Merge branch 'master' into nextnext

* master: (497 commits)
  Prepare 7.3.0-SNAPSHOT builds
  Prepare 7.2.1-SNAPSHOT builds
  JGit v7.2.0.202503040940-r
  JGit v7.2.0.202503040805-r
  CacheRegion: fix non translatable text warnings
  Ensure access to autoRefresh is thread-safe
  FileReftableStack: use FileSnapshot to detect modification
  FileReftableDatabase: consider ref updates by another process
  BlameRegionMerger: report invalid regions with checked exception.
  Prepare 7.2.0-SNAPSHOT builds
  [ssh known_hosts] Handle unknown keys better
  [releng] Remove unused target platform definitions
  JGit v7.2.0.202502261823-rc1
  [ssh known_hosts] Handle host certificates
  [ssh known_hosts] Improve updating modified keys
  [ssh known_hosts] Add tests and fix problems
  [ssh, releng] Remove net.i2p.crypto.eddsa
  AddCommand: Use parenthesis to make the operator precedence explicit
  AddCommand: implement --all/--no-all
  Do not load bitmap indexes during directory scans
  ...

Change-Id: I619c89071f5f7a05bcd0218840f7f47bd19b779d

20 files changed, 280 insertions, 125 deletions

diff --git a/org.eclipse.jgit.pgm/META-INF/MANIFEST.MF b/org.eclipse.jgit.pgm/META-INF/MANIFEST.MF
index bb0c23dd72..d91efd46dd 100644
--- a/org.eclipse.jgit.pgm/META-INF/MANIFEST.MF
+++ b/org.eclipse.jgit.pgm/META-INF/MANIFEST.MF
@@ -3,7 +3,7 @@ Bundle-ManifestVersion: 2
 Bundle-Name: %Bundle-Name
 Automatic-Module-Name: org.eclipse.jgit.pgm
 Bundle-SymbolicName: org.eclipse.jgit.pgm
-Bundle-Version: 7.0.0.qualifier
+Bundle-Version: 7.3.0.qualifier
 Bundle-Vendor: %Bundle-Vendor
 Bundle-Localization: OSGI-INF/l10n/plugin
 Bundle-RequiredExecutionEnvironment: JavaSE-17
@@ -14,49 +14,50 @@ Import-Package: jakarta.servlet;version="[6.0.0,7.0.0)",
  org.eclipse.jetty.server.handler;version="[12.0.0,13.0.0)",
  org.eclipse.jetty.util;version="[12.0.0,13.0.0)",
  org.eclipse.jetty.util.component;version="[12.0.0,13.0.0)",
- org.eclipse.jgit.api;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.api.errors;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.archive;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.awtui;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.blame;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.diff;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.dircache;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.errors;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.gitrepo;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.internal.storage.file;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.internal.diffmergetool;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.internal.storage.io;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.internal.storage.pack;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.internal.storage.reftable;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.lfs;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.lfs.server;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.lfs.server.fs;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.lfs.server.s3;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.lib;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.merge;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.lib.internal;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.nls;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.notes;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.revplot;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.revwalk;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.revwalk.filter;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.storage.file;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.storage.pack;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.transport;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.transport.http.apache;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.transport.resolver;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.transport.ssh.jsch;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.transport.sshd;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.treewalk;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.treewalk.filter;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.util;version="[7.0.0,7.1.0)",
- org.eclipse.jgit.util.io;version="[7.0.0,7.1.0)",
