHOD)
+@Deprecated
 public @interface EventHandler {
 
 	/**
diff --git a/src/main/java/org/scijava/event/EventHistory.java b/src/main/java/org/scijava/event/EventHistory.java
index 7caaaf022..3495f95eb 100644
--- a/src/main/java/org/scijava/event/EventHistory.java
+++ b/src/main/java/org/scijava/event/EventHistory.java
@@ -38,7 +38,11 @@
  * Interface for service that keeps a history of SciJava events.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated No replacement. A subscriber on {@code Object.class} reproduces
+ *             it in three lines.
  */
+@Deprecated
 public interface EventHistory extends SciJavaService {
 
 	/** Activates or deactivates event history tracking. */
diff --git a/src/main/java/org/scijava/event/EventHistoryListener.java b/src/main/java/org/scijava/event/EventHistoryListener.java
index 30a305c83..838d028c0 100644
--- a/src/main/java/org/scijava/event/EventHistoryListener.java
+++ b/src/main/java/org/scijava/event/EventHistoryListener.java
@@ -33,7 +33,10 @@
  * Listener for event history changes.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated No replacement; see {@link org.scijava.event.EventHistory}.
  */
+@Deprecated
 public interface EventHistoryListener {
 
 	void eventOccurred(EventDetails details);
diff --git a/src/main/java/org/scijava/event/EventService.java b/src/main/java/org/scijava/event/EventService.java
index 1b0907f7a..ac03f1d32 100644
--- a/src/main/java/org/scijava/event/EventService.java
+++ b/src/main/java/org/scijava/event/EventService.java
@@ -40,7 +40,13 @@
  * 
  * @author Curtis Rueden
  * @author Grant Harris
+ *
+ * @deprecated Use {@code org.scijava.events.EventBus} (scijava-events)
+ *             instead. Subscription takes a lambda rather than scanning
+ *             annotated methods, and returns a handle that cancels it; see
+ *             https://github.com/scijava/scijava/blob/main/docs/migration.md
  */
+@Deprecated
 public interface EventService extends SciJavaService {
 
 	/**
diff --git a/src/main/java/org/scijava/event/EventSubscriber.java b/src/main/java/org/scijava/event/EventSubscriber.java
index 9dcd25d94..5fffcd6e0 100644
--- a/src/main/java/org/scijava/event/EventSubscriber.java
+++ b/src/main/java/org/scijava/event/EventSubscriber.java
@@ -42,7 +42,11 @@
  * 
  * @author Curtis Rueden
  * @param <E> Type of event for which to listen
+ *
+ * @deprecated Use a {@link java.util.function.Consumer} with
+ *             {@code org.scijava.events.EventBus} (scijava-events) instead.
  */
+@Deprecated
 public interface EventSubscriber<E extends SciJavaEvent> extends
 	org.scijava.event.bushe.EventSubscriber<E>
 {
diff --git a/src/main/java/org/scijava/event/SciJavaEvent.java b/src/main/java/org/scijava/event/SciJavaEvent.java
index 4e51d775f..9be691035 100644
--- a/src/main/java/org/scijava/event/SciJavaEvent.java
+++ b/src/main/java/org/scijava/event/SciJavaEvent.java
@@ -36,7 +36,12 @@
  * Base class for all SciJava events.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated No replacement needed: {@code org.scijava.events.EventBus}
+ *             (scijava-events) accepts any object as an event, so no base type
+ *             is required.
  */
+@Deprecated
 public abstract class SciJavaEvent extends AbstractContextual {
 
 	/** Whether the event has been handled already. */
diff --git a/src/main/java/org/scijava/io/ByteArrayByteBank.java b/src/main/java/org/scijava/io/ByteArrayByteBank.java
index f0183f2d8..ee5ef866a 100644
--- a/src/main/java/org/scijava/io/ByteArrayByteBank.java
+++ b/src/main/java/org/scijava/io/ByteArrayByteBank.java
@@ -36,7 +36,11 @@
  * up to a maximum capacity of {@link Integer#MAX_VALUE}.
  *
  * @author Gabriel Einsdorf
+ *
+ * @deprecated Use {@code org.scijava.io3.ByteArrayByteBank} (scijava-io3)
+ *             instead.
  */
+@Deprecated
 public class ByteArrayByteBank implements ByteBank {
 
 	private final ByteArray buffer;
diff --git a/src/main/java/org/scijava/io/ByteBank.java b/src/main/java/org/scijava/io/ByteBank.java
index 8d466e8ce..6831ac852 100644
--- a/src/main/java/org/scijava/io/ByteBank.java
+++ b/src/main/java/org/scijava/io/ByteBank.java
@@ -34,7 +34,10 @@
  *
  * @author Gabriel Einsdorf
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.io3.ByteBank} (scijava-io3) instead.
  */
+@Deprecated
 public interface ByteBank {
 
 	/**
diff --git a/src/main/java/org/scijava/io/handle/AbstractDataHandle.java b/src/main/java/org/scijava/io/handle/AbstractDataHandle.java
index f2446f90a..e6f5c79ee 100644
--- a/src/main/java/org/scijava/io/handle/AbstractDataHandle.java
+++ b/src/main/java/org/scijava/io/handle/AbstractDataHandle.java
@@ -36,7 +36,11 @@
  * Abstract base class for {@link DataHandle} plugins.
  *
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.io3.handle.AbstractDataHandle}
+ *             (scijava-io3) instead.
  */
+@Deprecated
 public abstract class AbstractDataHandle<L extends Location> extends
 	AbstractWrapperPlugin<L> implements DataHandle<L>
 {
diff --git a/src/main/java/org/scijava/io/handle/AbstractHigherOrderHandle.java b/src/main/java/org/scijava/io/handle/AbstractHigherOrderHandle.java
index 7fa3d8df9..e1e4d97ae 100644
--- a/src/main/java/org/scijava/io/handle/AbstractHigherOrderHandle.java
+++ b/src/main/java/org/scijava/io/handle/AbstractHigherOrderHandle.java
@@ -38,7 +38,11 @@
  * {@link DataHandle}s.
  *
  * @author Gabriel Einsdorf
+ *
+ * @deprecated Use {@code org.scijava.io3.handle.AbstractHigherOrderHandle}
+ *             (scijava-io3) instead.
  */
+@Deprecated
 public abstract class AbstractHigherOrderHandle<L extends Location> extends
 	AbstractDataHandle<L>
 {
diff --git a/src/main/java/org/scijava/io/handle/AbstractSeekableStreamHandle.java b/src/main/java/org/scijava/io/handle/AbstractSeekableStreamHandle.java
index 5b56c5e93..a603ce3b5 100644
--- a/src/main/java/org/scijava/io/handle/AbstractSeekableStreamHandle.java
+++ b/src/main/java/org/scijava/io/handle/AbstractSeekableStreamHandle.java
@@ -33,6 +33,11 @@
 
 import org.scijava.io.location.Location;
 
+/**
+ * @deprecated Use {@code org.scijava.io3.handle.AbstractSeekableStreamHandle}
+ *             (scijava-io3) instead.
+ */
+@Deprecated
 public abstract class AbstractSeekableStreamHandle<L extends Location> extends
 	AbstractStreamHandle<L> implements SeekableStreamHandle<L>
 {
diff --git a/src/main/java/org/scijava/io/handle/AbstractStreamHandle.java b/src/main/java/org/scijava/io/handle/AbstractStreamHandle.java
index 75a9f4939..d89413659 100644
--- a/src/main/java/org/scijava/io/handle/AbstractStreamHandle.java
+++ b/src/main/java/org/scijava/io/handle/AbstractStreamHandle.java
@@ -36,7 +36,11 @@
  *
  * @author Curtis Rueden
  * @author Melissa Linkert
+ *
+ * @deprecated Use {@code org.scijava.io3.handle.AbstractStreamHandle}
+ *             (scijava-io3) instead.
  */
+@Deprecated
 public abstract class AbstractStreamHandle<L extends Location> extends
 	AbstractDataHandle<L> implements StreamHandle<L>
 {
diff --git a/src/main/java/org/scijava/io/handle/BytesHandle.java b/src/main/java/org/scijava/io/handle/BytesHandle.java
index b09228673..239e5cf5f 100644
--- a/src/main/java/org/scijava/io/handle/BytesHandle.java
+++ b/src/main/java/org/scijava/io/handle/BytesHandle.java
@@ -42,8 +42,12 @@
  * @author Curtis Rueden
  * @author Melissa Linkert
  * @author Gabriel Einsdorf
+ *
+ * @deprecated Use {@code org.scijava.io3.handle.BytesHandle} (scijava-io3)
+ *             instead.
  */
 @Plugin(type = DataHandle.class)
+@Deprecated
 public class BytesHandle extends AbstractDataHandle<BytesLocation> {
 
