Merge branch 'master' into next

* master:
  searchForReuse might impact performance in large repositories
  Retry loose object read upon "Stale file handle" exception
  Ignore missing javadoc in test bundles
  Upgrade maven-dependency-plugin to 3.2.0
  Upgrade jacoco-maven-plugin to 0.8.7
  Upgrade maven-jxr-plugin to 3.1.1
  Fix garbage collection failing to delete pack file
  Fix PathSuffixFilter: can decide only on full paths
  Update jetty to 9.4.42.v20210604
  [sshd] Log the full KEX negotiation result
  [releng] japicmp: update last release version
  CONTRIBUTING: add explicit link to ECA
  CONTRIBUTING: Use standard markdown format
  Add Eclipse code of conduct and security policy

Change-Id: I9e31cb6e22f5398db6e220f71693e87475c598bd

CODE_OF_CONDUCT.md

@@ -0,0 +1,46 @@
+# Community Code of Conduct
+
+**Version 1.2  
+August 19, 2020**
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as community members, contributors, committers, and project leaders pledge to make participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+*   Using welcoming and inclusive language
+*   Being respectful of differing viewpoints and experiences
+*   Gracefully accepting constructive criticism
+*   Focusing on what is best for the community
+*   Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+*   The use of sexualized language or imagery and unwelcome sexual attention or advances
+*   Trolling, insulting/derogatory comments, and personal or political attacks
+*   Public or private harassment
+*   Publishing others' private information, such as a physical or electronic address, without explicit permission
+*   Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+With the support of the Eclipse Foundation staff (the “Staff”), project committers and leaders are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project committers and leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies within all project spaces, and it also applies when an individual is representing the Eclipse Foundation project or its community in public spaces. Examples of representing a project or community include posting via an official social media account, or acting as a project representative at an online or offline event. Representation of a project may be further defined and clarified by project committers, leaders, or the EMO.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the Staff at codeofconduct@eclipse.org. All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The Staff is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+
+Project committers or leaders who do not follow the Code of Conduct in good faith may face temporary or permanent repercussions as determined by the Staff.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant](https://www.contributor-covenant.org) , version 1.4, available at [https://www.contributor-covenant.org/version/1/4/code-of-conduct.html](https://www.contributor-covenant.org/version/1/4/code-of-conduct/)

CONTRIBUTING.md

@@ -1,44 +1,33 @@
-Contributing
-============
+# Contributing
 
-Please refer to the contributor guide for all the details:
+Please refer to the [contributor guide](https://wiki.eclipse.org/EGit/Contributor_Guide) for all the details.
+Contributions require that you sign the [Eclipse Contributor Agreement](https://www.eclipse.org/legal/ECA.php).
 
-https://wiki.eclipse.org/EGit/Contributor_Guide
-
-
-Reporting bugs
---------------
+## Reporting bugs
 
 For anything other than small changes, it's a good idea to open a bug
 report for it (in case one doesn't already exist). This gives others the
-chance to give input and is useful for tracking. Create one here:
-
-https://bugs.eclipse.org/bugs/enter_bug.cgi?product=JGit
-
-
-Submitting changes
-------------------
+chance to give input and is useful for tracking. 
+[Create JGit bugs here](https://bugs.eclipse.org/bugs/enter_bug.cgi?product=JGit).
 
-We use Gerrit to review all changes by committers or contributors before
-they are merged:
+## Submitting changes
 
-https://git.eclipse.org/r/
-
-Make sure you have an account and have set up the `commit-msg` hook
+- We use [Gerrit](https://git.eclipse.org/r/) to review all changes by committers
+or contributors before they are merged.
+- Make sure you have an account and have set up the `commit-msg` hook
 before committing.
-
-When committing your changes, see the contributor guide or other commits
+- When committing your changes, see the contributor guide or other commits
 on what your commit message should include.
-
-Run the following to push your change for review (with `username`
+- Run the following to push your change for review (with `username`
 replaced by your Gerrit username):
 
-    git push ssh://username@git.eclipse.org:29418/jgit/jgit.git HEAD:refs/for/master
+```bash
+git push ssh://username@git.eclipse.org:29418/jgit/jgit.git HEAD:refs/for/master
+```
 
-Add the link to the review as a comment on the bug report, so that
+- Add the link to the review as a comment on the bug report, so that
 people coming from the bug report can find it.
-
-Then wait for someone to review your change. If there is something to be
+- Then wait for someone to review your change. If there is something to be
 corrected, amend your commit and push it again.
 
 Have fun :).

Documentation/config-options.md

@@ -102,6 +102,7 @@ Proxy configuration uses the standard Java mechanisms via class `java.net.ProxyS
 | `prunePreserved`, only via API of PackConfig | `false` | ⃞ | Whether to remove preserved pack files in a preserved directory. |
 | `pack.reuseDeltas` | `true` |⃞ | Whether to reuse deltas existing in repository. |
 | `pack.reuseObjects` | `true` | ⃞ | Whether to reuse existing objects representation in repository. |
+| `pack.searchForReuseTimeout` | | ⃞ | Search for reuse phase timeout. Expressed as a `Duration`, i.e.: `50sec`. |
 | `pack.singlePack` | `false` | ⃞ | Whether all of `refs/*` should be packed in a single pack. |
 | `pack.threads` | `0` (auto-detect number of processors) | ✅ | Number of threads to use for delta compression. |
 | `pack.waitPreventRacyPack` | `false` | ⃞ | Whether we wait before opening a newly written pack to prevent its lastModified timestamp could be racy. |

SECURITY.md

@@ -0,0 +1,49 @@
+<!--- https://www.eclipse.org/security/ --->
+_ISO 27005 defines vulnerability as:
+ "A weakness of an asset or group of assets that can be exploited by one or more threats."_
+
+## The Eclipse Security Team
+
+The Eclipse Security Team provides help and advice to Eclipse projects
+on vulnerability issues and is the first point of contact
+for handling security vulnerabilities.
+Members of the Security Team are committers on Eclipse Projects
+and members of the Eclipse Architecture Council.
+
+Contact the [Eclipse Security Team](mailto:security@eclipse.org).
+
+**Note that, as a matter of policy, the security team does not open attachments.**
+
+## Reporting a Security Vulnerability
+
+Vulnerabilities can be reported either via email to the Eclipse Security Team
+or directly with a project via the Eclipse Foundation's Bugzilla instance.
+
+The general security mailing list address is security@eclipse.org.
+Members of the Eclipse Security Team will receive messages sent to this address.
+This address should be used only for reporting undisclosed vulnerabilities;
+regular issue reports and questions unrelated to vulnerabilities in Eclipse software
+will be ignored.
+Note that this email address is not encrypted.
+
+The community is also encouraged to report vulnerabilities using the
+[Eclipse Foundation's Bugzilla instance](https://bugs.eclipse.org/bugs/enter_bug.cgi?product=Community&component=Vulnerability%20Reports&keywords=security&groups=Security_Advisories).
+Note that you will require an Eclipse Foundation account to create an issue report,
+but by doing so you will be able to participate directly in the resolution of the issue.
+
+Issue reports related to vulnerabilities must be marked as "committers-only",
+either automatically by clicking the provided link, by the reporter,
+or by a committer during the triage process.
+Note that issues marked "committers-only" are visible to all Eclipse committers.
+By default, a "committers-only" issue is also accessible to the reporter
+and individuals explicitly indicated in the "cc" list.
+
+## Disclosure
+
+Disclosure is initially limited to the reporter and all Eclipse Committers,
+but is expanded to include other individuals, and the general public.
+The timing and manner of disclosure is governed by the
+[Eclipse Security Policy](https://www.eclipse.org/security/policy.php).
+
+Publicly disclosed issues are listed on the
+[Disclosed Vulnerabilities Page](https://www.eclipse.org/security/known.php).

