Merge remote-tracking branch 'upstream/main' into fixUrlLink

* upstream/main:
  Bump guava from 31.0.1-jre to 31.1-jre (#8543)
  Bump org.beryx.jlink from 2.24.4 to 2.25.0 (#8548)
  Bump postgresql from 42.3.2 to 42.3.3 (#8546)
  Bump richtextfx from 0.10.7 to 0.10.9 (#8547)
  Bump archunit-junit5-engine from 0.22.0 to 0.23.1 (#8545)
  Bump actions/checkout from 2 to 3 (#8542)
  Squashed 'buildres/csl/csl-styles/' changes from eb97405..8f69d4e
  Bump classgraph from 4.8.139 to 4.8.141 (#8535)
  Bump archunit-junit5-api from 0.22.0 to 0.23.1 (#8536)
  issue(8448): allow URL with + sign in entry tabs (#8508)
  Add initial telemetry development documentation (#8530)
  Add existing "Remote storage" to index
  Disable telemetry client due to incompatibilites with jakarta (#8526)
  Update to jakarta xml everywhere and update PDFbox (#8521)
  Bump flexmark-ext-gfm-tasklist from 0.62.2 to 0.64.0 (#8515)
  Bump xmlunit-core from 2.8.4 to 2.9.0 (#8519)
  Bump org.openjfx.javafxplugin from 0.0.11 to 0.0.12 (#8518)
  Bump mockito-core from 4.3.0 to 4.3.1 (#8520)

.github/workflows/check-links.yaml

@@ -13,7 +13,7 @@ jobs:
   markdown-link-check:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: gaurav-nelson/github-action-markdown-link-check@v1
         with:
           use-quiet-mode: 'yes'

.github/workflows/deployment.yml

@@ -51,7 +51,7 @@ jobs:
     name: Create installer and portable version for ${{ matrix.displayName }}
     steps:
       - name: Fetch all history for all tags and branches
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - name: Install GitVersion
@@ -152,7 +152,7 @@ jobs:
         env:
           BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Fetch all history for all tags and branches
         run: git fetch --prune --unshallow
       - name: Install GitVersion

.github/workflows/gource.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: 'Checkout'
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - name: Determine dates

.github/workflows/refresh-csl-subtrees.yml

@@ -13,7 +13,7 @@ jobs:
     if: github.repository == 'JabRef/jabref'
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           ref: main
           fetch-depth: 0

.github/workflows/refresh-journal-lists.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Fetch all history for all tags and branches
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           ref: main
           persist-credentials: false

.github/workflows/snap.yml

@@ -30,7 +30,7 @@ jobs:
         env:
           SNAPCRAFT_LOGIN_FILE: ${{ secrets.SNAPCRAFT_LOGIN_FILE }}
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       # The image relies on https://builds.jabref.org/master/JabRef-5.0-portable_linux.tar.gz^
       # See snap/snapcraft.yml for details
       - name: Run snapcraft build

.github/workflows/tests-fetchers.yml

@@ -37,7 +37,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:

.github/workflows/tests.yml

@@ -26,7 +26,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
@@ -50,7 +50,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
@@ -82,7 +82,7 @@ jobs:
         options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
@@ -116,7 +116,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
@@ -154,7 +154,7 @@ jobs:
         env:
           SNAPCRAFT_LOGIN_FILE: ${{ secrets.CODECOV_TOKEN }}
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
@@ -174,5 +174,5 @@ jobs:
     name: "Validate Gradle Wrapper"
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: gradle/wrapper-validation-action@v1

.github/workflows/update-gradle-wrapper.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Update Gradle Wrapper
         uses: gradle-update/update-gradle-wrapper-action@v1