 	private long offset = 0;
diff --git a/src/main/java/org/scijava/io/handle/DataHandle.java b/src/main/java/org/scijava/io/handle/DataHandle.java
index 18cddadcb..9d4a0fb7a 100644
--- a/src/main/java/org/scijava/io/handle/DataHandle.java
+++ b/src/main/java/org/scijava/io/handle/DataHandle.java
@@ -49,7 +49,13 @@
  * @author Curtis Rueden
  * @see DataHandleInputStream
  * @see DataHandleOutputStream
+ *
+ * @deprecated Use {@code org.scijava.io3.handle.DataHandle} (scijava-io3)
+ *             instead. It no longer extends a wrapper plugin: the contract is
+ *             {@code locationType()}, {@code supports()}, {@code set()},
+ *             {@code get()} and {@code priority()}.
  */
+@Deprecated
 public interface DataHandle<L extends Location> extends WrapperPlugin<L>,
 	DataInput, DataOutput, Closeable
 {
diff --git a/src/main/java/org/scijava/io/handle/DataHandleInputStream.java b/src/main/java/org/scijava/io/handle/DataHandleInputStream.java
index 10e6b84e9..489c1da5d 100644
--- a/src/main/java/org/scijava/io/handle/DataHandleInputStream.java
+++ b/src/main/java/org/scijava/io/handle/DataHandleInputStream.java
@@ -39,7 +39,11 @@
  * 
  * @author Curtis Rueden
  * @author Melissa Linkert
+ *
+ * @deprecated Use {@code org.scijava.io3.handle.DataHandleInputStream}
+ *             (scijava-io3) instead.
  */
+@Deprecated
 public class DataHandleInputStream<L extends Location> extends InputStream {
 
 	// -- Fields --
diff --git a/src/main/java/org/scijava/io/handle/DataHandleOutputStream.java b/src/main/java/org/scijava/io/handle/DataHandleOutputStream.java
index 3328a4e0a..ebf79b9f4 100644
--- a/src/main/java/org/scijava/io/handle/DataHandleOutputStream.java
+++ b/src/main/java/org/scijava/io/handle/DataHandleOutputStream.java
@@ -39,7 +39,11 @@
  * 
  * @author Curtis Rueden
  * @author Melissa Linkert
+ *
+ * @deprecated Use {@code org.scijava.io3.handle.DataHandleOutputStream}
+ *             (scijava-io3) instead.
  */
+@Deprecated
 public class DataHandleOutputStream<L extends Location> extends OutputStream {
 
 	// -- Fields --
diff --git a/src/main/java/org/scijava/io/handle/DataHandleService.java b/src/main/java/org/scijava/io/handle/DataHandleService.java
index fae0e7f4a..1c0f1418d 100644
--- a/src/main/java/org/scijava/io/handle/DataHandleService.java
+++ b/src/main/java/org/scijava/io/handle/DataHandleService.java
@@ -43,7 +43,13 @@
  * @author Curtis Rueden
  * @see IOService
  * @see Location
+ *
+ * @deprecated Use {@code org.scijava.io3.handle.DataHandles} (scijava-io3)
+ *             instead, which creates handles through plain
+ *             {@link java.util.ServiceLoader} and so needs no application
+ *             context.
  */
+@Deprecated
 public interface DataHandleService extends
 	WrapperService<Location, DataHandle<Location>>, SciJavaService
 {
diff --git a/src/main/java/org/scijava/io/handle/DataHandles.java b/src/main/java/org/scijava/io/handle/DataHandles.java
index 1464f637e..59083d985 100644
--- a/src/main/java/org/scijava/io/handle/DataHandles.java
+++ b/src/main/java/org/scijava/io/handle/DataHandles.java
@@ -41,7 +41,14 @@
  *
  * @author Curtis Rueden
  * @author Gabriel Einsdorf
+ *
+ * @deprecated Use {@code org.scijava.io3.handle.DataHandles} (scijava-io3)
+ *             instead. NB: its {@code copy} reports progress to a
+ *             {@link java.util.function.LongConsumer} rather than a task, and
+ *             cancellation is thread interruption: it throws
+ *             {@link java.io.InterruptedIOException} with the partial count.
  */
+@Deprecated
 public final class DataHandles {
 
 	private DataHandles() {
diff --git a/src/main/java/org/scijava/io/handle/DefaultDataHandleService.java b/src/main/java/org/scijava/io/handle/DefaultDataHandleService.java
index 1cdbcdf46..79c48a177 100644
--- a/src/main/java/org/scijava/io/handle/DefaultDataHandleService.java
+++ b/src/main/java/org/scijava/io/handle/DefaultDataHandleService.java
@@ -38,8 +38,12 @@
  * Default implementation of {@link DataHandleService}.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.io3.handle.DataHandles} (scijava-io3)
+ *             instead.
  */
 @Plugin(type = Service.class)
+@Deprecated
 public class DefaultDataHandleService extends
 	AbstractWrapperService<Location, DataHandle<Location>> implements
 	DataHandleService
diff --git a/src/main/java/org/scijava/io/handle/DummyHandle.java b/src/main/java/org/scijava/io/handle/DummyHandle.java
index 74b2d24ab..9fe5cf9f7 100644
--- a/src/main/java/org/scijava/io/handle/DummyHandle.java
+++ b/src/main/java/org/scijava/io/handle/DummyHandle.java
@@ -39,8 +39,12 @@
  * A {@link DataHandle} which reads all zeroes, and writes no actual data.
  *
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.io3.handle.DummyHandle} (scijava-io3)
+ *             instead.
  */
 @Plugin(type = DataHandle.class)
+@Deprecated
 public class DummyHandle extends AbstractDataHandle<DummyLocation> {
 
 	// -- Fields --
diff --git a/src/main/java/org/scijava/io/handle/FileHandle.java b/src/main/java/org/scijava/io/handle/FileHandle.java
index 3734f7ebb..fc2a424f1 100644
--- a/src/main/java/org/scijava/io/handle/FileHandle.java
+++ b/src/main/java/org/scijava/io/handle/FileHandle.java
@@ -43,8 +43,12 @@
  * {@link DataHandle} for a {@link FileLocation}.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.io3.handle.FileHandle} (scijava-io3)
+ *             instead.
  */
 @Plugin(type = DataHandle.class)
+@Deprecated
 public class FileHandle extends AbstractDataHandle<FileLocation> {
 
 	// -- Fields --
diff --git a/src/main/java/org/scijava/io/handle/ReadBufferDataHandle.java b/src/main/java/org/scijava/io/handle/ReadBufferDataHandle.java
index fed7de110..ab66ba853 100644
--- a/src/main/java/org/scijava/io/handle/ReadBufferDataHandle.java
+++ b/src/main/java/org/scijava/io/handle/ReadBufferDataHandle.java
@@ -43,7 +43,11 @@
 /**
  * Read-only buffered {@link DataHandle}. It buffers the underlying handle into
  * a fixed number of pages, swapping them out when necessary.
+ *
+ * @deprecated Use {@code org.scijava.io3.handle.ReadBufferDataHandle}
+ *             (scijava-io3) instead.
  */
+@Deprecated
 public class ReadBufferDataHandle<L extends Location> extends AbstractHigherOrderHandle<L> {
 
 	private static final int DEFAULT_PAGE_SIZE = 10_000;
diff --git a/src/main/java/org/scijava/io/handle/ResettableStreamHandle.java b/src/main/java/org/scijava/io/handle/ResettableStreamHandle.java
index b4a7310f8..fc052c9f0 100644
--- a/src/main/java/org/scijava/io/handle/ResettableStreamHandle.java
+++ b/src/main/java/org/scijava/io/handle/ResettableStreamHandle.java
@@ -39,7 +39,11 @@
  * A {@link DataHandle} backed by an {@link InputStream} and/or
  * {@link OutputStream}. Supports resetting the handle to the start of the
  * internal stream(s).
+ *
+ * @deprecated Use {@code org.scijava.io3.handle.ResettableStreamHandle}
+ *             (scijava-io3) instead.
  */
+@Deprecated
 public interface ResettableStreamHandle<L extends Location> extends
 	StreamHandle<L>
 {
diff --git a/src/main/java/org/scijava/io/handle/SeekableStreamHandle.java b/src/main/java/org/scijava/io/handle/SeekableStreamHandle.java
index 6b4746f56..6535dc20e 100644
--- a/src/main/java/org/scijava/io/handle/SeekableStreamHandle.java
+++ b/src/main/java/org/scijava/io/handle/SeekableStreamHandle.java
@@ -41,7 +41,11 @@
  * stream.
  *
  * @author Gabriel Einsdorf
+ *
+ * @deprecated Use {@code org.scijava.io3.handle.SeekableStreamHandle}
+ *             (scijava-io3) instead.
  */
+@Deprecated
 public interface SeekableStreamHandle<L extends Location> extends
 	ResettableStreamHandle<L>
 {
diff --git a/src/main/java/org/scijava/io/handle/StreamHandle.java b/src/main/java/org/scijava/io/handle/StreamHandle.java
index 30a3e88ba..99e609c73 100644
--- a/src/main/java/org/scijava/io/handle/StreamHandle.java
+++ b/src/main/java/org/scijava/io/handle/StreamHandle.java
@@ -43,7 +43,11 @@
  * @author Curtis Rueden
  * @author Melissa Linkert
  * @author Gabriel Einsdorf
+ *
+ * @deprecated Use {@code org.scijava.io3.handle.StreamHandle} (scijava-io3)
+ *             instead.
  */
+@Deprecated
 public interface StreamHandle<L extends Location> extends DataHandle<L> {
 