+ org.eclipse.jgit.api;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.api.errors;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.archive;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.awtui;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.blame;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.diff;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.dircache;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.errors;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.gitrepo;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.internal.diffmergetool;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.internal.storage.file;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.internal.storage.io;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.internal.storage.midx;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.internal.storage.pack;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.internal.storage.reftable;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.lfs;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.lfs.server;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.lfs.server.fs;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.lfs.server.s3;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.lib;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.lib.internal;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.merge;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.nls;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.notes;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.revplot;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.revwalk;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.revwalk.filter;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.storage.file;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.storage.pack;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.transport;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.transport.http.apache;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.transport.resolver;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.transport.ssh.jsch;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.transport.sshd;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.treewalk;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.treewalk.filter;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.util;version="[7.3.0,7.4.0)",
+ org.eclipse.jgit.util.io;version="[7.3.0,7.4.0)",
  org.kohsuke.args4j;version="[2.33.0,3.0.0)",
  org.kohsuke.args4j.spi;version="[2.33.0,3.0.0)"
-Export-Package: org.eclipse.jgit.console;version="7.0.0";
+Export-Package: org.eclipse.jgit.console;version="7.3.0";
  uses:="org.eclipse.jgit.transport,
   org.eclipse.jgit.util",
- org.eclipse.jgit.pgm;version="7.0.0";
+ org.eclipse.jgit.pgm;version="7.3.0";
   uses:="org.eclipse.jgit.transport,
    org.eclipse.jgit.util.io,
    org.eclipse.jgit.awtui,
@@ -68,14 +69,14 @@ Export-Package: org.eclipse.jgit.console;version="7.0.0";
    org.eclipse.jgit.treewalk,
    org.eclipse.jgit.api,
    javax.swing",
- org.eclipse.jgit.pgm.debug;version="7.0.0";
+ org.eclipse.jgit.pgm.debug;version="7.3.0";
   uses:="org.eclipse.jgit.util.io,
    org.eclipse.jgit.pgm,
    org.eclipse.jetty.servlet",
- org.eclipse.jgit.pgm.internal;version="7.0.0";
+ org.eclipse.jgit.pgm.internal;version="7.3.0";
   x-friends:="org.eclipse.jgit.pgm.test,
    org.eclipse.jgit.test",
- org.eclipse.jgit.pgm.opt;version="7.0.0";
+ org.eclipse.jgit.pgm.opt;version="7.3.0";
   uses:="org.kohsuke.args4j,
    org.eclipse.jgit.lib,
    org.eclipse.jgit.revwalk,
diff --git a/org.eclipse.jgit.pgm/META-INF/SOURCE-MANIFEST.MF b/org.eclipse.jgit.pgm/META-INF/SOURCE-MANIFEST.MF
index 8bb1b64622..1c4a4812e5 100644
--- a/org.eclipse.jgit.pgm/META-INF/SOURCE-MANIFEST.MF
+++ b/org.eclipse.jgit.pgm/META-INF/SOURCE-MANIFEST.MF
@@ -3,5 +3,5 @@ Bundle-ManifestVersion: 2
 Bundle-Name: org.eclipse.jgit.pgm - Sources
 Bundle-SymbolicName: org.eclipse.jgit.pgm.source
 Bundle-Vendor: Eclipse.org - JGit
-Bundle-Version: 7.0.0.qualifier
-Eclipse-SourceBundle: org.eclipse.jgit.pgm;version="7.0.0.qualifier";roots="."
+Bundle-Version: 7.3.0.qualifier
+Eclipse-SourceBundle: org.eclipse.jgit.pgm;version="7.3.0.qualifier";roots="."
diff --git a/org.eclipse.jgit.pgm/META-INF/services/org.eclipse.jgit.pgm.TextBuiltin b/org.eclipse.jgit.pgm/META-INF/services/org.eclipse.jgit.pgm.TextBuiltin
index 08d37278de..6bf88d9aa8 100644
--- a/org.eclipse.jgit.pgm/META-INF/services/org.eclipse.jgit.pgm.TextBuiltin
+++ b/org.eclipse.jgit.pgm/META-INF/services/org.eclipse.jgit.pgm.TextBuiltin
@@ -26,6 +26,8 @@ org.eclipse.jgit.pgm.LsTree
 org.eclipse.jgit.pgm.Merge
 org.eclipse.jgit.pgm.MergeBase
 org.eclipse.jgit.pgm.MergeTool
+org.eclipse.jgit.pgm.MultiPackIndex
+org.eclipse.jgit.pgm.PackRefs
 org.eclipse.jgit.pgm.Push
 org.eclipse.jgit.pgm.ReceivePack
 org.eclipse.jgit.pgm.Reflog
diff --git a/org.eclipse.jgit.pgm/pom.xml b/org.eclipse.jgit.pgm/pom.xml
index 7cd76c3011..5890ce8256 100644
--- a/org.eclipse.jgit.pgm/pom.xml
+++ b/org.eclipse.jgit.pgm/pom.xml
@@ -17,7 +17,7 @@
   <parent>
     <groupId>org.eclipse.jgit</groupId>
     <artifactId>org.eclipse.jgit-parent</artifactId>
-    <version>7.0.0-SNAPSHOT</version>
+    <version>7.3.0-SNAPSHOT</version>
   </parent>
 