WORKSPACE

@@ -237,55 +237,55 @@ maven_jar(
     sha1 = "9180733b7df8542621dc12e21e87557e8c99b8cb",
 )
 
-JETTY_VER = "9.4.41.v20210516"
+JETTY_VER = "9.4.42.v20210604"
 
 maven_jar(
     name = "jetty-servlet",
     artifact = "org.eclipse.jetty:jetty-servlet:" + JETTY_VER,
-    sha1 = "ea45368ea7fd04026038f89e6910f17f70939641",
-    src_sha1 = "4acf6b0d1449ccd39b195783e3639ab0da51f7bf",
+    sha1 = "2b0529a22eab56f9a5553dd963e79edee7ffc1b5",
+    src_sha1 = "3351f1fdde7a9bc214f42283af82f002666c777d",
 )
 
 maven_jar(
     name = "jetty-security",
     artifact = "org.eclipse.jetty:jetty-security:" + JETTY_VER,
-    sha1 = "5ba69b1189a9d1f425ed03cbc2c901e0e6023c4d",
-    src_sha1 = "d46f8cb4dad66751d3a588309c6bbc15b80fbad4",
+    sha1 = "8f755242d4d73d98bef0055546aa53cf1ca456d9",
+    src_sha1 = "1442ba55bfdf147fdd9d8386627838b36af7a555",
 )
 
 maven_jar(
     name = "jetty-server",
     artifact = "org.eclipse.jetty:jetty-server:" + JETTY_VER,
-    sha1 = "25b1963b0a1c56202ec37046adc55861815107ce",
-    src_sha1 = "a7f82c9df737316cf0dfafe4a33ca4ae89d780db",
+    sha1 = "f5f95cdabe677bd8aad9e80f5e125c5b1c5011aa",
+    src_sha1 = "bdf93b825e7a7478a4a47d1c7569fc468f8c949e",
 )
 
 maven_jar(
     name = "jetty-http",
     artifact = "org.eclipse.jetty:jetty-http:" + JETTY_VER,
-    sha1 = "0d460bece4dd9666b46cbd18f8d7fd31cf02ecd9",
-    src_sha1 = "6fa009d950b8fdab8e94003e6295c08d42ee85b7",
+    sha1 = "2b0bb748d2388c6aa981ab29bc0a6a695dee31a4",
+    src_sha1 = "9f5b97a66ce62f03ce67b4f06936caa0ea9ba695",
 )
 
 maven_jar(
     name = "jetty-io",
     artifact = "org.eclipse.jetty:jetty-io:" + JETTY_VER,
-    sha1 = "820eea368623939c2113902b1ca7a98186f64a73",
-    src_sha1 = "4373285dafb5f79210815d9c15de106cc3e9ac4d",
+    sha1 = "581c5bb1aca96934e6961315fff066000c783659",
+    src_sha1 = "6822c5df4877b9d631543dd3e048bb1f0d9c7249",
 )
 
 maven_jar(
     name = "jetty-util",
     artifact = "org.eclipse.jetty:jetty-util:" + JETTY_VER,
-    sha1 = "548c76ea00d7eb3e2bcea273174e5d030639d109",
-    src_sha1 = "ba188de552a0c310f69cf12bea887413ce8f0e78",
+    sha1 = "16b116e9982c2037fd4bf05ce2525ccd5917eb9c",
+    src_sha1 = "e31bf18e992a5fd6e0e60f752b4edac4d57ca7cf",
 )
 
 maven_jar(
     name = "jetty-util-ajax",
     artifact = "org.eclipse.jetty:jetty-util-ajax:" + JETTY_VER,
-    sha1 = "d4c1d66fc62796a17548e6c344fbf89b5889f873",
-    src_sha1 = "b60cf77be68137eee4ee13d83c47d684d14b6d90",
+    sha1 = "dfff709928e92d8fd4888d53dbdfb024a4aa92f9",
+    src_sha1 = "6b59220ec832e41ed433581409006a567691a75c",
 )
 
 BOUNCYCASTLE_VER = "1.65"

org.eclipse.jgit.benchmarks/pom.xml

@@ -194,7 +194,7 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-jxr-plugin</artifactId>
-          <version>3.0.0</version>
+          <version>3.1.1</version>
         </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>

org.eclipse.jgit.lfs.server.test/.settings/org.eclipse.jdt.core.prefs

@@ -52,7 +52,7 @@ org.eclipse.jdt.core.compiler.problem.missingJavadocComments=ignore
 org.eclipse.jdt.core.compiler.problem.missingJavadocCommentsOverriding=disabled
 org.eclipse.jdt.core.compiler.problem.missingJavadocCommentsVisibility=protected
 org.eclipse.jdt.core.compiler.problem.missingJavadocTagDescription=return_tag
-org.eclipse.jdt.core.compiler.problem.missingJavadocTags=error
+org.eclipse.jdt.core.compiler.problem.missingJavadocTags=ignore
 org.eclipse.jdt.core.compiler.problem.missingJavadocTagsMethodTypeParameters=disabled
 org.eclipse.jdt.core.compiler.problem.missingJavadocTagsOverriding=disabled
 org.eclipse.jdt.core.compiler.problem.missingJavadocTagsVisibility=private

org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.10.target

@@ -1,28 +1,28 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
-<target name="jgit-4.10" sequenceNumber="1623012846">
+<target name="jgit-4.10" sequenceNumber="1623856101">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
-      <unit id="org.eclipse.jetty.client" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.client.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.continuation" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.continuation.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.http" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.http.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.io" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.io.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.security" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.security.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.server" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.server.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.servlet" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.servlet.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.util" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.util.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.util.ajax" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.util.ajax.source" version="9.4.41.v20210516"/>
-      <repository id="jetty-9.4.40" location="https://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.41.v20210516/"/>
+      <unit id="org.eclipse.jetty.client" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.client.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.continuation" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.continuation.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.http" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.http.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.io" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.io.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.security" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.security.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.server" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.server.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.servlet" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.servlet.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.util" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.util.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.util.ajax" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.util.ajax.source" version="9.4.42.v20210604"/>
+      <repository id="jetty-9.4.40" location="https://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.42.v20210604/"/>
     </location>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="com.google.gson" version="2.8.6.v20201231-1626"/>

org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.11.target

@@ -1,28 +1,28 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
-<target name="jgit-4.11" sequenceNumber="1623012873">
+<target name="jgit-4.11" sequenceNumber="1623856144">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
-      <unit id="org.eclipse.jetty.client" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.client.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.continuation" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.continuation.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.http" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.http.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.io" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.io.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.security" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.security.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.server" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.server.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.servlet" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.servlet.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.util" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.util.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.util.ajax" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.util.ajax.source" version="9.4.41.v20210516"/>
-      <repository id="jetty-9.4.40" location="https://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.41.v20210516/"/>
+      <unit id="org.eclipse.jetty.client" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.client.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.continuation" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.continuation.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.http" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.http.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.io" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.io.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.security" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.security.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.server" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.server.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.servlet" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.servlet.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.util" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.util.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.util.ajax" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.util.ajax.source" version="9.4.42.v20210604"/>
+      <repository id="jetty-9.4.40" location="https://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.42.v20210604/"/>
     </location>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="com.google.gson" version="2.8.6.v20201231-1626"/>

org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.12.target

@@ -1,28 +1,28 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
-<target name="jgit-4.12" sequenceNumber="1623012873">
+<target name="jgit-4.12" sequenceNumber="1623856144">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
-      <unit id="org.eclipse.jetty.client" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.client.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.continuation" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.continuation.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.http" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.http.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.io" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.io.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.security" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.security.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.server" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.server.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.servlet" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.servlet.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.util" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.util.source" version="9.4.41.v20210516"/>
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org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.13.target

@@ -1,28 +1,28 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
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+<target name="jgit-4.13" sequenceNumber="1623856144">
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org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.14.target

@@ -1,28 +1,28 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
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+<target name="jgit-4.14" sequenceNumber="1623856141">
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org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.15.target

@@ -1,28 +1,28 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
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org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.16.target

@@ -1,28 +1,28 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
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org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.17.target

@@ -1,28 +1,28 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
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org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.18.target

@@ -1,28 +1,28 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
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+<target name="jgit-4.18" sequenceNumber="1623856144">
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org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.19.target

@@ -1,28 +1,28 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
-<target name="jgit-4.19-staging" sequenceNumber="1623012870">
+<target name="jgit-4.19-staging" sequenceNumber="1623856140">
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+      <repository id="jetty-9.4.40" location="https://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.42.v20210604/"/>
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org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.20-staging.target