 	// -- StreamHandle methods --
diff --git a/src/main/java/org/scijava/io/handle/WriteBufferDataHandle.java b/src/main/java/org/scijava/io/handle/WriteBufferDataHandle.java
index f1549aa30..5b3715222 100644
--- a/src/main/java/org/scijava/io/handle/WriteBufferDataHandle.java
+++ b/src/main/java/org/scijava/io/handle/WriteBufferDataHandle.java
@@ -38,7 +38,11 @@
  * Wraps a {@link DataHandle} and acts as a write buffer.
  *
  * @author Gabriel Einsdorf
+ *
+ * @deprecated Use {@code org.scijava.io3.handle.WriteBufferDataHandle}
+ *             (scijava-io3) instead.
  */
+@Deprecated
 public class WriteBufferDataHandle extends AbstractHigherOrderHandle<Location> {
 
 	private static final int DEFAULT_BUFFERSIZE = 10_000;
diff --git a/src/main/java/org/scijava/io/location/AbstractLocation.java b/src/main/java/org/scijava/io/location/AbstractLocation.java
index 007a1a8a9..70c948807 100644
--- a/src/main/java/org/scijava/io/location/AbstractLocation.java
+++ b/src/main/java/org/scijava/io/location/AbstractLocation.java
@@ -36,7 +36,11 @@
  * Abstract base class for {@link Location} implementations.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.io3.location.AbstractLocation}
+ *             (scijava-io3) instead.
  */
+@Deprecated
 public abstract class AbstractLocation implements Location {
 
 	@Override
diff --git a/src/main/java/org/scijava/io/location/AbstractLocationResolver.java b/src/main/java/org/scijava/io/location/AbstractLocationResolver.java
index b40f6c0d9..868748cf4 100644
--- a/src/main/java/org/scijava/io/location/AbstractLocationResolver.java
+++ b/src/main/java/org/scijava/io/location/AbstractLocationResolver.java
@@ -37,7 +37,11 @@
  * Abstract super class for {@link LocationResolver} plugins.
  * 
  * @author Gabriel Einsdorf
+ *
+ * @deprecated Use {@code org.scijava.io3.location.AbstractLocationResolver}
+ *             (scijava-io3) instead.
  */
+@Deprecated
 public abstract class AbstractLocationResolver extends
 	AbstractHandlerPlugin<URI> implements LocationResolver
 {
diff --git a/src/main/java/org/scijava/io/location/AbstractRemoteLocation.java b/src/main/java/org/scijava/io/location/AbstractRemoteLocation.java
index 61b3f9735..2a1b5303e 100644
--- a/src/main/java/org/scijava/io/location/AbstractRemoteLocation.java
+++ b/src/main/java/org/scijava/io/location/AbstractRemoteLocation.java
@@ -33,7 +33,11 @@
  * Abstract base class for {@link RemoteLocation} implementations.
  *
  * @author Gabriel Einsdorf
+ *
+ * @deprecated Use {@code org.scijava.io3.location.AbstractRemoteLocation}
+ *             (scijava-io3) instead.
  */
+@Deprecated
 public abstract class AbstractRemoteLocation extends AbstractLocation implements
 	RemoteLocation
 {
diff --git a/src/main/java/org/scijava/io/location/BrowsableLocation.java b/src/main/java/org/scijava/io/location/BrowsableLocation.java
index f6efc3b99..bf5301dcc 100644
--- a/src/main/java/org/scijava/io/location/BrowsableLocation.java
+++ b/src/main/java/org/scijava/io/location/BrowsableLocation.java
@@ -39,7 +39,11 @@
  *
  * @author Gabriel Einsdorf
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.io3.location.BrowsableLocation}
+ *             (scijava-io3) instead.
  */
+@Deprecated
 public interface BrowsableLocation extends Location {
 
 	/**
diff --git a/src/main/java/org/scijava/io/location/BytesLocation.java b/src/main/java/org/scijava/io/location/BytesLocation.java
index 0b7f604ed..4de89f002 100644
--- a/src/main/java/org/scijava/io/location/BytesLocation.java
+++ b/src/main/java/org/scijava/io/location/BytesLocation.java
@@ -38,7 +38,11 @@
  *
  * @author Curtis Rueden
  * @author Gabriel Einsdorf
+ *
+ * @deprecated Use {@code org.scijava.io3.location.BytesLocation} (scijava-io3)
+ *             instead.
  */
+@Deprecated
 public class BytesLocation extends AbstractLocation {
 
 	private final ByteBank bytes;
diff --git a/src/main/java/org/scijava/io/location/DefaultLocationService.java b/src/main/java/org/scijava/io/location/DefaultLocationService.java
index 028dd807e..9e28a13fc 100644
--- a/src/main/java/org/scijava/io/location/DefaultLocationService.java
+++ b/src/main/java/org/scijava/io/location/DefaultLocationService.java
@@ -39,8 +39,12 @@
  * Default {@link LocationService} implementation.
  * 
  * @author Gabriel Einsdorf
+ *
+ * @deprecated Use {@code org.scijava.io3.location.Locations} (scijava-io3)
+ *             instead.
  */
 @Plugin(type = Service.class)
+@Deprecated
 public class DefaultLocationService extends
 	AbstractHandlerService<URI, LocationResolver> implements
 	LocationService
diff --git a/src/main/java/org/scijava/io/location/DummyLocation.java b/src/main/java/org/scijava/io/location/DummyLocation.java
index 0a9dd546f..e4091b798 100644
--- a/src/main/java/org/scijava/io/location/DummyLocation.java
+++ b/src/main/java/org/scijava/io/location/DummyLocation.java
@@ -33,7 +33,11 @@
  * {@link Location} backed by nothing whatsoever.
  *
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.io3.location.DummyLocation} (scijava-io3)
+ *             instead.
  */
+@Deprecated
 public class DummyLocation extends AbstractLocation {
 	// NB: No implementation needed.
 }
diff --git a/src/main/java/org/scijava/io/location/FileLocation.java b/src/main/java/org/scijava/io/location/FileLocation.java
index 4cf688d3b..db5216449 100644
--- a/src/main/java/org/scijava/io/location/FileLocation.java
+++ b/src/main/java/org/scijava/io/location/FileLocation.java
@@ -42,7 +42,11 @@
  *
  * @author Curtis Rueden
  * @author Gabriel Einsdorf
+ *
+ * @deprecated Use {@code org.scijava.io3.location.FileLocation} (scijava-io3)
+ *             instead.
  */
+@Deprecated
 public class FileLocation extends AbstractLocation implements
 	BrowsableLocation
 {
diff --git a/src/main/java/org/scijava/io/location/FileLocationResolver.java b/src/main/java/org/scijava/io/location/FileLocationResolver.java
index 5e6b19df0..32192dd4c 100644
--- a/src/main/java/org/scijava/io/location/FileLocationResolver.java
+++ b/src/main/java/org/scijava/io/location/FileLocationResolver.java
@@ -37,8 +37,12 @@
  * Implementation of {@link LocationResolver} for {@link FileLocation}.
  * 
  * @author Gabriel Einsdorf
+ *
+ * @deprecated Use {@code org.scijava.io3.location.FileLocationResolver}
+ *             (scijava-io3) instead.
  */
 @Plugin(type = LocationResolver.class)
+@Deprecated
 public class FileLocationResolver extends AbstractLocationResolver {
 
 	public FileLocationResolver() {
diff --git a/src/main/java/org/scijava/io/location/Location.java b/src/main/java/org/scijava/io/location/Location.java
index 2c579ad7e..d5888c4e6 100644
--- a/src/main/java/org/scijava/io/location/Location.java
+++ b/src/main/java/org/scijava/io/location/Location.java
@@ -47,7 +47,11 @@
  * 
  * @author Curtis Rueden
  * @author Gabriel Einsdorf
+ *
+ * @deprecated Use {@code org.scijava.io3.location.Location} (scijava-io3)
+ *             instead.
  */
+@Deprecated
 public interface Location {
 