   <artifactId>org.eclipse.jgit.pgm</artifactId>
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 50ee809b98..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
@@ -255,8 +256,11 @@ 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
 usage_bareClone=Make a bare Git repository. That is, instead of creating [DIRECTORY] and placing the administrative files in [DIRECTORY]/.git, make the [DIRECTORY] itself the $GIT_DIR.
 usage_extraArgument=Pass an extra argument to a merge driver. Currently supported are "-X ours" and "-X theirs".
@@ -278,6 +282,7 @@ usage_CreateAnEmptyGitRepository=Create an empty git repository
 usage_Describe=Show the most recent tag that is reachable from a commit
 usage_DiffAlgorithms=Test performance of jgit's diff algorithms
 usage_DisplayTheVersionOfJgit=Display the version of jgit
+usage_Exclude=Do not consider tags matching the given glob(7) pattern, excluding the "refs/tags/" prefix
 usage_Gc=Cleanup unnecessary files and optimize the local repository
 usage_Glog=View commit history as a graph
 usage_DiffGuiTool=When git-difftool is invoked with the -g or --gui option the default diff tool will be read from the configured diff.guitool variable instead of diff.tool.
@@ -299,7 +304,9 @@ usage_MakeCacheTree=Show the current cache tree structure
 usage_Match=Only consider tags matching the given glob(7) pattern or patterns, excluding the "refs/tags/" prefix.
 usage_MergeBase=Find as good common ancestors as possible for a merge
 usage_MergesTwoDevelopmentHistories=Merges two development histories
+usage_MultiPackIndex=Operations over the multipack index
 usage_PackKeptObjects=Include objects in packs locked by a ".keep" file when repacking
+usage_PackRefs=Pack heads and tags for efficient repository access
 usage_PreserveOldPacks=Preserve old pack files by moving them into the preserved subdirectory instead of deleting them after repacking
 usage_PrunePreserved=Remove the preserved subdirectory containing previously preserved old pack files before repacking, and before preserving more old pack files
 usage_ReadDirCache= Read the DirCache 100 times
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/Blame.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Blame.java
index d2285ae64a..285fe2a96a 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Blame.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Blame.java
@@ -18,7 +18,7 @@ import static org.eclipse.jgit.lib.Constants.OBJECT_ID_STRING_LENGTH;
 
 import java.io.IOException;
 import java.text.MessageFormat;
-import java.text.SimpleDateFormat;
+import java.time.format.DateTimeFormatter;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -91,7 +91,7 @@ class Blame extends TextBuiltin {
 
 	private final Map<RevCommit, String> abbreviatedCommits = new HashMap<>();
 
-	private SimpleDateFormat dateFmt;
+	private DateTimeFormatter dateFmt;
 
 	private int begin;
 
@@ -125,9 +125,9 @@ class Blame extends TextBuiltin {
 		}
 
 		if (showRawTimestamp) {
-			dateFmt = new SimpleDateFormat("ZZZZ"); //$NON-NLS-1$
+			dateFmt = DateTimeFormatter.ofPattern("ZZ"); //$NON-NLS-1$
 		} else {
-			dateFmt = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss ZZZZ"); //$NON-NLS-1$
+			dateFmt = DateTimeFormatter.ofPattern("yyyy-MM-dd HH:mm:ss ZZ"); //$NON-NLS-1$
 		}
 
 		try (ObjectReader reader = db.newObjectReader();
@@ -335,12 +335,14 @@ class Blame extends TextBuiltin {
 		if (author == null)
 			return ""; //$NON-NLS-1$
 