@@ -1,28 +1,28 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
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+<target name="jgit-4.20-staging" sequenceNumber="1623856145">
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org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.6.target

@@ -1,28 +1,28 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
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org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.7.target

@@ -1,28 +1,28 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
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org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.8.target

@@ -1,28 +1,28 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
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-      <unit id="org.eclipse.jetty.server.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.servlet" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.servlet.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.util" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.util.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.util.ajax" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.util.ajax.source" version="9.4.41.v20210516"/>
-      <repository id="jetty-9.4.40" location="https://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.41.v20210516/"/>
+      <unit id="org.eclipse.jetty.client" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.client.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.continuation" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.continuation.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.http" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.http.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.io" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.io.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.security" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.security.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.server" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.server.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.servlet" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.servlet.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.util" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.util.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.util.ajax" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.util.ajax.source" version="9.4.42.v20210604"/>
+      <repository id="jetty-9.4.40" location="https://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.42.v20210604/"/>
     </location>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="com.google.gson" version="2.8.6.v20201231-1626"/>

org.eclipse.jgit.packaging/org.eclipse.jgit.target/jgit-4.9.target

@@ -1,28 +1,28 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <?pde?>
 <!-- generated with https://github.com/eclipse-cbi/targetplatform-dsl -->
-<target name="jgit-4.9" sequenceNumber="1623012874">
+<target name="jgit-4.9" sequenceNumber="1623856144">
   <locations>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
-      <unit id="org.eclipse.jetty.client" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.client.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.continuation" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.continuation.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.http" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.http.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.io" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.io.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.security" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.security.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.server" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.server.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.servlet" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.servlet.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.util" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.util.source" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.util.ajax" version="9.4.41.v20210516"/>
-      <unit id="org.eclipse.jetty.util.ajax.source" version="9.4.41.v20210516"/>
-      <repository id="jetty-9.4.40" location="https://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.41.v20210516/"/>
+      <unit id="org.eclipse.jetty.client" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.client.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.continuation" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.continuation.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.http" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.http.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.io" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.io.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.security" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.security.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.server" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.server.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.servlet" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.servlet.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.util" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.util.source" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.util.ajax" version="9.4.42.v20210604"/>
+      <unit id="org.eclipse.jetty.util.ajax.source" version="9.4.42.v20210604"/>
+      <repository id="jetty-9.4.40" location="https://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.42.v20210604/"/>
     </location>
     <location includeMode="slicer" includeAllPlatforms="false" includeSource="true" includeConfigurePhase="true" type="InstallableUnit">
       <unit id="com.google.gson" version="2.8.6.v20201231-1626"/>

org.eclipse.jgit.packaging/org.eclipse.jgit.target/projects/jetty-9.4.x.tpd

@@ -1,22 +1,22 @@
 target "jetty-9.4.x" with source configurePhase
 
-location jetty-9.4.40 "https://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.41.v20210516/" {
-	org.eclipse.jetty.client [9.4.41.v20210516,9.4.41.v20210516]
-	org.eclipse.jetty.client.source [9.4.41.v20210516,9.4.41.v20210516]
-	org.eclipse.jetty.continuation [9.4.41.v20210516,9.4.41.v20210516]
-	org.eclipse.jetty.continuation.source [9.4.41.v20210516,9.4.41.v20210516]
-	org.eclipse.jetty.http [9.4.41.v20210516,9.4.41.v20210516]
-	org.eclipse.jetty.http.source [9.4.41.v20210516,9.4.41.v20210516]
-	org.eclipse.jetty.io [9.4.41.v20210516,9.4.41.v20210516]
-	org.eclipse.jetty.io.source [9.4.41.v20210516,9.4.41.v20210516]
-	org.eclipse.jetty.security [9.4.41.v20210516,9.4.41.v20210516]
-	org.eclipse.jetty.security.source [9.4.41.v20210516,9.4.41.v20210516]
-	org.eclipse.jetty.server [9.4.41.v20210516,9.4.41.v20210516]
-	org.eclipse.jetty.server.source [9.4.41.v20210516,9.4.41.v20210516]
-	org.eclipse.jetty.servlet [9.4.41.v20210516,9.4.41.v20210516]
-	org.eclipse.jetty.servlet.source [9.4.41.v20210516,9.4.41.v20210516]
-	org.eclipse.jetty.util [9.4.41.v20210516,9.4.41.v20210516]
-	org.eclipse.jetty.util.source [9.4.41.v20210516,9.4.41.v20210516]
-	org.eclipse.jetty.util.ajax [9.4.41.v20210516,9.4.41.v20210516]
-	org.eclipse.jetty.util.ajax.source [9.4.41.v20210516,9.4.41.v20210516]
+location jetty-9.4.40 "https://download.eclipse.org/jetty/updates/jetty-bundles-9.x/9.4.42.v20210604/" {
+	org.eclipse.jetty.client [9.4.42.v20210604,9.4.42.v20210604]
+	org.eclipse.jetty.client.source [9.4.42.v20210604,9.4.42.v20210604]
+	org.eclipse.jetty.continuation [9.4.42.v20210604,9.4.42.v20210604]
+	org.eclipse.jetty.continuation.source [9.4.42.v20210604,9.4.42.v20210604]
+	org.eclipse.jetty.http [9.4.42.v20210604,9.4.42.v20210604]
+	org.eclipse.jetty.http.source [9.4.42.v20210604,9.4.42.v20210604]
+	org.eclipse.jetty.io [9.4.42.v20210604,9.4.42.v20210604]
+	org.eclipse.jetty.io.source [9.4.42.v20210604,9.4.42.v20210604]
+	org.eclipse.jetty.security [9.4.42.v20210604,9.4.42.v20210604]
+	org.eclipse.jetty.security.source [9.4.42.v20210604,9.4.42.v20210604]
+	org.eclipse.jetty.server [9.4.42.v20210604,9.4.42.v20210604]
+	org.eclipse.jetty.server.source [9.4.42.v20210604,9.4.42.v20210604]
+	org.eclipse.jetty.servlet [9.4.42.v20210604,9.4.42.v20210604]
+	org.eclipse.jetty.servlet.source [9.4.42.v20210604,9.4.42.v20210604]
+	org.eclipse.jetty.util [9.4.42.v20210604,9.4.42.v20210604]
+	org.eclipse.jetty.util.source [9.4.42.v20210604,9.4.42.v20210604]
+	org.eclipse.jetty.util.ajax [9.4.42.v20210604,9.4.42.v20210604]
+	org.eclipse.jetty.util.ajax.source [9.4.42.v20210604,9.4.42.v20210604]
 }

org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/JGitClientSession.java

@@ -39,6 +39,7 @@ import org.apache.sshd.common.PropertyResolver;
 import org.apache.sshd.common.config.keys.KeyUtils;
 import org.apache.sshd.common.io.IoSession;
 import org.apache.sshd.common.io.IoWriteFuture;
+import org.apache.sshd.common.kex.KexProposalOption;
 import org.apache.sshd.common.util.Readable;
 import org.apache.sshd.common.util.buffer.Buffer;
 import org.eclipse.jgit.errors.InvalidPatternException;
@@ -200,6 +201,24 @@ public class JGitClientSession extends ClientSessionImpl {
 		}
 	}
 