 	/**
diff --git a/src/main/java/org/scijava/io/location/LocationResolver.java b/src/main/java/org/scijava/io/location/LocationResolver.java
index e4c60eada..9bfc11dbe 100644
--- a/src/main/java/org/scijava/io/location/LocationResolver.java
+++ b/src/main/java/org/scijava/io/location/LocationResolver.java
@@ -40,7 +40,12 @@
  * for easy implementation.
  * 
  * @author Gabriel Einsdorf
+ *
+ * @deprecated Use {@code org.scijava.io3.location.LocationResolver}
+ *             (scijava-io3) instead, which no longer extends a handler plugin
+ *             and carries its own {@code priority()}.
  */
+@Deprecated
 public interface LocationResolver extends HandlerPlugin<URI> {
 
 	/**
diff --git a/src/main/java/org/scijava/io/location/LocationService.java b/src/main/java/org/scijava/io/location/LocationService.java
index 078eca44c..9b7af2549 100644
--- a/src/main/java/org/scijava/io/location/LocationService.java
+++ b/src/main/java/org/scijava/io/location/LocationService.java
@@ -41,7 +41,13 @@
  * {@link LocationResolver} plugins for translation.
  * 
  * @author Gabriel Einsdorf
+ *
+ * @deprecated Use {@code org.scijava.io3.location.Locations} (scijava-io3)
+ *             instead, which resolves through plain
+ *             {@link java.util.ServiceLoader} and so needs no application
+ *             context.
  */
+@Deprecated
 public interface LocationService extends HandlerService<URI, LocationResolver>,
 	SciJavaService
 {
diff --git a/src/main/java/org/scijava/io/location/RemoteLocation.java b/src/main/java/org/scijava/io/location/RemoteLocation.java
index 20fd65fef..2322d0407 100644
--- a/src/main/java/org/scijava/io/location/RemoteLocation.java
+++ b/src/main/java/org/scijava/io/location/RemoteLocation.java
@@ -33,7 +33,11 @@
  * A {@link Location} which resides on a remote machine.
  * 
  * @author Gabriel Einsdorf
+ *
+ * @deprecated Use {@code org.scijava.io3.location.RemoteLocation}
+ *             (scijava-io3) instead.
  */
+@Deprecated
 public interface RemoteLocation extends Location {
 
 	/**
diff --git a/src/main/java/org/scijava/io/location/URILocation.java b/src/main/java/org/scijava/io/location/URILocation.java
index 52621ea91..88594b6d3 100644
--- a/src/main/java/org/scijava/io/location/URILocation.java
+++ b/src/main/java/org/scijava/io/location/URILocation.java
@@ -43,7 +43,11 @@
  * {@link Location} backed by a {@link URI} string.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.io3.location.URILocation} (scijava-io3)
+ *             instead.
  */
+@Deprecated
 public class URILocation extends AbstractLocation {
 
 	@Parameter
diff --git a/src/main/java/org/scijava/io/location/URLLocation.java b/src/main/java/org/scijava/io/location/URLLocation.java
index 396dedeae..212401d44 100644
--- a/src/main/java/org/scijava/io/location/URLLocation.java
+++ b/src/main/java/org/scijava/io/location/URLLocation.java
@@ -37,7 +37,11 @@
  * {@link Location} backed by a {@link URL}.
  *
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.io3.location.URLLocation} (scijava-io3)
+ *             instead.
  */
+@Deprecated
 public class URLLocation extends AbstractLocation {
 
 	/** The URL backing this location. */
diff --git a/src/main/java/org/scijava/io/nio/ByteBufferByteBank.java b/src/main/java/org/scijava/io/nio/ByteBufferByteBank.java
index 6f9ec504d..1991beb51 100644
--- a/src/main/java/org/scijava/io/nio/ByteBufferByteBank.java
+++ b/src/main/java/org/scijava/io/nio/ByteBufferByteBank.java
@@ -39,7 +39,13 @@
  * maximal capacity of {@link Integer#MAX_VALUE}
  *
  * @author Gabriel Einsdorf
+ *
+ * @deprecated Use {@code org.scijava.io3.ByteBufferByteBank} (scijava-io3)
+ *             instead, whose {@code direct()} factories make the off-heap case
+ *             explicit. NB: that version also fixes a bug here, where growing
+ *             a direct bank reallocated it on the heap.
  */
+@Deprecated
 public class ByteBufferByteBank implements ByteBank {
 
 	private static final int DEFAULT_CAPACITY = 10_000;
diff --git a/src/main/java/org/scijava/io/nio/DefaultNIOService.java b/src/main/java/org/scijava/io/nio/DefaultNIOService.java
index 2550caab8..3eebf0556 100644
--- a/src/main/java/org/scijava/io/nio/DefaultNIOService.java
+++ b/src/main/java/org/scijava/io/nio/DefaultNIOService.java
@@ -46,8 +46,11 @@
  * 
  * @author Chris Allan
  * @author Curtis Rueden
+ *
+ * @deprecated No replacement; see {@link org.scijava.io.nio.NIOService}.
  */
 @Plugin(type = Service.class)
+@Deprecated
 public class DefaultNIOService extends AbstractService implements NIOService {
 
 	// -- Fields --
diff --git a/src/main/java/org/scijava/io/nio/NIOService.java b/src/main/java/org/scijava/io/nio/NIOService.java
index 5e90ced72..e254565f5 100644
--- a/src/main/java/org/scijava/io/nio/NIOService.java
+++ b/src/main/java/org/scijava/io/nio/NIOService.java
@@ -42,7 +42,11 @@
  * 
  * @author Chris Allan
  * @author Curtis Rueden
+ *
+ * @deprecated No replacement. It wraps two JDK calls behind a system property;
+ *             use {@link java.nio.channels.FileChannel} directly.
  */
+@Deprecated
 public interface NIOService extends SciJavaService {
 
 	/**
diff --git a/src/main/java/org/scijava/task/DefaultTask.java b/src/main/java/org/scijava/task/DefaultTask.java
index 310dd8f15..a8654a286 100644
--- a/src/main/java/org/scijava/task/DefaultTask.java
+++ b/src/main/java/org/scijava/task/DefaultTask.java
@@ -65,7 +65,11 @@
  *
  * @author Curtis Rueden
  * @author Nicolas Chiaruttini
+ *
+ * @deprecated Use {@code org.scijava.progress.Task} (scijava-progress)
+ *             instead.
  */
+@Deprecated
 public class DefaultTask implements Task {
 
 	private final ThreadService threadService;
diff --git a/src/main/java/org/scijava/task/DefaultTaskService.java b/src/main/java/org/scijava/task/DefaultTaskService.java
index 7a2016f51..8bd5e4d39 100644
--- a/src/main/java/org/scijava/task/DefaultTaskService.java
+++ b/src/main/java/org/scijava/task/DefaultTaskService.java
@@ -40,8 +40,12 @@
  * Default implementation of {@link TaskService}.
  *
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.progress.Progress} (scijava-progress)
+ *             instead.
  */
 @Plugin(type = Service.class)
+@Deprecated
 public class DefaultTaskService extends AbstractService implements
 	TaskService
 {
diff --git a/src/main/java/org/scijava/task/Task.java b/src/main/java/org/scijava/task/Task.java
index 1dd539ab5..9ceecf193 100644
--- a/src/main/java/org/scijava/task/Task.java
+++ b/src/main/java/org/scijava/task/Task.java
@@ -58,7 +58,14 @@
  * See also {@link TaskService}, {@link DefaultTask}
  *
  * @author Curtis Rueden, Nicolas Chiaruttini
+ *
+ * @deprecated Use {@code org.scijava.progress.Task} (scijava-progress)
+ *             instead. NB: cancellation is no longer part of this contract; it
+ *             is thread interruption, with
+ *             {@link java.util.concurrent.Future#cancel(boolean)} as the
+ *             caller-facing API.
  */
+@Deprecated
 public interface Task extends Cancelable, Named {
 
 	/**
diff --git a/src/main/java/org/scijava/task/TaskService.java b/src/main/java/org/scijava/task/TaskService.java
index d3a46b7f9..ae421bc38 100644
--- a/src/main/java/org/scijava/task/TaskService.java
+++ b/src/main/java/org/scijava/task/TaskService.java
@@ -36,7 +36,11 @@
  *
  * @author Curtis Rueden
  * @see Task
+ *
+ * @deprecated Use {@code org.scijava.progress.Progress} (scijava-progress)
+ *             instead.
  */
+@Deprecated
 public interface TaskService extends SciJavaService {
 