-		dateFmt.setTimeZone(author.getTimeZone());
-		if (!showRawTimestamp)
-			return dateFmt.format(author.getWhen());
+		if (!showRawTimestamp) {
+			return dateFmt.withZone(author.getZoneId())
+					.format(author.getWhenAsInstant());
+		}
 		return String.format("%d %s", //$NON-NLS-1$
-				Long.valueOf(author.getWhen().getTime() / 1000L),
-				dateFmt.format(author.getWhen()));
+				Long.valueOf(author.getWhenAsInstant().getEpochSecond()),
+				dateFmt.withZone(author.getZoneId())
+						.format(author.getWhenAsInstant()));
 	}
 
 	private String abbreviate(ObjectReader reader, RevCommit commit)
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Config.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Config.java
index 52f40c2957..f5de7045d0 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Config.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Config.java
@@ -94,7 +94,7 @@ class Config extends TextBuiltin {
 		if (global || isListAll())
 			list(SystemReader.getInstance().openUserConfig(null, fs));
 		if (local || isListAll())
-			list(new FileBasedConfig(fs.resolve(getRepository().getDirectory(),
+			list(new FileBasedConfig(fs.resolve(getRepository().getCommonDirectory(),
 					Constants.CONFIG), fs));
 	}
 
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Describe.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Describe.java
index 913d7c790d..2633336e12 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Describe.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Describe.java
@@ -44,6 +44,9 @@ class Describe extends TextBuiltin {
 	@Option(name = "--match", usage = "usage_Match", metaVar = "metaVar_pattern")
 	private List<String> patterns = new ArrayList<>();
 
+	@Option(name = "--exclude", usage = "usage_Exclude", metaVar = "metaVar_pattern")
+	private List<String> excludes = new ArrayList<>();
+
 	@Option(name = "--abbrev", usage = "usage_Abbrev")
 	private Integer abbrev;
 
@@ -59,6 +62,7 @@ class Describe extends TextBuiltin {
 			cmd.setTags(useTags);
 			cmd.setAlways(always);
 			cmd.setMatch(patterns.toArray(new String[0]));
+			cmd.setExclude(excludes.toArray(new String[0]));
 			if (abbrev != null) {
 				cmd.setAbbrev(abbrev.intValue());
 			}
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Log.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Log.java
index 852a4b377b..958e566986 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Log.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Log.java
@@ -32,13 +32,12 @@ import org.eclipse.jgit.errors.LargeObjectException;
 import org.eclipse.jgit.lib.AnyObjectId;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.GpgConfig;
-import org.eclipse.jgit.lib.GpgSignatureVerifier;
-import org.eclipse.jgit.lib.GpgSignatureVerifier.SignatureVerification;
-import org.eclipse.jgit.lib.GpgSignatureVerifierFactory;
+import org.eclipse.jgit.lib.SignatureVerifier.SignatureVerification;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.PersonIdent;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.lib.SignatureVerifiers;
 import org.eclipse.jgit.notes.NoteMap;
 import org.eclipse.jgit.pgm.internal.CLIText;
 import org.eclipse.jgit.pgm.internal.VerificationUtils;
@@ -174,8 +173,6 @@ class Log extends RevWalkTextBuiltin {
 	// END -- Options shared with Diff
 
 
-	private GpgSignatureVerifier verifier;
-
 	private GpgConfig config;
 
 	Log() {
@@ -227,9 +224,6 @@ class Log extends RevWalkTextBuiltin {
 			throw die(e.getMessage(), e);
 		} finally {
 			diffFmt.close();
-			if (verifier != null) {
-				verifier.clear();
-			}
 		}
 	}
 
@@ -293,21 +287,13 @@ class Log extends RevWalkTextBuiltin {
 		if (c.getRawGpgSignature() == null) {
 			return;
 		}
-		if (verifier == null) {
-			GpgSignatureVerifierFactory factory = GpgSignatureVerifierFactory
-					.getDefault();
-			if (factory == null) {
-				throw die(CLIText.get().logNoSignatureVerifier, null);
-			}
-			verifier = factory.getVerifier();
-		}
-		SignatureVerification verification = verifier.verifySignature(c,
-				config);
+		SignatureVerification verification = SignatureVerifiers.verify(db,
+				config, c);
 		if (verification == null) {
 			return;
 		}
 		VerificationUtils.writeVerification(outw, verification,
-				verifier.getName(), c.getCommitterIdent());
+				verification.verifierName(), c.getCommitterIdent());
 	}
 