+	@Override
+	protected Map<KexProposalOption, String> setNegotiationResult(
+			Map<KexProposalOption, String> guess) {
+		Map<KexProposalOption, String> result = super.setNegotiationResult(
+				guess);
+		// This should be doable with a SessionListener, too, but I don't see
+		// how to add a listener in time to catch the negotiation end for sure
+		// given that the super-constructor already starts KEX.
+		//
+		// TODO: This override can be removed once we use sshd 2.8.0.
+		if (log.isDebugEnabled()) {
+			result.forEach((option, value) -> log.debug(
+					"setNegotiationResult({}) Kex: {} = {}", this, //$NON-NLS-1$
+					option.getDescription(), value));
+		}
+		return result;
+	}
+
 	@Override
 	protected String resolveAvailableSignaturesProposal(
 			FactoryManager manager) {

org.eclipse.jgit.test/tst/org/eclipse/jgit/diff/DiffFormatterTest.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2010, 2020 Google Inc. and others
+ * Copyright (C) 2010, 2021 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
@@ -18,6 +18,8 @@ import static org.junit.Assert.assertTrue;
 import java.io.BufferedOutputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
 
 import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.api.Status;
@@ -34,8 +36,12 @@ import org.eclipse.jgit.patch.FileHeader;
 import org.eclipse.jgit.patch.HunkHeader;
 import org.eclipse.jgit.revwalk.RevCommit;
 import org.eclipse.jgit.storage.file.FileBasedConfig;
+import org.eclipse.jgit.treewalk.CanonicalTreeParser;
 import org.eclipse.jgit.treewalk.FileTreeIterator;
+import org.eclipse.jgit.treewalk.filter.OrTreeFilter;
 import org.eclipse.jgit.treewalk.filter.PathFilter;
+import org.eclipse.jgit.treewalk.filter.PathSuffixFilter;
+import org.eclipse.jgit.treewalk.filter.TreeFilter;
 import org.eclipse.jgit.util.FileUtils;
 import org.eclipse.jgit.util.RawParseUtils;
 import org.eclipse.jgit.util.io.DisabledOutputStream;
@@ -491,6 +497,68 @@ public class DiffFormatterTest extends RepositoryTestCase {
 		}
 	}
 
+	@Test
+	public void testFilter() throws Exception {
+		RevCommit parent;
+		RevCommit head;
+		try (Git git = new Git(db)) {
+			writeTrashFile("foo.txt", "foo\n");
+			writeTrashFile("src/some.txt", "some\n");
+			writeTrashFile("src/image.png", "image\n");
+			writeTrashFile("src/test.pdf", "test\n");
+			writeTrashFile("src/xyz.txt", "xyz\n");
+			git.add().addFilepattern(".").call();
+			parent = git.commit().setMessage("initial").call();
+			writeTrashFile("foo.txt", "FOO\n");
+			writeTrashFile("src/some.txt", "SOME\n");
+			writeTrashFile("src/image.png", "IMAGE\n");
+			writeTrashFile("src/test.pdf", "TEST\n");
+			writeTrashFile("src/xyz.txt", "XYZ\n");
+			git.add().addFilepattern(".").call();
+			head = git.commit().setMessage("second").call();
+		}
+		try (ByteArrayOutputStream os = new ByteArrayOutputStream();
+				DiffFormatter dfmt = new DiffFormatter(os)) {
+			dfmt.setRepository(db);
+			List<TreeFilter> skip = new ArrayList<>();
+			skip.add(PathSuffixFilter.create(".png"));
+			skip.add(PathSuffixFilter.create(".pdf"));
+			dfmt.setPathFilter(OrTreeFilter.create(skip).negate());
+			dfmt.format(
+					new CanonicalTreeParser(null, db.newObjectReader(),
+							parent.getTree()),
+					new CanonicalTreeParser(null, db.newObjectReader(),
+							head.getTree()));
+			dfmt.flush();
+
+			String actual = os.toString("UTF-8");
+
+			String expected = "diff --git a/foo.txt b/foo.txt\n"
+					+ "index 257cc56..b7d6715 100644\n"
+					+ "--- a/foo.txt\n"
+					+ "+++ b/foo.txt\n"
+					+ "@@ -1 +1 @@\n"
+					+ "-foo\n"
+					+ "+FOO\n"
+					+ "diff --git a/src/some.txt b/src/some.txt\n"
+					+ "index 363ef61..76cea5f 100644\n"
+					+ "--- a/src/some.txt\n"
+					+ "+++ b/src/some.txt\n"
+					+ "@@ -1 +1 @@\n"
+					+ "-some\n"
+					+ "+SOME\n"
+					+ "diff --git a/src/xyz.txt b/src/xyz.txt\n"
+					+ "index cd470e6..d4e3ab0 100644\n"
+					+ "--- a/src/xyz.txt\n"
+					+ "+++ b/src/xyz.txt\n"
+					+ "@@ -1 +1 @@\n"
+					+ "-xyz\n"
+					+ "+XYZ\n";
+
+			assertEquals(expected, actual);
+		}
+	}
+
 	@Test
 	public void testTrackedFileInIgnoredFolderChanged()
 			throws Exception {

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/ObjectDirectoryTest.java

@@ -44,8 +44,12 @@ package org.eclipse.jgit.internal.storage.file;
 
 import static java.nio.charset.StandardCharsets.UTF_8;
 import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertThrows;
 import static org.junit.Assert.assertTrue;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.verify;
 
 import java.io.File;
 import java.io.IOException;
@@ -69,6 +73,7 @@ import org.eclipse.jgit.storage.file.FileBasedConfig;
 import org.eclipse.jgit.util.FS;
 import org.junit.Assume;
 import org.junit.Test;
+import org.mockito.Mockito;
 
 public class ObjectDirectoryTest extends RepositoryTestCase {
 
@@ -194,6 +199,42 @@ public class ObjectDirectoryTest extends RepositoryTestCase {
 		assertTrue(shallowCommits.isEmpty());
 	}
 
+	@Test
+	public void testOpenLooseObjectSuppressStaleFileHandleException()
+			throws Exception {
+		ObjectId id = ObjectId
+				.fromString("873fb8d667d05436d728c52b1d7a09528e6eb59b");
+		WindowCursor curs = new WindowCursor(db.getObjectDatabase());
+
+		LooseObjects mock = mock(LooseObjects.class);
+		UnpackedObjectCache unpackedObjectCacheMock = mock(
+				UnpackedObjectCache.class);
+
+		Mockito.when(mock.getObjectLoader(any(), any(), any()))
+				.thenThrow(new IOException("Stale File Handle"));
+		Mockito.when(mock.open(curs, id)).thenCallRealMethod();
+		Mockito.when(mock.unpackedObjectCache())
+				.thenReturn(unpackedObjectCacheMock);
+
+		assertNull(mock.open(curs, id));
+		verify(unpackedObjectCacheMock).remove(id);
+	}
+
+	@Test
+	public void testOpenLooseObjectPropagatesIOExceptions() throws Exception {
+		ObjectId id = ObjectId
+				.fromString("873fb8d667d05436d728c52b1d7a09528e6eb59b");
+		WindowCursor curs = new WindowCursor(db.getObjectDatabase());
+
+		LooseObjects mock = mock(LooseObjects.class);
+
+		Mockito.when(mock.getObjectLoader(any(), any(), any()))
+				.thenThrow(new IOException("some IO failure"));
+		Mockito.when(mock.open(curs, id)).thenCallRealMethod();
+
+		assertThrows(IOException.class, () -> mock.open(curs, id));
+	}
+
 	@Test
 	public void testShallowFileCorrupt() throws Exception {
 		FileRepository repository = createBareRepository();

org.eclipse.jgit.test/tst/org/eclipse/jgit/internal/storage/file/PackWriterTest.java

@@ -18,6 +18,10 @@ import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.doNothing;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
 
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
@@ -25,6 +29,7 @@ import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.text.ParseException;
+import java.time.Duration;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -32,6 +37,7 @@ import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
+import org.eclipse.jgit.api.Git;
 import org.eclipse.jgit.errors.MissingObjectException;
 import org.eclipse.jgit.internal.storage.file.PackIndex.MutableEntry;
 import org.eclipse.jgit.internal.storage.pack.PackExt;
@@ -43,6 +49,7 @@ import org.eclipse.jgit.lib.NullProgressMonitor;
 import org.eclipse.jgit.lib.ObjectId;
 import org.eclipse.jgit.lib.ObjectIdSet;
 import org.eclipse.jgit.lib.ObjectInserter;
+import org.eclipse.jgit.lib.Ref;
 import org.eclipse.jgit.lib.Repository;
 import org.eclipse.jgit.lib.Sets;
 import org.eclipse.jgit.revwalk.DepthWalk;
@@ -58,6 +65,7 @@ import org.eclipse.jgit.transport.PackParser;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
+import org.mockito.Mockito;
 
 public class PackWriterTest extends SampleDataRepositoryTestCase {
 
@@ -626,6 +634,131 @@ public class PackWriterTest extends SampleDataRepositoryTestCase {
 		}
 	}
 