 	/**
diff --git a/src/main/java/org/scijava/util/AbstractPrimitiveArray.java b/src/main/java/org/scijava/util/AbstractPrimitiveArray.java
index 6b284c0c3..1da41305f 100644
--- a/src/main/java/org/scijava/util/AbstractPrimitiveArray.java
+++ b/src/main/java/org/scijava/util/AbstractPrimitiveArray.java
@@ -45,7 +45,11 @@
  * @author Curtis Rueden
  * @param <ArrayType> Type of the primitive array; e.g., {@code double[]}.
  * @param <BaseType> Boxed type of the array element; e.g., {@code Double}.
+ *
+ * @deprecated Use {@code org.scijava.collections.AbstractPrimitiveArray}
+ *             (scijava-collections) instead.
  */
+@Deprecated
 public abstract class AbstractPrimitiveArray<ArrayType, BaseType> extends
 	AbstractList<BaseType> implements PrimitiveArray<ArrayType, BaseType>
 {
diff --git a/src/main/java/org/scijava/util/AppUtils.java b/src/main/java/org/scijava/util/AppUtils.java
index 134aa2ac4..d542c9eae 100644
--- a/src/main/java/org/scijava/util/AppUtils.java
+++ b/src/main/java/org/scijava/util/AppUtils.java
@@ -41,7 +41,10 @@
  * 
  * @author Johannes Schindelin
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.common3.Apps} (scijava-common3) instead.
  */
+@Deprecated
 public final class AppUtils {
 
 	private static final Class<?> mainClass;
diff --git a/src/main/java/org/scijava/util/ArrayUtils.java b/src/main/java/org/scijava/util/ArrayUtils.java
index 42afdfbcb..fad4b6c52 100644
--- a/src/main/java/org/scijava/util/ArrayUtils.java
+++ b/src/main/java/org/scijava/util/ArrayUtils.java
@@ -68,7 +68,14 @@
  * @author Curtis Rueden
  * @author Melissa Linkert
  * @author Chris Allan
+ *
+ * @deprecated Only the {@code safeMultiply} methods have a replacement, in
+ *             {@code org.scijava.common3.Numbers} (scijava-common3). For
+ *             {@code contains} and {@code indexOf}, use
+ *             {@link java.util.Arrays#asList} on object arrays, or a loop or
+ *             stream on primitive arrays.
  */
+@Deprecated
 public final class ArrayUtils {
 
 	private ArrayUtils() {
diff --git a/src/main/java/org/scijava/util/BoolArray.java b/src/main/java/org/scijava/util/BoolArray.java
index d0d6589b7..0612165be 100644
--- a/src/main/java/org/scijava/util/BoolArray.java
+++ b/src/main/java/org/scijava/util/BoolArray.java
@@ -37,7 +37,11 @@
  * @author Mark Hiner
  * @author Johannes Schindelin
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.collections.BoolArray}
+ *             (scijava-collections) instead.
  */
+@Deprecated
 public class BoolArray extends AbstractPrimitiveArray<boolean[], Boolean> {
 
 	/** The backing array. */
diff --git a/src/main/java/org/scijava/util/ByteArray.java b/src/main/java/org/scijava/util/ByteArray.java
index ad092abb5..967b88b09 100644
--- a/src/main/java/org/scijava/util/ByteArray.java
+++ b/src/main/java/org/scijava/util/ByteArray.java
@@ -36,7 +36,11 @@
  * 
  * @author Johannes Schindelin
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.collections.ByteArray}
+ *             (scijava-collections) instead.
  */
+@Deprecated
 public class ByteArray extends AbstractPrimitiveArray<byte[], Byte> {
 
 	/** The backing array. */
diff --git a/src/main/java/org/scijava/util/Bytes.java b/src/main/java/org/scijava/util/Bytes.java
index 5b56f8d03..7d71ca3c9 100644
--- a/src/main/java/org/scijava/util/Bytes.java
+++ b/src/main/java/org/scijava/util/Bytes.java
@@ -65,7 +65,10 @@
  * @author Curtis Rueden
  * @author Melissa Linkert
  * @author Chris Allan
+ *
+ * @deprecated Use {@code org.scijava.io3.Bytes} (scijava-io3) instead.
  */
+@Deprecated
 public final class Bytes {
 
 	private Bytes() {
diff --git a/src/main/java/org/scijava/util/CharArray.java b/src/main/java/org/scijava/util/CharArray.java
index 8459597da..1164a1730 100644
--- a/src/main/java/org/scijava/util/CharArray.java
+++ b/src/main/java/org/scijava/util/CharArray.java
@@ -37,7 +37,11 @@
  * @author Mark Hiner
  * @author Johannes Schindelin
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.collections.CharArray}
+ *             (scijava-collections) instead.
  */
+@Deprecated
 public class CharArray extends AbstractPrimitiveArray<char[], Character> {
 
 	/** The backing array. */
diff --git a/src/main/java/org/scijava/util/ClassUtils.java b/src/main/java/org/scijava/util/ClassUtils.java
index e9e7e4dc0..64777fd1e 100644
--- a/src/main/java/org/scijava/util/ClassUtils.java
+++ b/src/main/java/org/scijava/util/ClassUtils.java
@@ -47,7 +47,11 @@
  * Useful methods for working with {@link Class} objects and primitive types.
  *
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.common3.Classes} (scijava-common3)
+ *             instead.
  */
+@Deprecated
 public final class ClassUtils {
 
 	private ClassUtils() {
diff --git a/src/main/java/org/scijava/util/DebugUtils.java b/src/main/java/org/scijava/util/DebugUtils.java
index 44e28f780..ad0c61d5e 100644
--- a/src/main/java/org/scijava/util/DebugUtils.java
+++ b/src/main/java/org/scijava/util/DebugUtils.java
@@ -42,7 +42,11 @@
  * Useful methods for debugging programs.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.common3.Threads} (scijava-common3)
+ *             instead.
  */
+@Deprecated
 public final class DebugUtils {
 
 	private static final String NL = System.getProperty("line.separator");
diff --git a/src/main/java/org/scijava/util/DigestUtils.java b/src/main/java/org/scijava/util/DigestUtils.java
index 84a79eb66..a286ed53e 100644
--- a/src/main/java/org/scijava/util/DigestUtils.java
+++ b/src/main/java/org/scijava/util/DigestUtils.java
@@ -39,7 +39,12 @@
  * 
  * @author Curtis Rueden
  * @author Johannes Schindelin
+ *
+ * @deprecated Use {@code org.scijava.common3.Digests} (scijava-common3)
+ *             instead, whose {@code digest} throws for an unknown algorithm
+ *             rather than returning null.
  */
+@Deprecated
 public final class DigestUtils {
 
 	private final static char[] hex = { '0', '1', '2', '3', '4', '5', '6', '7',
diff --git a/src/main/java/org/scijava/util/DoubleArray.java b/src/main/java/org/scijava/util/DoubleArray.java
index de007478c..c4ee12fa7 100644
--- a/src/main/java/org/scijava/util/DoubleArray.java
+++ b/src/main/java/org/scijava/util/DoubleArray.java
@@ -36,7 +36,11 @@
  * 
  * @author Johannes Schindelin
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.collections.DoubleArray}
+ *             (scijava-collections) instead.
  */
+@Deprecated
 public class DoubleArray extends AbstractPrimitiveArray<double[], Double> {
 
 	/** The backing array. */
diff --git a/src/main/java/org/scijava/util/FileUtils.java b/src/main/java/org/scijava/util/FileUtils.java
index 897893e0d..702c1f6b9 100644
--- a/src/main/java/org/scijava/util/FileUtils.java
+++ b/src/main/java/org/scijava/util/FileUtils.java
@@ -63,7 +63,15 @@
  * @author Johannes Schindelin
  * @author Curtis Rueden
  * @author Grant Harris
+ *
+ * @deprecated Largely superseded. The filename logic is
+ *             {@code org.scijava.common3.FilePaths} and the URL methods are
+ *             {@code org.scijava.common3.URLs} (both scijava-common3); for
+ *             reading, writing, temporary directories and modification times,
+ *             use {@link java.nio.file.Files}. Method-by-method details:
+ *             https://github.com/scijava/scijava/blob/main/docs/migration.md
  */
+@Deprecated
 public final class FileUtils {
 
 	public static final int DEFAULT_SHORTENER_THRESHOLD = 4;
diff --git a/src/main/java/org/scijava/util/FloatArray.java b/src/main/java/org/scijava/util/FloatArray.java
index 49046497a..cb8c7a118 100644
--- a/src/main/java/org/scijava/util/FloatArray.java
+++ b/src/main/java/org/scijava/util/FloatArray.java
@@ -36,7 +36,11 @@
  * 
  * @author Johannes Schindelin
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.collections.FloatArray}
+ *             (scijava-collections) instead.
  */
+@Deprecated
 public class FloatArray extends AbstractPrimitiveArray<float[], Float> {
 
 	/** The backing array. */
diff --git a/src/main/java/org/scijava/util/IntArray.java b/src/main/java/org/scijava/util/IntArray.java
index f3c6a8e71..4c5efa13e 100644
--- a/src/main/java/org/scijava/util/IntArray.java
+++ b/src/main/java/org/scijava/util/IntArray.java
@@ -36,7 +36,11 @@
  * 
  * @author Johannes Schindelin
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.collections.IntArray}
+ *             (scijava-collections) instead.
  */
+@Deprecated
 public class IntArray extends AbstractPrimitiveArray<int[], Integer> {
 