 	/**
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/MergeBase.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/MergeBase.java
index aacde2f430..a29c4d9f36 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/MergeBase.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/MergeBase.java
@@ -26,11 +26,6 @@ class MergeBase extends TextBuiltin {
 	private boolean all;
 
 	@Argument(index = 0, metaVar = "metaVar_commitish", required = true)
-	void commit_0(final RevCommit c) {
-		commits.add(c);
-	}
-
-	@Argument(index = 1, metaVar = "metaVar_commitish", required = true)
 	private List<RevCommit> commits = new ArrayList<>();
 
 	@Override
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/MultiPackIndex.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/MultiPackIndex.java
new file mode 100644
index 0000000000..1844223cc9
--- /dev/null
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/MultiPackIndex.java
@@ -0,0 +1,107 @@
+/*
+ * Copyright (C) 2025, Google LLC.
+ *
+ * This program and the accompanying materials are made available under the
+ * terms of the Eclipse Distribution License v. 1.0 which is available at
+ * https://www.eclipse.org/org/documents/edl-v10.php.
+ *
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
+package org.eclipse.jgit.pgm;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.eclipse.jgit.internal.storage.file.ObjectDirectory;
+import org.eclipse.jgit.internal.storage.file.Pack;
+import org.eclipse.jgit.internal.storage.file.PackFile;
+import org.eclipse.jgit.internal.storage.file.PackIndex;
+import org.eclipse.jgit.internal.storage.midx.MultiPackIndexPrettyPrinter;
+import org.eclipse.jgit.internal.storage.midx.MultiPackIndexWriter;
+import org.eclipse.jgit.internal.storage.pack.PackExt;
+import org.eclipse.jgit.lib.NullProgressMonitor;
+import org.kohsuke.args4j.Argument;
+import org.kohsuke.args4j.Option;
+
+@Command(common = true, usage = "usage_MultiPackIndex")
+@SuppressWarnings("nls")
+class MultiPackIndex extends TextBuiltin {
+	@Argument(index = 0, required = true, usage = "write, print")
+	private String command;
+
+	@Option(name = "--midx")
+	private String midxPath;
+
+	/** {@inheritDoc} */
+	@Override
+	protected void run() throws IOException {
+		switch (command) {
+		case "print":
+			printMultiPackIndex();
+			break;
+		case "write":
+			writeMultiPackIndex();
+			break;
+		default:
+			outw.println("Unknown command " + command);
+		}
+	}
+
+	private void printMultiPackIndex() {
+		if (midxPath == null || midxPath.isEmpty()) {
+			throw die("'print' requires the path of a multipack "
+					+ "index file with --midx option.");
+		}
+
+		try (FileInputStream is = new FileInputStream(midxPath)) {
+			PrintWriter pw = new PrintWriter(outw, true);
+			MultiPackIndexPrettyPrinter.prettyPrint(is.readAllBytes(), pw);
+		} catch (FileNotFoundException e) {
+			throw die(true, e);
+		} catch (IOException e) {
+			throw die(true, e);
+		}
+	}
+
+	private void writeMultiPackIndex() throws IOException {
+		if (!(db.getObjectDatabase() instanceof ObjectDirectory)) {
+			throw die("This repository object db doesn't have packs");
+		}
+
+		File midx;
+		if (midxPath == null || midxPath.isEmpty()) {
+			midx = new File(((ObjectDirectory) db.getObjectDatabase())
+					.getPackDirectory(), "multi-pack-index");
+		} else {
+			midx = new File(midxPath);
+		}
+
+		errw.println("Writing " + midx.getAbsolutePath());
+
+		ObjectDirectory odb = (ObjectDirectory) db.getObjectDatabase();
+
+		Map<String, PackIndex> indexes = new HashMap<>();
+		for (Pack pack : odb.getPacks()) {
+			PackFile packFile = pack.getPackFile().create(PackExt.INDEX);
+			try {
+				indexes.put(packFile.getName(), pack.getIndex());
+			} catch (IOException e) {
+				throw die("Cannot open index in pack", e);
+			}
+		}
+
+		MultiPackIndexWriter writer = new MultiPackIndexWriter();
+		try (FileOutputStream out = new FileOutputStream(midxPath)) {
+			writer.write(NullProgressMonitor.INSTANCE, out, indexes);
+		} catch (IOException e) {
+			throw die("Cannot write midx " + midxPath, e);
+		}
+	}
+}
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/PackRefs.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/PackRefs.java
new file mode 100644
index 0000000000..ee05f5ca0b
--- /dev/null
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/PackRefs.java
@@ -0,0 +1,34 @@
+/*
+ * Copyright (c) 2024 Qualcomm Innovation Center, Inc.
+ * and other copyright owners as documented in the project's IP log.
+ *
+ * This program and the accompanying materials are made available under the
+ * terms of the Eclipse Distribution License v. 1.0 which is available at
+ * https://www.eclipse.org/org/documents/edl-v10.php.
+ *
+ * SPDX-License-Identifier: BSD-3-Clause
+ */
+
+package org.eclipse.jgit.pgm;
+
+import org.eclipse.jgit.api.Git;
+import org.eclipse.jgit.api.errors.GitAPIException;
+import org.eclipse.jgit.lib.TextProgressMonitor;
+import org.kohsuke.args4j.Option;
+
+@Command(common = true, usage = "usage_PackRefs")
+class PackRefs extends TextBuiltin {
+	@Option(name = "--all", usage = "usage_All")
+	private boolean all;
+
+	@Override
+	protected void run() {
+		Git git = Git.wrap(db);
+		try {
+			git.packRefs().setProgressMonitor(new TextProgressMonitor(errw))
+					.setAll(all).call();
+		} catch (GitAPIException e) {
+			throw die(e.getMessage(), e);
+		}
+	}
+}
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Show.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Show.java
index 4feb090032..a3a6782a71 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Show.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Show.java
@@ -14,11 +14,10 @@ package org.eclipse.jgit.pgm;
 