+	@Test
+	public void testTotalPackFilesScanWhenSearchForReuseTimeoutNotSet()
+			throws Exception {
+		FileRepository fileRepository = setUpRepoWithMultiplePackfiles();
+		PackWriter mockedPackWriter = Mockito
+				.spy(new PackWriter(config, fileRepository.newObjectReader()));
+
+		doNothing().when(mockedPackWriter).select(any(), any());
+
+		try (FileOutputStream packOS = new FileOutputStream(
+				getPackFileToWrite(fileRepository, mockedPackWriter))) {
+			mockedPackWriter.writePack(NullProgressMonitor.INSTANCE,
+					NullProgressMonitor.INSTANCE, packOS);
+		}
+
+		long numberOfPackFiles = new GC(fileRepository)
+				.getStatistics().numberOfPackFiles;
+		int expectedSelectCalls =
+				// Objects contained in multiple packfiles * number of packfiles
+				2 * (int) numberOfPackFiles +
+				// Objects in single packfile
+						1;
+		verify(mockedPackWriter, times(expectedSelectCalls)).select(any(),
+				any());
+	}
+
+	@Test
+	public void testTotalPackFilesScanWhenSkippingSearchForReuseTimeoutCheck()
+			throws Exception {
+		FileRepository fileRepository = setUpRepoWithMultiplePackfiles();
+		PackConfig packConfig = new PackConfig();
+		packConfig.setSearchForReuseTimeout(Duration.ofSeconds(-1));
+		PackWriter mockedPackWriter = Mockito.spy(
+				new PackWriter(packConfig, fileRepository.newObjectReader()));
+
+		doNothing().when(mockedPackWriter).select(any(), any());
+
+		try (FileOutputStream packOS = new FileOutputStream(
+				getPackFileToWrite(fileRepository, mockedPackWriter))) {
+			mockedPackWriter.writePack(NullProgressMonitor.INSTANCE,
+					NullProgressMonitor.INSTANCE, packOS);
+		}
+
+		long numberOfPackFiles = new GC(fileRepository)
+				.getStatistics().numberOfPackFiles;
+		int expectedSelectCalls =
+				// Objects contained in multiple packfiles * number of packfiles
+				2 * (int) numberOfPackFiles +
+				// Objects contained in single packfile
+						1;
+		verify(mockedPackWriter, times(expectedSelectCalls)).select(any(),
+				any());
+	}
+
+	@Test
+	public void testPartialPackFilesScanWhenDoingSearchForReuseTimeoutCheck()
+			throws Exception {
+		FileRepository fileRepository = setUpRepoWithMultiplePackfiles();
+		PackConfig packConfig = new PackConfig();
+		packConfig.setSearchForReuseTimeout(Duration.ofSeconds(-1));
+		PackWriter mockedPackWriter = Mockito.spy(
+				new PackWriter(packConfig, fileRepository.newObjectReader()));
+		mockedPackWriter.enableSearchForReuseTimeout();
+
+		doNothing().when(mockedPackWriter).select(any(), any());
+
+		try (FileOutputStream packOS = new FileOutputStream(
+				getPackFileToWrite(fileRepository, mockedPackWriter))) {
+			mockedPackWriter.writePack(NullProgressMonitor.INSTANCE,
+					NullProgressMonitor.INSTANCE, packOS);
+		}
+
+		int expectedSelectCalls = 3; // Objects in packfiles
+		verify(mockedPackWriter, times(expectedSelectCalls)).select(any(),
+				any());
+	}
+
+	/**
+	 * Creates objects and packfiles in the following order:
+	 * <ul>
+	 * <li>Creates 2 objects (C1 = commit, T1 = tree)
+	 * <li>Creates packfile P1 (containing C1, T1)
+	 * <li>Creates 1 object (C2 commit)
+	 * <li>Creates packfile P2 (containing C1, T1, C2)
+	 * <li>Create 1 object (C3 commit)
+	 * </ul>
+	 *
+	 * @throws Exception
+	 */
+	private FileRepository setUpRepoWithMultiplePackfiles() throws Exception {
+		FileRepository fileRepository = createWorkRepository();
+		try (Git git = new Git(fileRepository)) {
+			// Creates 2 objects (C1 = commit, T1 = tree)
+			git.commit().setMessage("First commit").call();
+			GC gc = new GC(fileRepository);
+			gc.setPackExpireAgeMillis(Long.MAX_VALUE);
+			gc.setExpireAgeMillis(Long.MAX_VALUE);
+			// Creates packfile P1 (containing C1, T1)
+			gc.gc();
+			// Creates 1 object (C2 commit)
+			git.commit().setMessage("Second commit").call();
+			// Creates packfile P2 (containing C1, T1, C2)
+			gc.gc();
+			// Create 1 object (C3 commit)
+			git.commit().setMessage("Third commit").call();
+		}
+		return fileRepository;
+	}
+
+	private PackFile getPackFileToWrite(FileRepository fileRepository,
+			PackWriter mockedPackWriter) throws IOException {
+		File packdir = fileRepository.getObjectDatabase().getPackDirectory();
+		PackFile packFile = new PackFile(packdir,
+				mockedPackWriter.computeName(), PackExt.PACK);
+
+		Set<ObjectId> all = new HashSet<>();
+		for (Ref r : fileRepository.getRefDatabase().getRefs()) {
+			all.add(r.getObjectId());
+		}
+
+		mockedPackWriter.preparePack(NullProgressMonitor.INSTANCE, all,
+				PackWriter.NONE);
+		return packFile;
+	}
+
 	private FileRepository setupRepoForShallowFetch() throws Exception {
 		FileRepository repo = createBareRepository();
 		// TestRepository will close the repo, but we need to return an open

org.eclipse.jgit.test/tst/org/eclipse/jgit/treewalk/filter/PathSuffixFilterTest.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2009, 2013 Google Inc. and others
+ * Copyright (C) 2009, 2021 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
@@ -41,10 +41,11 @@ public class PathSuffixFilterTest extends RepositoryTestCase {
 
 	@Test
 	public void testRecursiveFiltering() throws IOException {
-		ObjectId treeId = createTree("a.sth", "a.txt", "sub/b.sth", "sub/b.txt");
+		ObjectId treeId = createTree("a.sth", "a.txt", "sub/b.sth", "sub/b.txt",
+				"t.sth", "t.txt");
 
 		List<String> paths = getMatchingPaths(".txt", treeId, true);
-		List<String> expected = Arrays.asList("a.txt", "sub/b.txt");
+		List<String> expected = Arrays.asList("a.txt", "sub/b.txt", "t.txt");
 
 		assertEquals(expected, paths);
 	}
@@ -59,6 +60,17 @@ public class PathSuffixFilterTest extends RepositoryTestCase {
 		assertEquals(Arrays.asList("abc", "c"), getMatchingPaths("c", treeId));
 	}
 