 	/** The backing array. */
diff --git a/src/main/java/org/scijava/util/LongArray.java b/src/main/java/org/scijava/util/LongArray.java
index 12ae4a737..8fa6892ef 100644
--- a/src/main/java/org/scijava/util/LongArray.java
+++ b/src/main/java/org/scijava/util/LongArray.java
@@ -36,7 +36,11 @@
  * 
  * @author Johannes Schindelin
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.collections.LongArray}
+ *             (scijava-collections) instead.
  */
+@Deprecated
 public class LongArray extends AbstractPrimitiveArray<long[], Long> {
 
 	/** The backing array. */
diff --git a/src/main/java/org/scijava/util/Manifest.java b/src/main/java/org/scijava/util/Manifest.java
index 58100535e..a8bbb99a7 100644
--- a/src/main/java/org/scijava/util/Manifest.java
+++ b/src/main/java/org/scijava/util/Manifest.java
@@ -44,7 +44,10 @@
  * Helper class for working with JAR manifests.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.meta.Manifest} (scijava-meta) instead.
  */
+@Deprecated
 public class Manifest implements Versioned {
 
 	/** The JAR manifest backing this object. */
diff --git a/src/main/java/org/scijava/util/MersenneTwisterFast.java b/src/main/java/org/scijava/util/MersenneTwisterFast.java
index 852880483..e8cbd51ef 100644
--- a/src/main/java/org/scijava/util/MersenneTwisterFast.java
+++ b/src/main/java/org/scijava/util/MersenneTwisterFast.java
@@ -179,8 +179,12 @@
  *
  * @author Sean Luke
  * @version 17
+ *
+ * @deprecated Use {@code org.scijava.common3.MersenneTwisterFast}
+ *             (scijava-common3) instead.
  */
 @SuppressWarnings("all")
+@Deprecated
 public strictfp class MersenneTwisterFast implements Serializable, Cloneable
     {
 
diff --git a/src/main/java/org/scijava/util/MiscUtils.java b/src/main/java/org/scijava/util/MiscUtils.java
index eb9fad0c1..0d7097925 100644
--- a/src/main/java/org/scijava/util/MiscUtils.java
+++ b/src/main/java/org/scijava/util/MiscUtils.java
@@ -35,7 +35,11 @@
  * Miscellaneous utility methods. Every project needs a class like this, right?
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.common3.Comparisons} (scijava-common3)
+ *             instead.
  */
+@Deprecated
 public final class MiscUtils {
 
 	private MiscUtils() {
diff --git a/src/main/java/org/scijava/util/NumberUtils.java b/src/main/java/org/scijava/util/NumberUtils.java
index ba3fdc6d9..6646e0cd8 100644
--- a/src/main/java/org/scijava/util/NumberUtils.java
+++ b/src/main/java/org/scijava/util/NumberUtils.java
@@ -40,7 +40,13 @@
  * 
  * @author Curtis Rueden
  * @author Barry DeZonia
+ *
+ * @deprecated Use {@code org.scijava.common3.Numbers} (scijava-common3)
+ *             instead. Several methods are renamed, and its {@code toNumber}
+ *             consults no conversion framework; see
+ *             https://github.com/scijava/scijava/blob/main/docs/migration.md
  */
+@Deprecated
 public final class NumberUtils {
 
 	private NumberUtils() {
diff --git a/src/main/java/org/scijava/util/ObjectArray.java b/src/main/java/org/scijava/util/ObjectArray.java
index daaa6e7ed..2910f6f0b 100644
--- a/src/main/java/org/scijava/util/ObjectArray.java
+++ b/src/main/java/org/scijava/util/ObjectArray.java
@@ -48,7 +48,11 @@
  * @author Mark Hiner
  * @author Johannes Schindelin
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.collections.ObjectArray}
+ *             (scijava-collections) instead.
  */
+@Deprecated
 public class ObjectArray<E> extends AbstractPrimitiveArray<E[], E> {
 
 	/** The backing array. */
diff --git a/src/main/java/org/scijava/util/POM.java b/src/main/java/org/scijava/util/POM.java
index ed7dc8009..e98d58c27 100644
--- a/src/main/java/org/scijava/util/POM.java
+++ b/src/main/java/org/scijava/util/POM.java
@@ -48,7 +48,10 @@
  * Helper class for working with Maven POMs.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.meta.POM} (scijava-meta) instead.
  */
+@Deprecated
 public class POM extends XML implements Comparable<POM>, Versioned {
 
 	private String version;
diff --git a/src/main/java/org/scijava/util/PlatformUtils.java b/src/main/java/org/scijava/util/PlatformUtils.java
index a8b8cf909..020b4a8fc 100644
--- a/src/main/java/org/scijava/util/PlatformUtils.java
+++ b/src/main/java/org/scijava/util/PlatformUtils.java
@@ -34,7 +34,11 @@
  * 
  * @author Curtis Rueden
  * @author Johannes Schindelin
+ *
+ * @deprecated Use {@code org.scijava.common3.Platforms} (scijava-common3)
+ *             instead.
  */
+@Deprecated
 public final class PlatformUtils {
 
 	private PlatformUtils() {
diff --git a/src/main/java/org/scijava/util/PrimitiveArray.java b/src/main/java/org/scijava/util/PrimitiveArray.java
index 6efb5e463..713f128dd 100644
--- a/src/main/java/org/scijava/util/PrimitiveArray.java
+++ b/src/main/java/org/scijava/util/PrimitiveArray.java
@@ -44,7 +44,11 @@
  * @author Curtis Rueden
  * @param <ArrayType> Type of the primitive array; e.g., {@code double[]}.
  * @param <BaseType> Boxed type of the array element; e.g., {@code Double}.
+ *
+ * @deprecated Use {@code org.scijava.collections.PrimitiveArray}
+ *             (scijava-collections) instead.
  */
+@Deprecated
 public interface PrimitiveArray<ArrayType, BaseType> extends List<BaseType>,
 	Sizable
 {
diff --git a/src/main/java/org/scijava/util/ProcessUtils.java b/src/main/java/org/scijava/util/ProcessUtils.java
index 2e5cb62e5..21f017c08 100644
--- a/src/main/java/org/scijava/util/ProcessUtils.java
+++ b/src/main/java/org/scijava/util/ProcessUtils.java
@@ -39,7 +39,11 @@
  * Useful methods for working with processes.
  * 
  * @author Johannes Schindelin
+ *
+ * @deprecated Use {@code org.scijava.common3.Processes} (scijava-common3)
+ *             instead.
  */
+@Deprecated
 public final class ProcessUtils {
 
 	private ProcessUtils() {
diff --git a/src/main/java/org/scijava/util/ShortArray.java b/src/main/java/org/scijava/util/ShortArray.java
index 935bf6b96..417bbc0fe 100644
--- a/src/main/java/org/scijava/util/ShortArray.java
+++ b/src/main/java/org/scijava/util/ShortArray.java
@@ -36,7 +36,11 @@
  * 
  * @author Johannes Schindelin
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.collections.ShortArray}
+ *             (scijava-collections) instead.
  */
+@Deprecated
 public class ShortArray extends AbstractPrimitiveArray<short[], Short> {
 
 	/** The backing array. */
diff --git a/src/main/java/org/scijava/util/StringUtils.java b/src/main/java/org/scijava/util/StringUtils.java
index a38afb144..bf1e0573a 100644
--- a/src/main/java/org/scijava/util/StringUtils.java
+++ b/src/main/java/org/scijava/util/StringUtils.java
@@ -69,7 +69,12 @@
  * @author Chris Allan
  * @author Melissa Linkert
  * @author Richard Domander (Royal Veterinary College, London)
+ *
+ * @deprecated Use {@code org.scijava.common3.Strings} (scijava-common3)
+ *             instead, which carries the padding, {@code isNullOrEmpty} and
+ *             {@code splitUnquoted} methods; the rest have no replacement.
  */
+@Deprecated
 public final class StringUtils {
 
 	public static final char DEFAULT_PAD_CHAR = ' ';
diff --git a/src/main/java/org/scijava/util/Types.java b/src/main/java/org/scijava/util/Types.java
index 495ca4a40..10f05c8d1 100644
--- a/src/main/java/org/scijava/util/Types.java
+++ b/src/main/java/org/scijava/util/Types.java
@@ -102,7 +102,14 @@
  *
  * @author Curtis Rueden
  * @author Gabe Selzer
+ *
+ * @deprecated Use {@code org.scijava.common3.Types} (scijava-common3) instead.
+ *             It is not a drop-in superset: the class-oriented methods moved
+ *             to {@code org.scijava.common3.Classes}, and a few have no
+ *             replacement; see
+ *             https://github.com/scijava/scijava/blob/main/docs/migration.md
  */
+@Deprecated
 public final class Types {
 
 	private Types() {
diff --git a/src/main/java/org/scijava/util/VersionUtils.java b/src/main/java/org/scijava/util/VersionUtils.java
index 2d7e97a32..5655eb362 100644
--- a/src/main/java/org/scijava/util/VersionUtils.java
+++ b/src/main/java/org/scijava/util/VersionUtils.java
@@ -35,7 +35,10 @@
  *
  * @author Curtis Rueden
  * @author Mark Hiner
+ *
+ * @deprecated Use {@code org.scijava.meta.Versions} (scijava-meta) instead.
  */
+@Deprecated
 public class VersionUtils {
 