 import java.io.BufferedOutputStream;
 import java.io.IOException;
-import java.text.DateFormat;
 import java.text.MessageFormat;
-import java.text.SimpleDateFormat;
+import java.time.ZoneId;
+import java.time.format.DateTimeFormatter;
 import java.util.Locale;
-import java.util.TimeZone;
 
 import org.eclipse.jgit.diff.DiffFormatter;
 import org.eclipse.jgit.diff.RawTextComparator;
@@ -30,12 +29,11 @@ import org.eclipse.jgit.errors.RevisionSyntaxException;
 import org.eclipse.jgit.lib.Constants;
 import org.eclipse.jgit.lib.FileMode;
 import org.eclipse.jgit.lib.GpgConfig;
-import org.eclipse.jgit.lib.GpgSignatureVerifier;
-import org.eclipse.jgit.lib.GpgSignatureVerifierFactory;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.PersonIdent;
 import org.eclipse.jgit.lib.Repository;
-import org.eclipse.jgit.lib.GpgSignatureVerifier.SignatureVerification;
+import org.eclipse.jgit.lib.SignatureVerifier.SignatureVerification;
+import org.eclipse.jgit.lib.SignatureVerifiers;
 import org.eclipse.jgit.pgm.internal.CLIText;
 import org.eclipse.jgit.pgm.internal.VerificationUtils;
 import org.eclipse.jgit.pgm.opt.PathTreeFilterHandler;
@@ -52,9 +50,9 @@ import org.kohsuke.args4j.Option;
 
 @Command(common = true, usage = "usage_show")
 class Show extends TextBuiltin {
-	private final TimeZone myTZ = TimeZone.getDefault();
+	private final ZoneId myTZ = ZoneId.systemDefault();
 
-	private final DateFormat fmt;
+	private final DateTimeFormatter fmt;
 
 	private DiffFormatter diffFmt;
 
@@ -158,7 +156,8 @@ class Show extends TextBuiltin {
 	// END -- Options shared with Diff
 
 	Show() {
-		fmt = new SimpleDateFormat("EEE MMM dd HH:mm:ss yyyy ZZZZZ", Locale.US); //$NON-NLS-1$
+		fmt = DateTimeFormatter.ofPattern("EEE MMM dd HH:mm:ss yyyy ZZ", //$NON-NLS-1$
+				Locale.US);
 	}
 