+	@Test
+	public void testNegated() throws IOException {
+		ObjectId treeId = createTree("a.sth", "a.txt", "sub/b.sth",
+				"sub/b.txt", "t.sth", "t.txt");
+
+		List<String> paths = getMatchingPaths(".txt", treeId, true, true);
+		List<String> expected = Arrays.asList("a.sth", "sub/b.sth", "t.sth");
+
+		assertEquals(expected, paths);
+	}
+
 	private ObjectId createTree(String... paths) throws IOException {
 		final ObjectInserter odi = db.newObjectInserter();
 		final DirCache dc = db.readDirCache();
@@ -80,8 +92,18 @@ public class PathSuffixFilterTest extends RepositoryTestCase {
 
 	private List<String> getMatchingPaths(String suffixFilter,
 			final ObjectId treeId, boolean recursiveWalk) throws IOException {
+		return getMatchingPaths(suffixFilter, treeId, recursiveWalk, false);
+	}
+
+	private List<String> getMatchingPaths(String suffixFilter,
+			final ObjectId treeId, boolean recursiveWalk, boolean negated)
+			throws IOException {
 		try (TreeWalk tw = new TreeWalk(db)) {
-			tw.setFilter(PathSuffixFilter.create(suffixFilter));
+			TreeFilter filter = PathSuffixFilter.create(suffixFilter);
+			if (negated) {
+				filter = filter.negate();
+			}
+			tw.setFilter(filter);
 			tw.setRecursive(recursiveWalk);
 			tw.addTree(treeId);
 

org.eclipse.jgit/.settings/.api_filters

@@ -1,5 +1,13 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <component id="org.eclipse.jgit" version="2">
+    <resource path="src/org/eclipse/jgit/storage/pack/PackConfig.java" type="org.eclipse.jgit.storage.pack.PackConfig">
+        <filter id="336658481">
+            <message_arguments>
+                <message_argument value="org.eclipse.jgit.storage.pack.PackConfig"/>
+                <message_argument value="DEFAULT_SEARCH_FOR_REUSE_TIMEOUT"/>
+            </message_arguments>
+        </filter>
+    </resource>
     <resource path="src/org/eclipse/jgit/transport/SshConstants.java" type="org.eclipse.jgit.transport.SshConstants">
         <filter id="1142947843">
             <message_arguments>

org.eclipse.jgit/resources/org/eclipse/jgit/internal/JGitText.properties

@@ -442,6 +442,7 @@ logInconsistentFiletimeDiff={}: inconsistent duration from file timestamps on {}
 logLargerFiletimeDiff={}: inconsistent duration from file timestamps on {}, {}: diff = {} > {} (last good value). Aborting measurement.
 logSmallerFiletime={}: got smaller file timestamp on {}, {}: {} < {}. Aborting measurement at resolution {}.
 logXDGConfigHomeInvalid=Environment variable XDG_CONFIG_HOME contains an invalid path {}
+looseObjectHandleIsStale=loose-object {0} file handle is stale. retry {1} of {2}
 maxCountMustBeNonNegative=max count must be >= 0
 mergeConflictOnNonNoteEntries=Merge conflict on non-note entries: base = {0}, ours = {1}, theirs = {2}
 mergeConflictOnNotes=Merge conflict on note {0}. base = {1}, ours = {2}, theirs = {2}
@@ -632,6 +633,7 @@ s3ActionWriting=Writing
 searchForReachableBranches=Finding reachable branches
 saveFileStoreAttributesFailed=Saving measured FileStore attributes to user config failed
 searchForReuse=Finding sources
+searchForReuseTimeout=Search for reuse timed out after {0} seconds
 searchForSizes=Getting sizes
 secondsAgo={0} seconds ago
 selectingCommits=Selecting commits

org.eclipse.jgit/src/org/eclipse/jgit/errors/SearchForReuseTimeout.java

@@ -0,0 +1,42 @@
+/*
+ * Copyright (C) 2021, Fabio Ponciroli <ponch@gerritforge.com>
+ *
+ * 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.errors;
+
+import org.eclipse.jgit.internal.JGitText;
+
+import java.io.IOException;
+import java.text.MessageFormat;
+import java.time.Duration;
+
+/**
+ * Thrown when the search for reuse phase times out.
+ *
+ * @since 5.13
+ */
+public class SearchForReuseTimeout extends IOException {
+	private static final long serialVersionUID = 1L;
+
+	/**
+	 * Construct a search for reuse timeout error.
+	 *
+	 * @param timeout
+	 *            time exceeded during the search for reuse phase.
+	 */
+	public SearchForReuseTimeout(Duration timeout) {
+		super(MessageFormat.format(JGitText.get().searchForReuseTimeout,
+				Long.valueOf(timeout.getSeconds())));
+	}
+
+	@Override
+	public synchronized Throwable fillInStackTrace() {
+		return this;
+	}
+}

org.eclipse.jgit/src/org/eclipse/jgit/internal/JGitText.java

@@ -470,6 +470,7 @@ public class JGitText extends TranslationBundle {
 	/***/ public String logLargerFiletimeDiff;
 	/***/ public String logSmallerFiletime;
 	/***/ public String logXDGConfigHomeInvalid;
+	/***/ public String looseObjectHandleIsStale;
 	/***/ public String maxCountMustBeNonNegative;
 	/***/ public String mergeConflictOnNonNoteEntries;
 	/***/ public String mergeConflictOnNotes;
@@ -660,6 +661,7 @@ public class JGitText extends TranslationBundle {
 	/***/ public String saveFileStoreAttributesFailed;
 	/***/ public String searchForReachableBranches;
 	/***/ public String searchForReuse;
+	/***/ public String searchForReuseTimeout;
 	/***/ public String searchForSizes;
 	/***/ public String secondsAgo;
 	/***/ public String selectingCommits;

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java

@@ -344,10 +344,10 @@ public class GC {
 					&& repo.getFS()
 							.lastModifiedInstant(oldPack.getPackFile())
 							.toEpochMilli() < packExpireDate) {
-				oldPack.close();
 				if (shouldLoosen) {
 					loosen(inserter, reader, oldPack, ids);
 				}
+				oldPack.close();
 				prunePack(oldPack.getPackFile());
 			}
 		}

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/LooseObjects.java

@@ -17,8 +17,10 @@ import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.NoSuchFileException;
 import java.nio.file.StandardCopyOption;
+import java.text.MessageFormat;
 import java.util.Set;
 
+import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.internal.storage.file.FileObjectDatabase.InsertLooseObjectResult;
 import org.eclipse.jgit.lib.AbbreviatedObjectId;
 import org.eclipse.jgit.lib.AnyObjectId;
@@ -40,6 +42,12 @@ class LooseObjects {
 	private static final Logger LOG = LoggerFactory
 			.getLogger(LooseObjects.class);
 
+	/**
+	 * Maximum number of attempts to read a loose object for which a stale file
+	 * handle exception is thrown
+	 */
+	private final static int MAX_LOOSE_OBJECT_STALE_READ_ATTEMPTS = 5;
+
 	private final File directory;
 
 	private final UnpackedObjectCache unpackedObjectCache;
@@ -69,7 +77,7 @@ class LooseObjects {
 	}
 
 	void close() {
-		unpackedObjectCache.clear();
+		unpackedObjectCache().clear();
 	}
 
 	/** {@inheritDoc} */
@@ -79,7 +87,7 @@ class LooseObjects {
 	}
 
 	boolean hasCached(AnyObjectId id) {
-		return unpackedObjectCache.isUnpacked(id);
+		return unpackedObjectCache().isUnpacked(id);
 	}
 
 	/**
@@ -133,29 +141,77 @@ class LooseObjects {
 	}
 
 	ObjectLoader open(WindowCursor curs, AnyObjectId id) throws IOException {
-		File path = fileFor(id);
+		int readAttempts = 0;
+		while (readAttempts < MAX_LOOSE_OBJECT_STALE_READ_ATTEMPTS) {
+			readAttempts++;
+			File path = fileFor(id);
+			try {
+				return getObjectLoader(curs, path, id);
+			} catch (FileNotFoundException noFile) {
+				if (path.exists()) {
+					throw noFile;
+				}
+				break;
+			} catch (IOException e) {
+				if (!FileUtils.isStaleFileHandleInCausalChain(e)) {
+					throw e;
+				}
+				if (LOG.isDebugEnabled()) {
+					LOG.debug(MessageFormat.format(
+							JGitText.get().looseObjectHandleIsStale, id.name(),
+							Integer.valueOf(readAttempts), Integer.valueOf(
+									MAX_LOOSE_OBJECT_STALE_READ_ATTEMPTS)));
+				}
+			}
+		}
+		unpackedObjectCache().remove(id);
+		return null;
+	}
+
+	/**
+	 * Provides a loader for an objectId
+	 *
+	 * @param curs
+	 *            cursor on the database
+	 * @param path
+	 *            the path of the loose object
+	 * @param id
+	 *            the object id
+	 * @return a loader for the loose file object
+	 * @throws IOException
+	 *             when file does not exist or it could not be opened
+	 */
+	ObjectLoader getObjectLoader(WindowCursor curs, File path, AnyObjectId id)
+			throws IOException {
 		try (FileInputStream in = new FileInputStream(path)) {
-			unpackedObjectCache.add(id);
+			unpackedObjectCache().add(id);
 			return UnpackedObject.open(in, path, id, curs);
-		} catch (FileNotFoundException noFile) {
-			if (path.exists()) {
-				throw noFile;
-			}
-			unpackedObjectCache.remove(id);
-			return null;
 		}
 	}
 