CHANGELOG.md

@@ -25,6 +25,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where an exception could occur when saving the preferences [#7614](https://github.com/JabRef/jabref/issues/7614)
 - We fixed an issue where "Copy DOI url" in the right-click menu of the Entry List would just copy the DOI and not the DOI url. [#8389](https://github.com/JabRef/jabref/issues/8389)
 - We fixed an issue where opening the console from the drop-down menu would cause an exception. [#8466](https://github.com/JabRef/jabref/issues/8466)
+- We fixed an issue where pasting a URL was replacing + signs by spaces making the URL unreachable. [#8448](https://github.com/JabRef/jabref/issues/8448)
 
 ### Removed
 

build.gradle

@@ -16,9 +16,9 @@ plugins {
 
     id 'org.javamodularity.moduleplugin' version '1.8.10'
 
-    id 'org.openjfx.javafxplugin' version '0.0.11'
+    id 'org.openjfx.javafxplugin' version '0.0.12'
 
-    id 'org.beryx.jlink' version '2.24.4'
+    id 'org.beryx.jlink' version '2.25.0'
 
     // nicer test outputs during running and completion
     // Homepage: https://github.com/radarsh/gradle-test-logger-plugin
@@ -114,9 +114,9 @@ dependencies {
     // Include all jar-files in the 'lib' folder as dependencies
     implementation fileTree(dir: 'lib', includes: ['*.jar'])
 
-    implementation 'org.apache.pdfbox:pdfbox:2.0.25'
-    implementation 'org.apache.pdfbox:fontbox:2.0.25'
-    implementation 'org.apache.pdfbox:xmpbox:2.0.25'
+    implementation 'org.apache.pdfbox:pdfbox:3.0.0-RC1'
+    implementation 'org.apache.pdfbox:fontbox:3.0.0-RC1'
+    implementation 'org.apache.pdfbox:xmpbox:3.0.0-RC1'
 
     implementation group: 'org.apache.commons', name: 'commons-csv', version: '1.9.0'
     implementation 'com.h2database:h2-mvstore:2.1.210'
@@ -147,14 +147,14 @@ dependencies {
 
     implementation group: 'org.mariadb.jdbc', name: 'mariadb-java-client', version: '2.7.5'
 
-    implementation 'org.postgresql:postgresql:42.3.2'
+    implementation 'org.postgresql:postgresql:42.3.3'
 
     implementation ('com.oracle.ojdbc:ojdbc10:19.3.0.0') {
         // causing module issues
         exclude module: 'oraclepki'
     }
 
-    implementation ('com.google.guava:guava:31.0.1-jre') {
+    implementation ('com.google.guava:guava:31.1-jre') {
         // TODO: Remove this as soon as https://github.com/google/guava/issues/2960 is fixed
         exclude module: "jsr305"
     }
@@ -168,7 +168,7 @@ dependencies {
     implementation 'de.saxsys:mvvmfx:1.8.0'
     implementation 'com.tobiasdiez:easybind:2.2'
     implementation 'org.fxmisc.flowless:flowless:0.6.8'
-    implementation 'org.fxmisc.richtext:richtextfx:0.10.7'
+    implementation 'org.fxmisc.richtext:richtextfx:0.10.9'
     implementation group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
     implementation 'com.jfoenix:jfoenix:9.0.10'
     implementation 'org.controlsfx:controlsfx:11.1.1'
@@ -183,9 +183,9 @@ dependencies {
 
     implementation 'de.undercouch:citeproc-java:3.0.0-alpha.3'
 
