AddCommand: implement --all/--no-all

Command-line git stages deletions if file paths are given. (i.e., --all
is implied.) File paths are also optional if --update or --all (or
--no-all) are given.

Add a setter and getter for an "all" flag on AddCommand.

Check consistency with the "update" flag in call(). Make file paths
optional (imply a "." path) if update is set or if setAll() had been
called. If file paths are given, set the all flag.

Stage deletions if update is set, or if the "all" flag is set.

Add the C git command-line options for the "all" flag to jgit.pgm.Add.

Bug: jgit-122
Change-Id: Iedddedcaa2d7a2e75162454ea047f34ec1cf3660

7 files changed, 183 insertions, 26 deletions

diff --git a/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/AddTest.java b/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/AddTest.java
index 6d6374f172..a48fcbcd5a 100644
--- a/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/AddTest.java
+++ b/org.eclipse.jgit.pgm.test/tst/org/eclipse/jgit/pgm/AddTest.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2012 Google Inc. and others
+ * Copyright (C) 2012, 2025 Google Inc. and others
  *
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Distribution License v. 1.0 which is available at
@@ -12,7 +12,10 @@ package org.eclipse.jgit.pgm;
 import static org.junit.Assert.assertArrayEquals;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.fail;
+import static org.junit.Assert.assertThrows;
+import static org.junit.Assert.assertTrue;
+
+import java.io.File;
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.dircache.DirCache;
@@ -32,12 +35,7 @@ public class AddTest extends CLIRepositoryTestCase {
 
 	@Test
 	public void testAddNothing() throws Exception {
-		try {
-			execute("git add");
-			fail("Must die");
-		} catch (Die e) {
-			// expected, requires argument
-		}
+		assertThrows(Die.class, () -> execute("git add"));
 	}
 
 	@Test
@@ -46,6 +44,17 @@ public class AddTest extends CLIRepositoryTestCase {
 	}
 
 	@Test
+	public void testAddInvalidOptionCombinations() throws Exception {
+		writeTrashFile("greeting", "Hello, world!");
+		assertThrows(Die.class, () -> execute("git add -u -A greeting"));
+		assertThrows(Die.class,
+				() -> execute("git add -u --ignore-removed greeting"));
+		// --renormalize implies -u
+		assertThrows(Die.class,
+				() -> execute("git add --renormalize --all greeting"));
+	}
+
+	@Test
 	public void testAddAFile() throws Exception {
 		writeTrashFile("greeting", "Hello, world!");
 		assertArrayEquals(new String[] { "" }, //
@@ -78,4 +87,34 @@ public class AddTest extends CLIRepositoryTestCase {
 		assertNotNull(cache.getEntry("greeting"));
 		assertEquals(1, cache.getEntryCount());
 	}
+
+	@Test
+	public void testAddDeleted() throws Exception {
+		File greeting = writeTrashFile("greeting", "Hello, world!");
+		git.add().addFilepattern("greeting").call();
+		DirCache cache = db.readDirCache();
+		assertNotNull(cache.getEntry("greeting"));
+		assertEquals(1, cache.getEntryCount());
+		assertTrue(greeting.delete());
+		assertArrayEquals(new String[] { "" }, //
+				execute("git add greeting"));
+
+		cache = db.readDirCache();
+		assertEquals(0, cache.getEntryCount());
+	}
+
+	@Test
+	public void testAddDeleted2() throws Exception {
+		File greeting = writeTrashFile("greeting", "Hello, world!");
+		git.add().addFilepattern("greeting").call();
+		DirCache cache = db.readDirCache();
+		assertNotNull(cache.getEntry("greeting"));
+		assertEquals(1, cache.getEntryCount());
+		assertTrue(greeting.delete());
+		assertArrayEquals(new String[] { "" }, //
+				execute("git add -A"));
+
+		cache = db.readDirCache();
+		assertEquals(0, cache.getEntryCount());
+	}
 }
diff --git a/org.eclipse.jgit.pgm/resources/org/eclipse/jgit/pgm/internal/CLIText.properties b/org.eclipse.jgit.pgm/resources/org/eclipse/jgit/pgm/internal/CLIText.properties
index 80829b6638..e9630e9499 100644
--- a/org.eclipse.jgit.pgm/resources/org/eclipse/jgit/pgm/internal/CLIText.properties
+++ b/org.eclipse.jgit.pgm/resources/org/eclipse/jgit/pgm/internal/CLIText.properties
@@ -12,6 +12,7 @@ ARGS=ARGS
 # default meta variable defined in the org.kohsuke.args4j.spi.OneArgumentOptionHandler
 N=N
 
