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

* upstream/main: (1565 commits)
  Enable journal information fetcher directly in popup (#10598)
  Make generate button wider (#10588)
  make openRewrite stable again
  Rename cleanup_pr.yml to cleanup-pr.yml
  Changelog
  Fix failing fetcher tests (#10613)
  ShortDoi
  Fix CHANGELOG.md
  Bump commons-cli:commons-cli from 1.5.0 to 1.6.0 (#10607)
  Fix issue #9306: Move "Open only one instance of JabRef" preference option to somewhere else (#10602)
  Update README.md (#10604)
  Bump me.champeau.jmh from 0.7.1 to 0.7.2
  Bump org.beryx.jlink from 3.0.0 to 3.0.1
  Bump com.dlsc.gemsfx:gemsfx from 1.82.0 to 1.84.0
  Bump org.apache.logging.log4j:log4j-to-slf4j from 2.21.0 to 2.21.1
  Synchronize scrollbars in the change resolver dialog (#10587)
  Add button for a user to reset the cite command to the default value. (#10580)
  openrerwrite
  Update .github/PULL_REQUEST_TEMPLATE.md
  Update PULL_REQUEST_TEMPLATE.md
  ...

# Conflicts:
#	.devcontainer/devcontainer.json
#	build.gradle
#	src/main/java/org/jabref/gui/DefaultInjector.java
#	src/main/java/org/jabref/gui/libraryproperties/general/GeneralProperties.fxml
#	src/main/java/org/jabref/gui/libraryproperties/general/GeneralPropertiesView.java
#	src/main/java/org/jabref/gui/libraryproperties/general/GeneralPropertiesViewModel.java
#	src/main/java/org/jabref/logic/exporter/MetaDataSerializer.java
#	src/main/java/org/jabref/logic/importer/util/MetaDataParser.java
#	src/main/java/org/jabref/model/metadata/MetaData.java
#	src/main/java/org/jabref/preferences/JabRefPreferences.java

.devcontainer/devcontainer.json

@@ -1,43 +1,39 @@
-// For format details, see https://aka.ms/devcontainer.json. For config options, see the README at:
-// https://github.com/microsoft/vscode-dev-containers/tree/v0.245.2/containers/java
 {
     "name": "Java",
-    "image": "mcr.microsoft.com/vscode/devcontainers/base:bullseye",
-
-    // Configure tool-specific properties.
+    "image": "mcr.microsoft.com/devcontainers/base:debian",
     "customizations": {
-        // Configure properties specific to VS Code.
         "vscode": {
-            // Set *default* container specific settings.json values on container create.
-            "settings": { 
-            },
-
-            // Add the IDs of extensions you want installed when the container is created.
             "extensions": [
                 "vscjava.vscode-java-pack",
                 "vscjava.vscode-gradle",
-                "shengchen.vscode-checkstyle"
+                "shengchen.vscode-checkstyle",
+                "DavidAnson.vscode-markdownlint"
             ]
         }
     },
 
-    "onCreateCommand": "gradle assemble || true",
+    // Source code generation needs to be done before hand-over to VS Code.
+    // Otherwise, the Java extension will go mad.
+    "onCreateCommand": "./gradlew testClasses --console=plain --no-daemon",
 
-    // Forward the noVNC port (desktop-lite: https://github.com/devcontainers/features/tree/main/src/desktop-lite)  
-    "forwardPorts": [6080],
+    // Forward the vncPort and noVNC port.
+    // They are provided by desktop-lite:
+    // https://github.com/devcontainers/features/tree/main/src/desktop-lite#options
+    "forwardPorts": [5901, 6080],
 
     // Need to connect as root otherwise we run into issues with gradle.
     // default option is "vscode". More info: https://aka.ms/vscode-remote/containers/non-root.
     "remoteUser": "root",
     "features": {
         // Adds a lightweight desktop that can be accessed using a VNC viewer or the web
-        "desktop-lite": "latest",
+        "ghcr.io/devcontainers/features/desktop-lite:1": {},
 