 	/**
diff --git a/src/main/java/org/scijava/util/XML.java b/src/main/java/org/scijava/util/XML.java
index 0dcbb1126..fda818328 100644
--- a/src/main/java/org/scijava/util/XML.java
+++ b/src/main/java/org/scijava/util/XML.java
@@ -64,7 +64,10 @@
  * Helper class for working with XML documents.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.meta.XML} (scijava-meta) instead.
  */
+@Deprecated
 public class XML {
 
 	/** Path to the XML document (e.g., a file or URL). */
diff --git a/src/main/java/org/scijava/widget/AbstractInputHarvester.java b/src/main/java/org/scijava/widget/AbstractInputHarvester.java
index 0785fa157..178e72f2a 100644
--- a/src/main/java/org/scijava/widget/AbstractInputHarvester.java
+++ b/src/main/java/org/scijava/widget/AbstractInputHarvester.java
@@ -55,6 +55,10 @@
  * @author Curtis Rueden
  * @param <P> The type of UI component housing the input panel itself.
  * @param <W> The type of UI component housing each input widget.
+ *
+ * @deprecated Use {@code org.scijava.ui3.InputHarvester} (scijava-ui3)
+ *             instead; {@code org.scijava.ui3.WidgetPanels} does the
+ *             tree-walking this class did.
  */
 public abstract class AbstractInputHarvester<P, W> extends AbstractContextual
 	implements InputHarvester<P, W>
diff --git a/src/main/java/org/scijava/widget/AbstractInputPanel.java b/src/main/java/org/scijava/widget/AbstractInputPanel.java
index 756f5ed15..1e2f94e10 100644
--- a/src/main/java/org/scijava/widget/AbstractInputPanel.java
+++ b/src/main/java/org/scijava/widget/AbstractInputPanel.java
@@ -38,6 +38,9 @@
  * @author Curtis Rueden
  * @param <P> The type of UI component housing the input panel itself.
  * @param <W> The type of UI component housing each input widget.
+ *
+ * @deprecated Use {@code org.scijava.swing.SwingPanel} (scijava-swing), or the
+ *             equivalent of another toolkit binding, instead.
  */
 public abstract class AbstractInputPanel<P, W> implements InputPanel<P, W> {
 
diff --git a/src/main/java/org/scijava/widget/AbstractInputWidget.java b/src/main/java/org/scijava/widget/AbstractInputWidget.java
index b6304cfd3..a53fcd32b 100644
--- a/src/main/java/org/scijava/widget/AbstractInputWidget.java
+++ b/src/main/java/org/scijava/widget/AbstractInputWidget.java
@@ -37,6 +37,9 @@
  * @author Curtis Rueden
  * @param <T> The input type of the widget.
  * @param <W> The type of UI component housing the widget.
+ *
+ * @deprecated Use {@code org.scijava.swing.SwingWidget} (scijava-swing), or
+ *             the equivalent base class of another toolkit binding, instead.
  */
 public abstract class AbstractInputWidget<T, W> extends
 	AbstractWrapperPlugin<WidgetModel> implements InputWidget<T, W>
diff --git a/src/main/java/org/scijava/widget/Button.java b/src/main/java/org/scijava/widget/Button.java
index 3ddfa0217..2fd3937ff 100644
--- a/src/main/java/org/scijava/widget/Button.java
+++ b/src/main/java/org/scijava/widget/Button.java
@@ -36,6 +36,9 @@
  * button fields.
  * 
  * @author Barry DeZonia
+ *
+ * @deprecated Not ported: a button in a dialog earns its place when something
+ *             asks for it.
  */
 public interface Button extends Optional {
 	// marker : nothing to implement
diff --git a/src/main/java/org/scijava/widget/ButtonWidget.java b/src/main/java/org/scijava/widget/ButtonWidget.java
index c836c522d..3a26c7150 100644
--- a/src/main/java/org/scijava/widget/ButtonWidget.java
+++ b/src/main/java/org/scijava/widget/ButtonWidget.java
@@ -33,6 +33,9 @@
  * Widget interface for buttons.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Not ported: a button in a dialog earns its place when something
+ *             asks for it.
  */
 public interface ButtonWidget<U> extends InputWidget<Button, U> {
 	// NB: No changes to interface.
diff --git a/src/main/java/org/scijava/widget/ChoiceWidget.java b/src/main/java/org/scijava/widget/ChoiceWidget.java
index 275b39607..4e5727f81 100644
--- a/src/main/java/org/scijava/widget/ChoiceWidget.java
+++ b/src/main/java/org/scijava/widget/ChoiceWidget.java
@@ -33,6 +33,11 @@
  * Widget interface for multiple choice selectors.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.swing.SwingChoiceWidget} (scijava-swing)
+ *             instead, or the equivalent of another toolkit binding. Which
+ *             widget a parameter gets is decided by a
+ *             {@code org.scijava.ui3.WidgetFactory}, not by a marker interface.
  */
 public interface ChoiceWidget<U> extends InputWidget<String, U> {
 
diff --git a/src/main/java/org/scijava/widget/ColorWidget.java b/src/main/java/org/scijava/widget/ColorWidget.java
index 93573a5ca..80953453f 100644
--- a/src/main/java/org/scijava/widget/ColorWidget.java
+++ b/src/main/java/org/scijava/widget/ColorWidget.java
@@ -35,6 +35,8 @@
  * Widget interface for color choosers.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Not ported yet: it earns its place when something asks for it.
  */
 public interface ColorWidget<U> extends InputWidget<ColorRGB, U> {
 	// NB: No changes to interface.
diff --git a/src/main/java/org/scijava/widget/DateWidget.java b/src/main/java/org/scijava/widget/DateWidget.java
index ecd9953cb..8b986eb89 100644
--- a/src/main/java/org/scijava/widget/DateWidget.java
+++ b/src/main/java/org/scijava/widget/DateWidget.java
@@ -35,6 +35,8 @@
  * Widget interface for dates.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Not ported yet: it earns its place when something asks for it.
  */
 public interface DateWidget<U> extends InputWidget<Date, U> {
 	// NB: No changes to interface.
diff --git a/src/main/java/org/scijava/widget/DefaultWidgetModel.java b/src/main/java/org/scijava/widget/DefaultWidgetModel.java
index e7d6b9352..65ada5c65 100644
--- a/src/main/java/org/scijava/widget/DefaultWidgetModel.java
+++ b/src/main/java/org/scijava/widget/DefaultWidgetModel.java
@@ -53,6 +53,8 @@
  * The backing data model for a particular {@link InputWidget}.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated No replacement; see {@code org.scijava.ui3.Widgets}.
  */
 public class DefaultWidgetModel extends AbstractContextual implements WidgetModel {
 
diff --git a/src/main/java/org/scijava/widget/DefaultWidgetService.java b/src/main/java/org/scijava/widget/DefaultWidgetService.java
index 7ceaf2c45..f13ebdf35 100644
--- a/src/main/java/org/scijava/widget/DefaultWidgetService.java
+++ b/src/main/java/org/scijava/widget/DefaultWidgetService.java
@@ -37,6 +37,8 @@
  * Default service for managing available {@link InputWidget}s.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated No replacement; see {@code org.scijava.ui3.WidgetPanels}.
  */
 @Plugin(type = Service.class)
 public class DefaultWidgetService extends
diff --git a/src/main/java/org/scijava/widget/FileListWidget.java b/src/main/java/org/scijava/widget/FileListWidget.java
index 466f51d2f..41f42ecd1 100644
--- a/src/main/java/org/scijava/widget/FileListWidget.java
+++ b/src/main/java/org/scijava/widget/FileListWidget.java
@@ -30,6 +30,9 @@
 
 import java.io.File;
 