+addIncompatibleOptions=--update/-u cannot be combined with --all/-A/--no-ignore-removal or --no-all/--ignore-removal. Note that --renormalize implies --update.
 alreadyOnBranch=Already on ''{0}''
 alreadyUpToDate=Already up-to-date.
 answerNo=n
@@ -255,7 +256,9 @@ unsupportedOperation=Unsupported operation: {0}
 untrackedFiles=Untracked files:
 updating=Updating {0}..{1}
 usage_Abbrev=Instead of using the default number of hexadecimal digits (which will vary according to the number of objects in the repository with a default of 7) of the abbreviated object name, use <n> digits, or as many digits as needed to form a unique object name. An <n> of 0 will suppress long format, only showing the closest tag.
-usage_addRenormalize=Apply the "clean" process freshly to tracked files to forcibly add them again to the index. This implies -u.
+usage_addRenormalize=Apply the "clean" process freshly to tracked files to forcibly add them again to the index. This implies --update/-u.
+usage_addStageDeletions=Add, modify, or remove index entries to match the working tree. Cannot be used with --update/-u.
+usage_addDontStageDeletions=Only add or modify index entries, but do not remove index entries for which there is no file. (Don''t stage deletions.) Cannot be used with --update/-u.
 usage_Aggressive=This option will cause gc to more aggressively optimize the repository at the expense of taking much more time
 usage_All=Pack all refs, except hidden refs, broken refs, and symbolic refs.
 usage_AlwaysFallback=Show uniquely abbreviated commit object as fallback
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Add.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Add.java
index 2ebab5e5d2..dc9d77df35 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Add.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Add.java
@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2010, Sasa Zivkov <sasa.zivkov@sap.com> and others
+ * Copyright (C) 2010, 2025 Sasa Zivkov <sasa.zivkov@sap.com> and others
  *
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Distribution License v. 1.0 which is available at
@@ -16,6 +16,7 @@ import java.util.List;
 import org.eclipse.jgit.api.AddCommand;
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.errors.GitAPIException;
+import org.eclipse.jgit.pgm.internal.CLIText;
 import org.kohsuke.args4j.Argument;
 import org.kohsuke.args4j.Option;
 
@@ -28,17 +29,33 @@ class Add extends TextBuiltin {
 	@Option(name = "--update", aliases = { "-u" }, usage = "usage_onlyMatchAgainstAlreadyTrackedFiles")
 	private boolean update = false;
 
-	@Argument(required = true, metaVar = "metaVar_filepattern", usage = "usage_filesToAddContentFrom")
+	@Option(name = "--all", aliases = { "-A",
+			"--no-ignore-removal" }, usage = "usage_addStageDeletions")
+	private Boolean all;
+
+	@Option(name = "--no-all", aliases = {
+			"--ignore-removal" }, usage = "usage_addDontStageDeletions")
+	private void noAll(@SuppressWarnings("unused") boolean ignored) {
+		all = Boolean.FALSE;
+	}
+
+	@Argument(metaVar = "metaVar_filepattern", usage = "usage_filesToAddContentFrom")
 	private List<String> filepatterns = new ArrayList<>();
 