+	/**
+	 * <p>
+	 * Getter for the field <code>unpackedObjectCache</code>.
+	 * </p>
+	 * This accessor is particularly useful to allow mocking of this class for
+	 * testing purposes.
+	 *
+	 * @return the cache of the objects currently unpacked.
+	 */
+	UnpackedObjectCache unpackedObjectCache() {
+		return unpackedObjectCache;
+	}
+
 	long getSize(WindowCursor curs, AnyObjectId id) throws IOException {
 		File f = fileFor(id);
 		try (FileInputStream in = new FileInputStream(f)) {
-			unpackedObjectCache.add(id);
+			unpackedObjectCache().add(id);
 			return UnpackedObject.getSize(in, id, curs);
 		} catch (FileNotFoundException noFile) {
 			if (f.exists()) {
 				throw noFile;
 			}
-			unpackedObjectCache.remove(id);
+			unpackedObjectCache().remove(id);
 			return -1;
 		}
 	}
@@ -207,7 +263,7 @@ class LooseObjects {
 		Files.move(FileUtils.toPath(tmp), FileUtils.toPath(dst),
 				StandardCopyOption.ATOMIC_MOVE);
 		dst.setReadOnly();
-		unpackedObjectCache.add(id);
+		unpackedObjectCache().add(id);
 		return InsertLooseObjectResult.INSERTED;
 	}
 

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/PackDirectory.java

@@ -33,6 +33,7 @@ import org.eclipse.jgit.annotations.Nullable;
 import org.eclipse.jgit.errors.CorruptObjectException;
 import org.eclipse.jgit.errors.PackInvalidException;
 import org.eclipse.jgit.errors.PackMismatchException;
+import org.eclipse.jgit.errors.SearchForReuseTimeout;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.internal.storage.pack.ObjectToPack;
 import org.eclipse.jgit.internal.storage.pack.PackExt;
@@ -264,7 +265,10 @@ class PackDirectory {
 					p.resetTransientErrorCount();
 					if (rep != null) {
 						packer.select(otp, rep);
+						packer.checkSearchForReuseTimeout();
 					}
+				} catch (SearchForReuseTimeout e) {
+					break SEARCH;
 				} catch (PackMismatchException e) {
 					// Pack was modified; refresh the entire pack list.
 					//

org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/pack/PackWriter.java

@@ -25,6 +25,7 @@ import java.io.OutputStream;
 import java.lang.ref.WeakReference;
 import java.security.MessageDigest;
 import java.text.MessageFormat;
+import java.time.Duration;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -54,6 +55,7 @@ import org.eclipse.jgit.errors.CorruptObjectException;
 import org.eclipse.jgit.errors.IncorrectObjectTypeException;
 import org.eclipse.jgit.errors.LargeObjectException;
 import org.eclipse.jgit.errors.MissingObjectException;
+import org.eclipse.jgit.errors.SearchForReuseTimeout;
 import org.eclipse.jgit.errors.StoredObjectRepresentationNotAvailableException;
 import org.eclipse.jgit.internal.JGitText;
 import org.eclipse.jgit.internal.storage.file.PackBitmapIndexBuilder;
@@ -262,6 +264,12 @@ public class PackWriter implements AutoCloseable {
 
 	private boolean indexDisabled;
 
+	private boolean checkSearchForReuseTimeout = false;
+
+	private final Duration searchForReuseTimeout;
+
+	private long searchForReuseStartTimeEpoc;
+
 	private int depth;
 
 	private Collection<? extends ObjectId> unshallowObjects;
@@ -356,6 +364,7 @@ public class PackWriter implements AutoCloseable {
 
 		deltaBaseAsOffset = config.isDeltaBaseAsOffset();
 		reuseDeltas = config.isReuseDeltas();
+		searchForReuseTimeout = config.getSearchForReuseTimeout();
 		reuseValidate = true; // be paranoid by default
 		stats = statsAccumulator != null ? statsAccumulator
 				: new PackStatistics.Accumulator();
@@ -404,6 +413,24 @@ public class PackWriter implements AutoCloseable {
 		return deltaBaseAsOffset;
 	}
 
+	/**
+	 * Check whether the search for reuse phase is taking too long. This could
+	 * be the case when the number of objects and pack files is high and the
+	 * system is under pressure. If that's the case and
+	 * checkSearchForReuseTimeout is true abort the search.
+	 *
+	 * @throws SearchForReuseTimeout
+	 *             if the search for reuse is taking too long.
+	 */
+	public void checkSearchForReuseTimeout() throws SearchForReuseTimeout {
+		if (checkSearchForReuseTimeout
+				&& Duration.ofMillis(System.currentTimeMillis()
+						- searchForReuseStartTimeEpoc)
+				.compareTo(searchForReuseTimeout) > 0) {
+			throw new SearchForReuseTimeout(searchForReuseTimeout);
+		}
+	}
+
 	/**
 	 * Set writer delta base format. Delta base can be written as an offset in a
 	 * pack file (new approach reducing file size) or as an object id (legacy
@@ -419,6 +446,22 @@ public class PackWriter implements AutoCloseable {
 		this.deltaBaseAsOffset = deltaBaseAsOffset;
 	}
 
+	/**
+	 * Set the writer to check for long search for reuse, exceeding the timeout.
+	 * Selecting an object representation can be an expensive operation. It is
+	 * possible to set a max search for reuse time (see
+	 * PackConfig#CONFIG_KEY_SEARCH_FOR_REUSE_TIMEOUT for more details).
+	 *
+	 * However some operations, i.e.: GC, need to find the best candidate
+	 * regardless how much time the operation will need to finish.
+	 *
+	 * This method enables the search for reuse timeout check, otherwise
+	 * disabled.
+	 */
+	public void enableSearchForReuseTimeout() {
+		this.checkSearchForReuseTimeout = true;
+	}
+
 	/**
 	 * Check if the writer will reuse commits that are already stored as deltas.
 	 *
@@ -1306,6 +1349,7 @@ public class PackWriter implements AutoCloseable {
 		cnt += objectsLists[OBJ_TAG].size();
 
 		long start = System.currentTimeMillis();
+		searchForReuseStartTimeEpoc = start;
 		beginPhase(PackingPhase.FINDING_SOURCES, monitor, cnt);
 		if (cnt <= 4096) {
 			// For small object counts, do everything as one list.

org.eclipse.jgit/src/org/eclipse/jgit/lib/ConfigConstants.java

@@ -736,4 +736,12 @@ public final class ConfigConstants {
 	 * @since 5.11
 	 */
 	public static final String CONFIG_KEY_DEFAULT_BRANCH = "defaultbranch";
+
+	/**
+	 * The "pack.searchForReuseTimeout" key
+	 *
+	 * @since 5.13
+	 */
+	public static final String CONFIG_KEY_SEARCH_FOR_REUSE_TIMEOUT = "searchforreusetimeout";
+
 }

org.eclipse.jgit/src/org/eclipse/jgit/storage/pack/PackConfig.java

@@ -29,6 +29,7 @@ import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_INDEXVERSION;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_MIN_SIZE_PREVENT_RACYPACK;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_REUSE_DELTAS;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_REUSE_OBJECTS;
+import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_SEARCH_FOR_REUSE_TIMEOUT;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_SINGLE_PACK;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_THREADS;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_WAIT_PREVENT_RACYPACK;
@@ -36,7 +37,9 @@ import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_WINDOW;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_KEY_WINDOW_MEMORY;
 import static org.eclipse.jgit.lib.ConfigConstants.CONFIG_PACK_SECTION;
 
+import java.time.Duration;
 import java.util.concurrent.Executor;
+import java.util.concurrent.TimeUnit;
 import java.util.zip.Deflater;
 
 import org.eclipse.jgit.internal.storage.file.PackIndexWriter;
@@ -222,6 +225,16 @@ public class PackConfig {
 	 */
 	public static final int DEFAULT_BITMAP_INACTIVE_BRANCH_AGE_IN_DAYS = 90;
 