 	@Override
@@ -233,15 +232,17 @@ class Show extends TextBuiltin {
 		outw.print(tag.getTagName());
 		outw.println();
 
-		final PersonIdent tagger = tag.getTaggerIdent();
+		PersonIdent tagger = tag.getTaggerIdent();
 		if (tagger != null) {
 			outw.println(MessageFormat.format(CLIText.get().taggerInfo,
 					tagger.getName(), tagger.getEmailAddress()));
 
-			final TimeZone taggerTZ = tagger.getTimeZone();
-			fmt.setTimeZone(taggerTZ != null ? taggerTZ : myTZ);
+			ZoneId taggerTZ = tagger.getZoneId();
+			String formattedTaggerTime = fmt
+					.withZone(taggerTZ != null ? taggerTZ : myTZ)
+					.format(tagger.getWhenAsInstant());
 			outw.println(MessageFormat.format(CLIText.get().dateInfo,
-					fmt.format(tagger.getWhen())));
+					formattedTaggerTime));
 		}
 
 		outw.println();
@@ -294,10 +295,12 @@ class Show extends TextBuiltin {
 		outw.println(MessageFormat.format(CLIText.get().authorInfo,
 				author.getName(), author.getEmailAddress()));
 
-		final TimeZone authorTZ = author.getTimeZone();
-		fmt.setTimeZone(authorTZ != null ? authorTZ : myTZ);
+		final ZoneId authorTZ = author.getZoneId();
+		String formattedAuthorTime = fmt
+				.withZone(authorTZ != null ? authorTZ : myTZ)
+				.format(author.getWhenAsInstant());
 		outw.println(MessageFormat.format(CLIText.get().dateInfo,
-				fmt.format(author.getWhen())));
+				formattedAuthorTime));
 
 		outw.println();
 		final String[] lines = c.getFullMessage().split("\n"); //$NON-NLS-1$
@@ -335,23 +338,13 @@ class Show extends TextBuiltin {
 		if (c.getRawGpgSignature() == null) {
 			return;
 		}
-		GpgSignatureVerifierFactory factory = GpgSignatureVerifierFactory
-				.getDefault();
-		if (factory == null) {
-			throw die(CLIText.get().logNoSignatureVerifier, null);
-		}
-		GpgSignatureVerifier verifier = factory.getVerifier();
 		GpgConfig config = new GpgConfig(db.getConfig());
-		try {
-			SignatureVerification verification = verifier.verifySignature(c,
-					config);
-			if (verification == null) {
-				return;
-			}
-			VerificationUtils.writeVerification(outw, verification,
-					verifier.getName(), c.getCommitterIdent());
-		} finally {
-			verifier.clear();
+		SignatureVerification verification = SignatureVerifiers.verify(db,
+				config, c);
+		if (verification == null) {
+			throw die(CLIText.get().logNoSignatureVerifier, null);
 		}
+		VerificationUtils.writeVerification(outw, verification,
+				verification.verifierName(), c.getCommitterIdent());
 	}
 }
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Tag.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Tag.java
index 4ea67ab92c..6be30c9447 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Tag.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/Tag.java
@@ -27,10 +27,10 @@ import org.eclipse.jgit.api.VerifySignatureCommand;
 import org.eclipse.jgit.api.errors.GitAPIException;
 import org.eclipse.jgit.api.errors.RefAlreadyExistsException;
 import org.eclipse.jgit.lib.Constants;
-import org.eclipse.jgit.lib.GpgSignatureVerifier.SignatureVerification;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.Repository;
+import org.eclipse.jgit.lib.SignatureVerifier.SignatureVerification;
 import org.eclipse.jgit.pgm.internal.CLIText;
 import org.eclipse.jgit.pgm.internal.VerificationUtils;
 import org.eclipse.jgit.revwalk.RevCommit;
@@ -106,7 +106,8 @@ class Tag extends TextBuiltin {
 						if (error != null) {
 							throw die(error.getMessage(), error);
 						}
-						writeVerification(verifySig.getVerifier().getName(),
+						writeVerification(
+								verification.getVerification().verifierName(),
 								(RevTag) verification.getObject(),
 								verification.getVerification());
 					}
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildCommitGraph.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildCommitGraph.java
index 2f96ef7d57..22d9e3440a 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildCommitGraph.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/RebuildCommitGraph.java
@@ -18,8 +18,8 @@ import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.text.MessageFormat;
+import java.time.Instant;
 import java.util.ArrayList;
-import java.util.Date;
 import java.util.HashMap;
 import java.util.List;
 import java.util.ListIterator;
@@ -166,7 +166,8 @@ class RebuildCommitGraph extends TextBuiltin {
 