-        // Install java
-        "java": {
-            "version": "18",
-            "installGradle": true,
-            "jdkDistro": "sem"
+        // Install java.
+        // See https://github.com/devcontainers/features/tree/main/src/java#options for details.
+        "ghcr.io/devcontainers/features/java:1": {
+            "version": "21.0.1-librca",
+            "installGradle": false,
+            "jdkDistro": "librca"
         }
     }
 }

.gitattributes

@@ -12,6 +12,8 @@ gradlew text eol=lf
 
 # .bib files have to be written using OS specific line endings to enable our tests working
 *.bib text !eol
+# Exception: The files used for the http server test - they should have linux line endings
+src/test/resources/org/jabref/http/server/*.bib text eol=lf
 
 # Citavi needs to be LF line ending
 # This overwrites the setting of "*.bib"

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -12,8 +12,7 @@ body:
     attributes:
       label: JabRef version
       options:
-        - "5.7 (latest release)"
-        - "3.8.2"
+        - "5.11 (latest release)"
         - Latest development branch build (please note build date below)
         - Other (please describe below)
       description: The version as shown in the about dialog.
@@ -42,7 +41,7 @@ body:
 
   - type: checkboxes
     attributes:
-      label: Checked with the latest development build
+      label: Checked with the latest development build (copy version output from About dialog)
       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.**

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,10 +1,12 @@
 <!-- 
 Describe the changes you have made here: what, why, ... 
-Link issues that are fixed, e.g. "Fixes #333".
-If you fixed a koppor issue, link it, e.g. "Fixes https://github.com/koppor/jabref/issues/47".
-The title of the PR must not reference an issue, because GitHub does not support autolinking there.
+Link the issue that will be closed, e.g., "Closes #333".
+If your PR closes a koppor issue, link it using its URL, e.g., "Closes https://github.com/koppor/jabref/issues/47".
+"Closes" is a keyword GitHub uses to link PRs with issues; do not change it.
+Don't reference an issue in the PR title because GitHub does not support auto-linking there.
 -->
 
+### Mandatory checks
 
 <!-- 
 - Go through the list below. Please don't remove any items.

.github/dependabot.yml

@@ -5,7 +5,7 @@ updates:
     schedule:
       interval: weekly
     labels:
-      - "type: dependencies"
+      - "dependencies"
     ignore:
       - dependency-name: com.microsoft.azure:applicationinsights-core
         versions:
@@ -18,10 +18,10 @@ updates:
     schedule:
       interval: weekly
     labels:
-      - "type: dependencies"
+      - "dependencies"
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:
       interval: weekly
     labels:
-      - "type: dependencies"
+      - "dependencies"

.github/heylogs.java

@@ -0,0 +1,6 @@
+//DEPS com.github.nbbrd.heylogs:heylogs-cli:0.7.1
+public class heylogs {
+    public static void main(String... args) throws Exception {
+        nbbrd.heylogs.cli.HeylogsCommand.main(args);
+    }
+}

.github/workflows/add-greeting-to-issue.yml

@@ -0,0 +1,22 @@
+name: Add greeting to issues for first time contributors
+
+on: 
+  issues:
+     types:
+       - labeled
+
+jobs:
+  GreetingFirstTimeCodeContribution:
+    if: ${{ github.event.label.name == 'FirstTimeCodeContribution' }}
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+    steps:
+    - name: GreetingFirstTimeCodeContribution
+      uses: peter-evans/create-or-update-comment@v3
+      with:
+        issue-number: ${{ github.event.issue.number }}
+        body: |
+            As a general advice for newcomers: check out [Contributing](https://github.com/JabRef/jabref/blob/main/CONTRIBUTING.md) for a start. Also, [guidelines for setting up a local workspace](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace) is worth having a look at.
+            
+            Feel free to ask here at GitHub, if you have any issue related questions. If you have questions about how to setup your workspace use JabRef's [Gitter](https://gitter.im/JabRef/jabref) chat. Try to open a (draft) pull-request early on, so that people can see you are working on the issue and so that they can see the direction the pull request is heading towards. This way, you will likely receive valuable feedback.

