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

* upstream/main: (110 commits)
  Extract PushTo names into model (#8005)
  Refactor processCitation in GrobidService to match processPdf (#8003)
  Improved progress indication for fulltext-index operations (#7981)
  Reordered Pdf-Importer priorities (#8001)
  Implement more pdf importers (#7947)
  Adding icon picker for group dialog issue#6142 (#7776)
  Fix possible NPE in exporter with empty charset (#7979)
  Fix icon color (#7994)
  Bump slf4j-api from 2.0.0-alpha2 to 2.0.0-alpha4 (#7991)
  Bump classgraph from 4.8.112 to 4.8.114 (#7990)
  Bump mariadb-java-client from 2.7.3 to 2.7.4 (#7992)
  Bump jsoup from 1.14.1 to 1.14.2 (#7993)
  New yaml issue template (#7983)
  [Bot] Update CSL styles (#7985)
  Reordered items in main table right-click menu (#7952)
  Fulltext Index: Only index local pdf files (#7980)
  Bump WyriHaximus/github-action-wait-for-status from 1.3 to 1.4 (#7973)
  Bump byte-buddy-parent from 1.11.9 to 1.11.12 (#7974)
  Bump classgraph from 4.8.110 to 4.8.112 (#7975)
  Bump checkstyle from 8.45 to 8.45.1 (#7978)
  ...

# Conflicts:
#	src/main/java/module-info.java

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,79 @@
+name: "Bug report"
+description: Create a report to help us improve
+body:
+  - type: markdown
+    attributes:
+      value:
+        "Please use the GitHub issue tracker only for bug reports.
+        Feature requests, questions and general feedback is now handled at http://discourse.jabref.org.
+        Please make sure you looked into our [list of existing issues](https://github.com/jabref/JabRef/issues) before creating a new issue to avoid duplicates!"
+
+  - type: dropdown
+    attributes:
+      label: JabRef version
+      options:
+        - "5.3 (latest release)"
+        - "3.8.2"
+        - Latest development branch build (please note build date below)
+        - Other (please describe below)
+      description: The version as shown in the about dialog.
+    validations:
+      required: true
+
+  - type: dropdown
+    attributes:
+      label: Operating system
+      multiple: false
+      options:
+        - Windows
+        - GNU / Linux
+        - mac OS
+        - Other (please describe below)
+    validations:
+      required: true
+
+  - type: input
+    attributes:
+      label: Details on version and operating system
+      description: OS Version, distribution, desktop environment, older JabRef version etc.
+      placeholder: Ubuntu 21.04 with Plasma 5.22 / Windows 10 21H1 / Mac OS 10.14
+    validations:
+      required: false
+
+  - type: checkboxes
+    attributes:
+      label: Checked with the latest development build
+      description: |
+        Please always test if the bug is still reproducible in the latest development version. We are constantly improving JabRef and some bugs may already be fixed. If you already use a development version, ensure that you use the latest one.
+        You can download the latest development build at: https://builds.jabref.org/main/ . **Please make a backup of your library before you try out this version.**
+      options:
+        - label: I made a backup of my libraries before testing the latest development version.
+          required: true
+        - label: I have tested the latest development version and the problem persists
+          required: true
+
+  - type: textarea
+    attributes:
+      label: Steps to reproduce the behaviour
+      description: A clear and concise description of what the bug is and how to make it occur.
+      value: |
+        1. ...
+        2. ...
+        3. ...
+    validations:
+      required: true
+
+  - type: textarea
+    attributes:
+      label: Appendix
+      description: "If applicable: An excerpt of the bibliography file, a screenshot, an excerpt of log (available in the error console) etc."
+      value: |
+        ...
+        <details>
+        <summary>Log File</summary>
+        ```
+        Paste an excerpt of your log file here
+        ```
+        </details>
+    validations:
+      required: false