 	@Override
 	protected void run() throws Exception {
 		try (Git git = new Git(db)) {
-			AddCommand addCmd = git.add();
 			if (renormalize) {
 				update = true;
 			}
+			if (update && all != null) {
+				throw die(CLIText.get().addIncompatibleOptions);
+			}
+			AddCommand addCmd = git.add();
 			addCmd.setUpdate(update).setRenormalize(renormalize);
+			if (all != null) {
+				addCmd.setAll(all.booleanValue());
+			}
 			for (String p : filepatterns) {
 				addCmd.addFilepattern(p);
 			}
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/internal/CLIText.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/internal/CLIText.java
index b5bf6d2bc3..bb1e950542 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/internal/CLIText.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/internal/CLIText.java
@@ -1,6 +1,6 @@
 /*
  * Copyright (C) 2010, 2013 Sasa Zivkov <sasa.zivkov@sap.com>
- * Copyright (C) 2013, 2021 Obeo and others
+ * Copyright (C) 2013, 2025 Obeo and others
  *
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Distribution License v. 1.0 which is available at
@@ -91,6 +91,7 @@ public class CLIText extends TranslationBundle {
 	}
 
 	// @formatter:off
+	/***/ public String addIncompatibleOptions;
 	/***/ public String alreadyOnBranch;
 	/***/ public String alreadyUpToDate;
 	/***/ public String answerNo;
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java
index 1c2e995bbb..226677229c 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/api/AddCommandTest.java
@@ -1,6 +1,6 @@
 /*
  * Copyright (C) 2010, Stefan Lay <stefan.lay@sap.com>
- * Copyright (C) 2010, Christian Halstrick <christian.halstrick@sap.com> and others
+ * Copyright (C) 2010, 2025 Christian Halstrick <christian.halstrick@sap.com> and others
  *
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Distribution License v. 1.0 which is available at
@@ -665,11 +665,13 @@ public class AddCommandTest extends RepositoryTestCase {
 			FileUtils.delete(file);
 
 			// is supposed to do nothing
-			dc = git.add().addFilepattern("a.txt").call();
+			dc = git.add().addFilepattern("a.txt").setAll(false).call();
 			assertEquals(oid, dc.getEntry(0).getObjectId());
 			assertEquals(
 					"[a.txt, mode:100644, content:content]",
 					indexState(CONTENT));
+			git.add().addFilepattern("a.txt").call();
+			assertEquals("", indexState(CONTENT));
 		}
 	}
 
@@ -690,11 +692,13 @@ public class AddCommandTest extends RepositoryTestCase {
 			FileUtils.delete(file);
 
 			// is supposed to do nothing
-			dc = git.add().addFilepattern("a.txt").call();
+			dc = git.add().addFilepattern("a.txt").setAll(false).call();
 			assertEquals(oid, dc.getEntry(0).getObjectId());
 			assertEquals(
 					"[a.txt, mode:100644, content:content]",
 					indexState(CONTENT));
+			git.add().addFilepattern("a.txt").call();
+			assertEquals("", indexState(CONTENT));
 		}
 	}
 
@@ -964,7 +968,7 @@ public class AddCommandTest extends RepositoryTestCase {
 			// file sub/b.txt is deleted
 			FileUtils.delete(file2);
 
-			git.add().addFilepattern("sub").call();
+			git.add().addFilepattern("sub").setAll(false).call();
 			// change in sub/a.txt is staged
 			// deletion of sub/b.txt is not staged
 			// sub/c.txt is staged
@@ -973,6 +977,12 @@ public class AddCommandTest extends RepositoryTestCase {
 					"[sub/b.txt, mode:100644, content:content b]" +
 					"[sub/c.txt, mode:100644, content:content c]",
 					indexState(CONTENT));
+			git.add().addFilepattern("sub").call();
+			// deletion of sub/b.txt is staged
+			assertEquals(
+					"[sub/a.txt, mode:100644, content:modified content]"
+							+ "[sub/c.txt, mode:100644, content:content c]",
+					indexState(CONTENT));
 		}
 	}
 