+/**
+ * @deprecated Not ported yet: it earns its place when something asks for it.
+ */
 public interface FileListWidget<U> extends InputWidget<File[], U> {
 	/**
 	 * Widget style to allow file selection only
diff --git a/src/main/java/org/scijava/widget/FileWidget.java b/src/main/java/org/scijava/widget/FileWidget.java
index dcf38039d..faec1726e 100644
--- a/src/main/java/org/scijava/widget/FileWidget.java
+++ b/src/main/java/org/scijava/widget/FileWidget.java
@@ -35,6 +35,9 @@
  * Widget interface for file selectors.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.swing.SwingFileWidget} (scijava-swing)
+ *             instead, or the equivalent of another toolkit binding.
  */
 public interface FileWidget<U> extends InputWidget<File, U> {
 
diff --git a/src/main/java/org/scijava/widget/InputHarvester.java b/src/main/java/org/scijava/widget/InputHarvester.java
index c0638cd96..481df0e71 100644
--- a/src/main/java/org/scijava/widget/InputHarvester.java
+++ b/src/main/java/org/scijava/widget/InputHarvester.java
@@ -51,6 +51,11 @@
  * @author Curtis Rueden
  * @param <P> The type of UI component housing the input panel itself.
  * @param <W> The type of UI component housing each input widget.
+ *
+ * @deprecated Use {@code org.scijava.ui3.InputHarvester} (scijava-ui3)
+ *             instead. It is an {@code org.scijava.execute.Preprocessor}, and
+ *             a dismissed dialog calls {@code Execution.decline} rather than
+ *             setting a flag on the harvester.
  */
 public interface InputHarvester<P, W> {
 
diff --git a/src/main/java/org/scijava/widget/InputPanel.java b/src/main/java/org/scijava/widget/InputPanel.java
index 27869b777..bc7cbcdfe 100644
--- a/src/main/java/org/scijava/widget/InputPanel.java
+++ b/src/main/java/org/scijava/widget/InputPanel.java
@@ -36,6 +36,10 @@
  * @author Curtis Rueden
  * @param <P> The type of UI component housing the input panel itself.
  * @param <W> The type of UI component housing each input widget.
+ *
+ * @deprecated Use {@code org.scijava.ui3.WidgetPanel} (scijava-ui3) instead.
+ *             A panel is itself a widget there, so a group of parameters nests
+ *             inside another panel with no special case.
  */
 public interface InputPanel<P, W> extends UIComponent<P> {
 
diff --git a/src/main/java/org/scijava/widget/InputWidget.java b/src/main/java/org/scijava/widget/InputWidget.java
index fe12174a0..ff5a81905 100644
--- a/src/main/java/org/scijava/widget/InputWidget.java
+++ b/src/main/java/org/scijava/widget/InputWidget.java
@@ -52,6 +52,11 @@
  * @see WidgetService
  * @see InputHarvester
  * @see InputPanel
+ *
+ * @deprecated Use {@code org.scijava.ui3.Widget} (scijava-ui3) instead. A
+ *             widget is a view of an {@code org.scijava.harvest.ParameterNode}
+ *             and writes through the {@code ParameterModel}, so callbacks and
+ *             dynamic groups need nothing from the widget itself.
  */
 public interface InputWidget<T, W> extends WrapperPlugin<WidgetModel>,
 	UIComponent<W>
diff --git a/src/main/java/org/scijava/widget/MessageWidget.java b/src/main/java/org/scijava/widget/MessageWidget.java
index fe4877975..93271e62b 100644
--- a/src/main/java/org/scijava/widget/MessageWidget.java
+++ b/src/main/java/org/scijava/widget/MessageWidget.java
@@ -33,6 +33,8 @@
  * Widget interface for message labels.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Not ported yet: it earns its place when something asks for it.
  */
 public interface MessageWidget<U> extends InputWidget<String, U> {
 	// NB: No changes to interface.
diff --git a/src/main/java/org/scijava/widget/NumberWidget.java b/src/main/java/org/scijava/widget/NumberWidget.java
index f0aaefe28..a9e63d99e 100644
--- a/src/main/java/org/scijava/widget/NumberWidget.java
+++ b/src/main/java/org/scijava/widget/NumberWidget.java
@@ -33,6 +33,9 @@
  * Widget interface for number choosers.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.swing.SwingNumberWidget} (scijava-swing)
+ *             instead, or the equivalent of another toolkit binding.
  */
 public interface NumberWidget<U> extends InputWidget<Number, U> {
 
diff --git a/src/main/java/org/scijava/widget/ObjectWidget.java b/src/main/java/org/scijava/widget/ObjectWidget.java
index 925826ab9..99404240f 100644
--- a/src/main/java/org/scijava/widget/ObjectWidget.java
+++ b/src/main/java/org/scijava/widget/ObjectWidget.java
@@ -33,6 +33,11 @@
  * Widget interface for object selectors.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.ui3.WidgetFactory} with
+ *             {@code @Parameter(choicesFrom = ...)} instead: the candidate
+ *             objects are the parameter's resolved choices, so an ordinary
+ *             choice widget renders them.
  */
 public interface ObjectWidget<U> extends InputWidget<Object, U> {
 	// NB: No changes to interface.
diff --git a/src/main/java/org/scijava/widget/TextWidget.java b/src/main/java/org/scijava/widget/TextWidget.java
index 401d22076..1677bf8f6 100644
--- a/src/main/java/org/scijava/widget/TextWidget.java
+++ b/src/main/java/org/scijava/widget/TextWidget.java
@@ -33,6 +33,9 @@
  * Widget interface for text fields and areas.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.swing.SwingTextWidget} (scijava-swing)
+ *             instead, or the equivalent of another toolkit binding.
  */
 public interface TextWidget<U> extends InputWidget<String, U> {
 
diff --git a/src/main/java/org/scijava/widget/ToggleWidget.java b/src/main/java/org/scijava/widget/ToggleWidget.java
index 11c028862..c65ffa25d 100644
--- a/src/main/java/org/scijava/widget/ToggleWidget.java
+++ b/src/main/java/org/scijava/widget/ToggleWidget.java
@@ -33,6 +33,9 @@
  * Widget interface for boolean toggles.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated Use {@code org.scijava.swing.SwingToggleWidget} (scijava-swing)
+ *             instead, or the equivalent of another toolkit binding.
  */
 public interface ToggleWidget<U> extends InputWidget<Boolean, U> {
 	// NB: No changes to interface.
diff --git a/src/main/java/org/scijava/widget/UIComponent.java b/src/main/java/org/scijava/widget/UIComponent.java
index e36fcd919..839c48a7a 100644
--- a/src/main/java/org/scijava/widget/UIComponent.java
+++ b/src/main/java/org/scijava/widget/UIComponent.java
@@ -34,6 +34,10 @@
  * 
  * @author Curtis Rueden
  * @param <C> The type of UI component housing the object.
+ *
+ * @deprecated No replacement: a toolkit binding exposes its own component
+ *             type directly, as {@code org.scijava.swing.SwingWidget.component}
+ *             does.
  */
 public interface UIComponent<C> {
 
diff --git a/src/main/java/org/scijava/widget/WidgetModel.java b/src/main/java/org/scijava/widget/WidgetModel.java
index 4eb8e2703..8b85e8243 100644
--- a/src/main/java/org/scijava/widget/WidgetModel.java
+++ b/src/main/java/org/scijava/widget/WidgetModel.java
@@ -40,6 +40,11 @@
  * The backing data model for a particular {@link InputWidget}.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated No replacement: a widget reads its
+ *             {@code org.scijava.harvest.ParameterNode} for label, description,
+ *             bounds, style and resolved choices, and writes through
+ *             {@code org.scijava.harvest.ParameterModel}.
  */
 public interface WidgetModel extends Contextual {
 
diff --git a/src/main/java/org/scijava/widget/WidgetService.java b/src/main/java/org/scijava/widget/WidgetService.java
index 88bb00e93..f951767f3 100644
--- a/src/main/java/org/scijava/widget/WidgetService.java
+++ b/src/main/java/org/scijava/widget/WidgetService.java
@@ -40,6 +40,10 @@
  * Interface for services that manage available {@link InputWidget}s.
  * 
  * @author Curtis Rueden
+ *
+ * @deprecated No replacement: {@code org.scijava.ui3.WidgetPanels} picks the
+ *             widget for each parameter, from the
+ *             {@code org.scijava.ui3.WidgetFactory} plugins available.
  */
 public interface WidgetService extends
 	WrapperService<WidgetModel, InputWidget<?, ?>>, SciJavaService
diff --git a/src/main/java/org/scijava/widget/WidgetStyle.java b/src/main/java/org/scijava/widget/WidgetStyle.java
index ddd56824d..95e7771c4 100644
--- a/src/main/java/org/scijava/widget/WidgetStyle.java
+++ b/src/main/java/org/scijava/widget/WidgetStyle.java
@@ -30,6 +30,11 @@
 
 import org.scijava.module.ModuleItem;
 
+/**
+ * @deprecated Use {@code org.scijava.ui3.Widgets.isStyle} and
+ *             {@code org.scijava.ui3.Widgets.styleValue} (scijava-ui3)
+ *             instead.
+ */
 public class WidgetStyle {
 	private WidgetStyle() {
 		// prevent instantiation of utility class