+	/**
+	 * Default max time to spend during the search for reuse phase. This
+	 * optimization is disabled by default: {@value}
+	 *
+	 * @see #setSearchForReuseTimeout(Duration)
+	 * @since 5.13
+	 */
+	public static final Duration DEFAULT_SEARCH_FOR_REUSE_TIMEOUT = Duration
+			.ofSeconds(Integer.MAX_VALUE);
+
 	private int compressionLevel = Deflater.DEFAULT_COMPRESSION;
 
 	private boolean reuseDeltas = DEFAULT_REUSE_DELTAS;
@@ -272,6 +285,8 @@ public class PackConfig {
 
 	private int bitmapInactiveBranchAgeInDays = DEFAULT_BITMAP_INACTIVE_BRANCH_AGE_IN_DAYS;
 
+	private Duration searchForReuseTimeout = DEFAULT_SEARCH_FOR_REUSE_TIMEOUT;
+
 	private boolean cutDeltaChains;
 
 	private boolean singlePack;
@@ -342,6 +357,7 @@ public class PackConfig {
 		this.bitmapInactiveBranchAgeInDays = cfg.bitmapInactiveBranchAgeInDays;
 		this.cutDeltaChains = cfg.cutDeltaChains;
 		this.singlePack = cfg.singlePack;
+		this.searchForReuseTimeout = cfg.searchForReuseTimeout;
 	}
 
 	/**
@@ -1103,6 +1119,18 @@ public class PackConfig {
 		return bitmapInactiveBranchAgeInDays;
 	}
 
+	/**
+	 * Get the max time to spend during the search for reuse phase.
+	 *
+	 * Default setting: {@value #DEFAULT_SEARCH_FOR_REUSE_TIMEOUT}
+	 *
+	 * @return the maximum time to spend during the search for reuse phase.
+	 * @since 5.13
+	 */
+	public Duration getSearchForReuseTimeout() {
+		return searchForReuseTimeout;
+	}
+
 	/**
 	 * Set the age in days that marks a branch as "inactive".
 	 *
@@ -1116,6 +1144,19 @@ public class PackConfig {
 		bitmapInactiveBranchAgeInDays = ageInDays;
 	}
 
+	/**
+	 * Set the max time to spend during the search for reuse phase.
+	 *
+	 * @param timeout
+	 *            max time allowed during the search for reuse phase
+	 *
+	 *            Default setting: {@value #DEFAULT_SEARCH_FOR_REUSE_TIMEOUT}
+	 * @since 5.13
+	 */
+	public void setSearchForReuseTimeout(Duration timeout) {
+		searchForReuseTimeout = timeout;
+	}
+
 	/**
 	 * Update properties by setting fields from the configuration.
 	 *
@@ -1179,6 +1220,10 @@ public class PackConfig {
 		setBitmapInactiveBranchAgeInDays(rc.getInt(CONFIG_PACK_SECTION,
 				CONFIG_KEY_BITMAP_INACTIVE_BRANCH_AGE_INDAYS,
 				getBitmapInactiveBranchAgeInDays()));
+		setSearchForReuseTimeout(Duration.ofSeconds(rc.getTimeUnit(
+				CONFIG_PACK_SECTION, null,
+				CONFIG_KEY_SEARCH_FOR_REUSE_TIMEOUT,
+				getSearchForReuseTimeout().getSeconds(), TimeUnit.SECONDS)));
 		setWaitPreventRacyPack(rc.getBoolean(CONFIG_PACK_SECTION,
 				CONFIG_KEY_WAIT_PREVENT_RACYPACK, isWaitPreventRacyPack()));
 		setMinSizePreventRacyPack(rc.getLong(CONFIG_PACK_SECTION,
@@ -1216,6 +1261,8 @@ public class PackConfig {
 				.append(getBitmapExcessiveBranchCount());
 		b.append(", bitmapInactiveBranchAge=") //$NON-NLS-1$
 				.append(getBitmapInactiveBranchAgeInDays());
+		b.append(", searchForReuseTimeout") //$NON-NLS-1$
+				.append(getSearchForReuseTimeout());
 		b.append(", singlePack=").append(getSinglePack()); //$NON-NLS-1$
 		return b.toString();
 	}

org.eclipse.jgit/src/org/eclipse/jgit/transport/UploadPack.java

@@ -2359,6 +2359,7 @@ public class UploadPack {
 							GitProtocolConstants.SECTION_PACKFILE + '\n');
 				}
 			}
+			pw.enableSearchForReuseTimeout();
 			pw.writePack(pm, NullProgressMonitor.INSTANCE, packOut);
 
 			if (msgOut != NullOutputStream.INSTANCE) {

org.eclipse.jgit/src/org/eclipse/jgit/treewalk/filter/PathSuffixFilter.java

@@ -1,5 +1,5 @@
 /*
- * Copyright (C) 2009, Google Inc. and others
+ * Copyright (C) 2009, 2021 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
@@ -73,6 +73,15 @@ public class PathSuffixFilter extends TreeFilter {
 
 	}
 
+	@Override
+	public int matchFilter(TreeWalk walker) throws MissingObjectException,
+			IncorrectObjectTypeException, IOException {
+		if (walker.isSubtree()) {
+			return -1;
+		}
+		return super.matchFilter(walker);
+	}
+
 	/** {@inheritDoc} */
 	@Override
 	public boolean shouldBeRecursive() {

pom.xml

@@ -151,7 +151,7 @@
     <maven.compiler.target>1.8</maven.compiler.target>
     <bundle-manifest>${project.build.directory}/META-INF/MANIFEST.MF</bundle-manifest>
 
-    <jgit-last-release-version>5.10.0.202012080955-r</jgit-last-release-version>
+    <jgit-last-release-version>5.12.0.202106070339-r</jgit-last-release-version>
     <apache-sshd-version>2.6.0</apache-sshd-version>
     <jsch-version>0.1.55</jsch-version>
     <jzlib-version>1.1.1</jzlib-version>
@@ -162,7 +162,7 @@
     <commons-compress-version>1.19</commons-compress-version>
     <osgi-core-version>4.3.1</osgi-core-version>
     <servlet-api-version>3.1.0</servlet-api-version>
-    <jetty-version>9.4.40.v20210413</jetty-version>
+    <jetty-version>9.4.42.v20210604</jetty-version>
     <japicmp-version>0.15.3</japicmp-version>
     <httpclient-version>4.5.13</httpclient-version>
     <httpcore-version>4.4.14</httpcore-version>
@@ -172,9 +172,9 @@
     <tycho-extras-version>1.7.0</tycho-extras-version>
     <gson-version>2.8.6</gson-version>
     <bouncycastle-version>1.65</bouncycastle-version>
-    <spotbugs-maven-plugin-version>4.2.2</spotbugs-maven-plugin-version>
-    <maven-project-info-reports-plugin-version>3.1.1</maven-project-info-reports-plugin-version>
-    <maven-jxr-plugin-version>3.0.0</maven-jxr-plugin-version>
+    <spotbugs-maven-plugin-version>4.2.3</spotbugs-maven-plugin-version>
+    <maven-project-info-reports-plugin-version>3.1.2</maven-project-info-reports-plugin-version>
+    <maven-jxr-plugin-version>3.1.1</maven-jxr-plugin-version>
     <maven-surefire-plugin-version>3.0.0-M5</maven-surefire-plugin-version>
     <maven-surefire-report-plugin-version>${maven-surefire-plugin-version}</maven-surefire-report-plugin-version>
     <maven-compiler-plugin-version>3.8.1</maven-compiler-plugin-version>
@@ -247,7 +247,7 @@
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>
           <artifactId>maven-dependency-plugin</artifactId>
-          <version>3.1.2</version>
+          <version>3.2.0</version>
         </plugin>
 
         <plugin>
@@ -337,7 +337,7 @@
         <plugin>
           <groupId>org.jacoco</groupId>
           <artifactId>jacoco-maven-plugin</artifactId>
-          <version>0.8.6</version>
+          <version>0.8.7</version>
         </plugin>
         <plugin>
           <groupId>org.apache.maven.plugins</groupId>