diff --git a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexDiffTest.java b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexDiffTest.java
index 2b7b6ca76c..cd98606e53 100644
--- a/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexDiffTest.java
+++ b/org.eclipse.jgit.test/tst/org/eclipse/jgit/lib/IndexDiffTest.java
@@ -2,7 +2,7 @@
  * Copyright (C) 2007, Dave Watson <dwatson@mimvista.com>
  * Copyright (C) 2008, Robin Rosenberg <robin.rosenberg@dewire.com>
  * Copyright (C) 2008, Shawn O. Pearce <spearce@spearce.org>
- * Copyright (C) 2013, Robin Stocker <robin@nibor.org> and others
+ * Copyright (C) 2013, 2025 Robin Stocker <robin@nibor.org> and others
  *
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Distribution License v. 1.0 which is available at
@@ -539,7 +539,7 @@ public class IndexDiffTest extends RepositoryTestCase {
 			assertTrue(diff.getAssumeUnchanged().contains("file3"));
 			assertTrue(diff.getModified().contains("file"));
 
-			git.add().addFilepattern(".").call();
+			git.add().addFilepattern(".").setAll(false).call();
 
 			iterator = new FileTreeIterator(db);
 			diff = new IndexDiff(db, Constants.HEAD, iterator);
@@ -551,6 +551,18 @@ public class IndexDiffTest extends RepositoryTestCase {
 			assertTrue(diff.getAssumeUnchanged().contains("file3"));
 			assertTrue(diff.getChanged().contains("file"));
 			assertEquals(Collections.EMPTY_SET, diff.getUntrackedFolders());
+
+			git.add().addFilepattern(".").call();
+
+			iterator = new FileTreeIterator(db);
+			diff = new IndexDiff(db, Constants.HEAD, iterator);
+			diff.diff();
+			assertEquals(1, diff.getAssumeUnchanged().size());
+			assertEquals(0, diff.getModified().size());
+			assertEquals(1, diff.getChanged().size());
+			assertTrue(diff.getAssumeUnchanged().contains("file2"));
+			assertTrue(diff.getChanged().contains("file"));
+			assertEquals(Collections.EMPTY_SET, diff.getUntrackedFolders());
 		}
 	}
 
diff --git a/org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java b/org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java
index c895dc9aaa..fd2ed37bb8 100644
--- a/org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java
+++ b/org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java
@@ -1,6 +1,6 @@
 /*
  * Copyright (C) 2010, Christian Halstrick <christian.halstrick@sap.com>
- * Copyright (C) 2010, Stefan Lay <stefan.lay@sap.com> and others
+ * Copyright (C) 2010, 2025 Stefan Lay <stefan.lay@sap.com> and others
  *
  * This program and the accompanying materials are made available under the
  * terms of the Eclipse Distribution License v. 1.0 which is available at
@@ -17,6 +17,7 @@ import static org.eclipse.jgit.lib.FileMode.TYPE_TREE;
 
 import java.io.IOException;
 import java.io.InputStream;
+import java.text.MessageFormat;
 import java.time.Instant;
 import java.util.ArrayList;
 import java.util.List;
@@ -59,8 +60,15 @@ public class AddCommand extends GitCommand<DirCache> {
 
 	private WorkingTreeIterator workingTreeIterator;
 
+	// Update only known index entries, don't add new ones. If there's no file
+	// for an index entry, remove it: stage deletions.
 	private boolean update = false;
 