.github/workflows/automerge.yml

@@ -9,7 +9,7 @@ jobs:
     steps:
       - name: 'Wait for status checks'
         id: waitforstatuschecks
-        uses: "WyriHaximus/github-action-wait-for-status@v1.3"
+        uses: "WyriHaximus/github-action-wait-for-status@v1.4"
         with:
           ignoreActions: Automerge Dependabot,Code coverage,Create snapcraft image,Deploy binaries on builds.jabref.org,codecov/project,markdown-link-check
           checkInterval: 13

.github/workflows/check-outdated-dependencies.yml

@@ -14,7 +14,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
-          java-version: 14
+          java-version: 16
           distribution: 'adopt'
       - name: Look for outdated dependencies
         run: ./gradlew -q checkOutdatedDependencies

.github/workflows/deployment.yml

@@ -10,6 +10,8 @@ on:
       - 'docs/**'
       - 'src/test/**'
       - 'README.md'
+    tags:
+       - '*'
   pull_request:
     paths-ignore:
       - 'docs/**'
@@ -43,20 +45,20 @@ jobs:
     name: Create installer and portable version for ${{ matrix.displayName }}
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/[email protected].0
+        uses: styfle/[email protected].1
         with:
           access_token: ${{ github.token }}
       - name: Fetch all history for all tags and branches
         uses: actions/checkout@v2
         with:
           fetch-depth: 0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].9
+        uses: gittools/actions/gitversion/[email protected].10
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].9
+        uses: gittools/actions/gitversion/[email protected].10
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
@@ -103,7 +105,7 @@ jobs:
           jpackage --type pkg --dest build/distribution --name JabRef --mac-package-identifier JabRef --app-version "${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}" --app-image build/distribution/JabRef.app --verbose --type pkg --vendor JabRef --app-version "${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}" --file-associations buildres/mac/bibtexAssociations.properties --resource-dir buildres/mac
           productsign --sign "Developer ID Installer: JabRef e.V. (6792V39SK3)" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.pkg" "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg"
       - name: Notarize dmg and pkg installer
-        if: matrix.os == 'macos-latest' && github.ref == 'refs/heads/main'
+        if: matrix.os == 'macos-latest' && startsWith(github.ref, 'refs/tags/') 
         shell: bash
         run: |
           REQUEST_UUID_DMG=$(xcrun altool --verbose --notarize-app --primary-bundle-id "org.jabref" --username ${{ secrets.OSX_NOTARIZATION_APP_USERNAME }} --password ${{ secrets.OSX_NOTARIZATION_APP_PWD }} --asc-provider "6792V39SK3" --file "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg" | grep RequestUUID | awk '{print $3}')
@@ -160,12 +162,12 @@ jobs:
       - name: Fetch all history for all tags and branches
         run: git fetch --prune --unshallow
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].9
+        uses: gittools/actions/gitversion/[email protected].10
         with:
           versionSpec: '5.x'
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].9
+        uses: gittools/actions/gitversion/[email protected].10
       - name: Get linux binaries
         uses: actions/download-artifact@master
         with:

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

@@ -18,7 +18,8 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
-          java-version: 14
+          java-version: 16
+          distribution: 'adopt'
       - uses: actions/cache@v1
         name: Restore gradle wrapper
         with:

.github/workflows/stale.yml

@@ -1,15 +1,14 @@
 name: Mark stale issues and pull requests
 
 on:
-  schedule:
-  - cron: "20 19 * * *"
+  workflow_dispatch:
 
 jobs:
   stale:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/stale@v3
+    - uses: actions/stale@v4
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         days-before-stale: 180

.github/workflows/tests-fetchers.yml

@@ -36,7 +36,7 @@ jobs:
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
-          java-version: 14
+          java-version: 16
           distribution: 'adopt'
       - uses: actions/cache@v2
         name: Restore gradle cache

.github/workflows/tests.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/[email protected].0
+        uses: styfle/[email protected].1
         with:
           access_token: ${{ github.token }}
       - name: Checkout source