-    implementation group: 'jakarta.activation', name: 'jakarta.activation-api', version: '1.2.1'
-    implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '2.3.2'
-    implementation group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '2.3.2'
+    // jakarta.activation is already depdency of glassfish
+    implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '3.0.1'
+    implementation group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '3.0.2'
 
     implementation ('com.github.tomtung:latex2unicode_2.12:0.2.6') {
         exclude module: 'fastparse_2.12'
@@ -198,27 +198,29 @@ dependencies {
 
     implementation 'com.vladsch.flexmark:flexmark:0.62.2'
     implementation 'com.vladsch.flexmark:flexmark-ext-gfm-strikethrough:0.64.0'
-    implementation 'com.vladsch.flexmark:flexmark-ext-gfm-tasklist:0.62.2'
+    implementation 'com.vladsch.flexmark:flexmark-ext-gfm-tasklist:0.64.0'
 
     implementation group: 'net.harawata', name: 'appdirs', version: '1.2.1'
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.139'
+    testImplementation 'io.github.classgraph:classgraph:4.8.141'
     testImplementation 'org.junit.jupiter:junit-jupiter:5.8.2'
     testImplementation 'org.junit.platform:junit-platform-launcher:1.8.2'
 
     testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
-    testImplementation 'org.mockito:mockito-core:4.3.0'
-    testImplementation 'org.xmlunit:xmlunit-core:2.8.4'
+    testImplementation 'org.mockito:mockito-core:4.3.1'
+    testImplementation 'org.xmlunit:xmlunit-core:2.9.0'
     testImplementation 'org.xmlunit:xmlunit-matchers:2.9.0'
-    testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.22.0'
-    testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.22.0'
+    testRuntimeOnly 'com.tngtech.archunit:archunit-junit5-engine:0.23.1'
+    testImplementation 'com.tngtech.archunit:archunit-junit5-api:0.23.1'
     testImplementation "org.testfx:testfx-core:4.0.17-alpha-SNAPSHOT"
     testImplementation "org.testfx:testfx-junit5:4.0.17-alpha-SNAPSHOT"
     testImplementation "org.hamcrest:hamcrest-library:2.2"
 
     checkstyle 'com.puppycrawl.tools:checkstyle:9.3'
-    xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '2.3.3'
+    // xjc needs the runtime as well for the ant task, otherwise it fails
+    xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '3.0.2'
+    xjc group: 'org.glassfish.jaxb', name: 'jaxb-runtime', version: '3.0.2'
 }
 
 clean {
@@ -555,8 +557,6 @@ jlink {
         requires 'jdk.security.jgss'
         requires 'jdk.xml.dom'
         requires 'com.google.gson'
-        requires 'com.sun.xml.fastinfoset'
-        requires 'com.sun.xml.txw2'
         requires 'org.slf4j'
         uses 'org.controlsfx.glyphfont.GlyphFont'
         uses 'com.airhacks.afterburner.views.ResourceLocator'
@@ -567,7 +567,6 @@ jlink {
         uses 'org.mariadb.jdbc.LocalInfileInterceptor'
         uses 'org.eclipse.jgit.transport.SshSessionFactory'
         uses 'org.eclipse.jgit.lib.GpgSigner'
-        uses 'javax.xml.bind.JAXBContextFactory'
         provides 'org.apache.lucene.codecs.DocValuesFormat' with 'org.apache.lucene.codecs.lucene80.Lucene80DocValuesFormat'
         provides 'org.controlsfx.glyphfont.GlyphFont' with 'org.controlsfx.glyphfont.FontAwesome'
         provides 'org.mariadb.jdbc.tls.TlsSocketPlugin' with 'org.mariadb.jdbc.internal.protocol.tls.DefaultTlsSocketPlugin'

buildres/csl/csl-styles/american-journal-of-archaeology.csl

@@ -15,7 +15,7 @@
     <issn>0002-9114</issn>
     <eissn>1939-828X</eissn>
     <summary>The American Journal of Archaeology style</summary>
-    <updated>2021-11-12T14:22:00+00:00</updated>
+    <updated>2022-02-27T11:00:00+00:00</updated>
     <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
   </info>
   <locale>
@@ -262,7 +262,7 @@
         <text macro="container-prefix" suffix=" "/>
       </if>
     </choose>
-    <text variable="container-title" font-style="italic"/>
+    <text variable="container-title" text-case="title" font-style="italic"/>
   </macro>
   <macro name="publisher">
     <group>