+	// If TRUE, also stage deletions, otherwise only update and add index
+	// entries.
+	// If not set explicitly
+	private Boolean all;
+
 	// This defaults to true because it's what JGit has been doing
 	// traditionally. The C git default would be false.
 	private boolean renormalize = true;
@@ -82,6 +90,17 @@ public class AddCommand extends GitCommand<DirCache> {
 	 * A directory name (e.g. <code>dir</code> to add <code>dir/file1</code> and
 	 * <code>dir/file2</code>) can also be given to add all files in the
 	 * directory, recursively. Fileglobs (e.g. *.c) are not yet supported.
+	 * </p>
+	 * <p>
+	 * If a pattern {@code "."} is added, all changes in the git repository's
+	 * working tree will be added.
+	 * </p>
+	 * <p>
+	 * File patterns are required unless {@code isUpdate() == true} or
+	 * {@link #setAll(boolean)} is called. If so and no file patterns are given,
+	 * all changes will be added (i.e., a file pattern of {@code "."} is
+	 * implied).
+	 * </p>
 	 *
 	 * @param filepattern
 	 *            repository-relative path of file/directory to add (with
@@ -113,15 +132,41 @@ public class AddCommand extends GitCommand<DirCache> {
 	 * Executes the {@code Add} command. Each instance of this class should only
 	 * be used for one invocation of the command. Don't call this method twice
 	 * on an instance.
+	 * </p>
+	 *
+	 * @throws JGitInternalException
+	 *             on errors, but also if {@code isUpdate() == true} _and_
+	 *             {@link #setAll(boolean)} had been called
+	 * @throws NoFilepatternException
+	 *             if no file patterns are given if {@code isUpdate() == false}
+	 *             and {@link #setAll(boolean)} was not called
 	 */
 	@Override
 	public DirCache call() throws GitAPIException, NoFilepatternException {
-
-		if (filepatterns.isEmpty())
-			throw new NoFilepatternException(JGitText.get().atLeastOnePatternIsRequired);
 		checkCallable();
+
+		if (update && all != null) {
+			throw new JGitInternalException(MessageFormat.format(
+					JGitText.get().illegalCombinationOfArguments,
+					"--update", "--all/--no-all")); //$NON-NLS-1$ //$NON-NLS-2$
+		}
+		boolean addAll;
+		if (filepatterns.isEmpty()) {
+			if (update || all != null) {
+				addAll = true;
+			} else {
+				throw new NoFilepatternException(
+						JGitText.get().atLeastOnePatternIsRequired);
+			}
+		} else {
+			addAll = filepatterns.contains("."); //$NON-NLS-1$
+			if (all == null && !update) {
+				all = Boolean.TRUE;
+			}
+		}
+		boolean stageDeletions = update || all != null && all.booleanValue();
+
 		DirCache dc = null;
-		boolean addAll = filepatterns.contains("."); //$NON-NLS-1$
 
 		try (ObjectInserter inserter = repo.newObjectInserter();
 				NameConflictTreeWalk tw = new NameConflictTreeWalk(repo)) {
@@ -181,7 +226,8 @@ public class AddCommand extends GitCommand<DirCache> {
 
 				if (f == null) { // working tree file does not exist
 					if (entry != null
-							&& (!update || GITLINK == entry.getFileMode())) {
+							&& (!stageDeletions
+									|| GITLINK == entry.getFileMode())) {
 						builder.add(entry);
 					}
 					continue;
@@ -252,7 +298,8 @@ public class AddCommand extends GitCommand<DirCache> {
 	}
 
 	/**
-	 * Set whether to only match against already tracked files
+	 * Set whether to only match against already tracked files. If
+	 * {@code update == true}, re-sets a previous {@link #setAll(boolean)}.
 	 *
 	 * @param update
 	 *            If set to true, the command only matches {@code filepattern}
@@ -314,4 +361,32 @@ public class AddCommand extends GitCommand<DirCache> {
 	public boolean isRenormalize() {
 		return renormalize;
 	}
+
+	/**
+	 * Defines whether the command will use '--all' mode: update existing index
+	 * entries, add new entries, and remove index entries for which there is no
+	 * file. (In other words: also stage deletions.)
+	 * <p>
+	 * The setting is independent of {@link #setUpdate(boolean)}.
+	 * </p>
+	 *
+	 * @param all
+	 *            whether to enable '--all' mode
+	 * @return {@code this}
+	 * @since 7.2
+	 */
+	public AddCommand setAll(boolean all) {
+		this.all = Boolean.valueOf(all);
+		return this;
+	}
+
+	/**
+	 * Tells whether '--all' has been set for this command.
+	 *
+	 * @return {@code true} if it was set; {@code false} otherwise
+	 * @since 7.2
+	 */
+	public boolean isAll() {
+		return all != null && all.booleanValue();
+	}
 }