 					final CommitBuilder newc = new CommitBuilder();
 					newc.setTreeId(emptyTree);
-					newc.setAuthor(new PersonIdent(me, new Date(t.commitTime)));
+					newc.setAuthor(new PersonIdent(me,
+							Instant.ofEpochSecond(t.commitTime)));
 					newc.setCommitter(newc.getAuthor());
 					newc.setParentIds(newParents);
 					newc.setMessage("ORIGINAL " + t.oldId.name() + "\n"); //$NON-NLS-1$ //$NON-NLS-2$
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowPackDelta.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowPackDelta.java
index c95f1384e8..74e322ff7f 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowPackDelta.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/ShowPackDelta.java
@@ -31,6 +31,7 @@ import org.eclipse.jgit.pgm.Command;
 import org.eclipse.jgit.pgm.TextBuiltin;
 import org.eclipse.jgit.revwalk.RevObject;
 import org.eclipse.jgit.revwalk.RevWalk;
+import org.eclipse.jgit.storage.pack.PackConfig;
 import org.eclipse.jgit.util.TemporaryBuffer;
 import org.kohsuke.args4j.Argument;
 
@@ -68,7 +69,7 @@ class ShowPackDelta extends TextBuiltin {
 		ObjectReuseAsIs asis = (ObjectReuseAsIs) reader;
 		ObjectToPack target = asis.newObjectToPack(obj, obj.getType());
 
-		PackWriter pw = new PackWriter(reader) {
+		PackWriter pw = new PackWriter(new PackConfig(), reader) {
 			@Override
 			public void select(ObjectToPack otp, StoredObjectRepresentation next) {
 				otp.select(next);
diff --git a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/WriteReftable.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/WriteReftable.java
index faa2bceb74..7aff2dd9cd 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/WriteReftable.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/debug/WriteReftable.java
@@ -24,6 +24,8 @@ import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.OutputStream;
+import java.time.Instant;
+import java.time.ZoneOffset;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
@@ -209,14 +211,15 @@ class WriteReftable extends TextBuiltin {
 				}
 				String ref = m.group(1);
 				double t = Double.parseDouble(m.group(2));
-				long time = ((long) t) * 1000L;
+				Instant time = Instant.ofEpochSecond((long) t);
 				long index = (long) (t * 1e6);
 				String user = m.group(3);
 				ObjectId oldId = parseId(m.group(4));
 				ObjectId newId = parseId(m.group(5));
 				String msg = m.group(6);
 				String email = user + "@gerrit"; //$NON-NLS-1$
-				PersonIdent who = new PersonIdent(user, email, time, -480);
+				PersonIdent who = new PersonIdent(user, email, time,
+						ZoneOffset.ofHours(-8));
 				log.add(new LogEntry(ref, index, who, oldId, newId, msg));
 			}
 		}
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.pgm/src/org/eclipse/jgit/pgm/internal/VerificationUtils.java b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/internal/VerificationUtils.java
index c1f8a86a8c..64ee602620 100644
--- a/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/internal/VerificationUtils.java
+++ b/org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/internal/VerificationUtils.java
@@ -11,7 +11,7 @@ package org.eclipse.jgit.pgm.internal;
 
 import java.io.IOException;
 
-import org.eclipse.jgit.lib.GpgSignatureVerifier.SignatureVerification;
+import org.eclipse.jgit.lib.SignatureVerifier.SignatureVerification;
 import org.eclipse.jgit.lib.PersonIdent;
 import org.eclipse.jgit.util.GitDateFormatter;
 import org.eclipse.jgit.util.SignatureUtils;