.github/workflows/add-to-projects.yml

@@ -0,0 +1,42 @@
+name: Add to Project on Label
+
+on:
+  issues:
+    types: [labeled]
+
+permissions:
+  issues: write
+
+jobs:
+  add-to-project:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: "good first issue"
+        if: "${{ github.event.label.name == 'good first issue' }}"
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          ISSUE_URL=$(jq --raw-output .issue.html_url "$GITHUB_EVENT_PATH")
+          gh project item-add 5 --owner jabref --url $ISSUE_URL
+      - name: needs-refinement
+        if: github.event.label.name == 'needs-refinement'
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          ISSUE_URL=$(jq --raw-output .issue.html_url "$GITHUB_EVENT_PATH")
+          gh project item-add 15 --owner jabref --url $ISSUE_URL
+      - name: "status: freeze"
+        if: "${{ github.event.label.name == 'status: freeze' }}"
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          ISSUE_URL=$(jq --raw-output .issue.html_url "$GITHUB_EVENT_PATH")
+          gh project item-add 9 --owner jabref --url $ISSUE_URL
+      - name: ui
+        if: "${{ github.event.label.name == 'ui' }}"
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          ISSUE_URL=$(jq --raw-output .issue.html_url "$GITHUB_EVENT_PATH")
+          gh project item-add 8 --owner jabref --url $ISSUE_URL

.github/workflows/automerge.yml

@@ -1,29 +1,33 @@
-name: Automerge Pull Requests
-on: [pull_request]
+name: Auto Merge
+on: [pull_request_target, workflow_dispatch]
+
+permissions:
+  contents: write
+  pull-requests: write
 
 jobs:
   automerge:
-    name: Automerge Dependency Updates
     runs-on: ubuntu-latest
-    if: github.actor == 'dependabot[bot]' || github.actor == 'dependabot-preview[bot]' || contains(github.event.pull_request.labels.*.name, 'dependencies')
+    # Run only if PR is inside JabRef's main repository and created by dependabot or by an update workflow
+    if: >
+      (github.repository == 'JabRef/jabref') && 
+      (github.event.pull_request.head.repo.full_name == 'JabRef/jabref') &&
+      (
+        (github.actor == 'dependabot[bot]') ||
+        (
+          startsWith(github.event.pull_request.title, '[Bot] ') || 
+          startsWith(github.event.pull_request.title, 'Bump ') || 
+          startsWith(github.event.pull_request.title, 'New Crowdin updates')
+        )
+      )
     steps:
-      - name: 'Wait for status checks'
-        id: waitforstatuschecks
-        uses: "WyriHaximus/github-action-wait-for-status@v1.7.1"
-        with:
-          ignoreActions: Automerge Dependabot,Code coverage,Create snapcraft image,Deploy binaries on builds.jabref.org,codecov/project,markdown-link-check
-          checkInterval: 13
+      - name: Approve PR
+        run: gh pr review --approve "$PR_URL"
         env:
-          GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
-      - name: Auto approve
-        uses: hmarr/auto-approve-action@v3.1.0
-        if: steps.waitforstatuschecks.outputs.status == 'success'
-        with:
-          github-token: "${{ secrets.GITHUB_TOKEN }}"
-      - name: Merge pull requests
-        uses: pascalgn/automerge-action@v0.15.5
-        if: steps.waitforstatuschecks.outputs.status == 'success'
+          PR_URL: ${{github.event.pull_request.html_url}}
+          GITHUB_TOKEN: ${{secrets.GH_TOKEN_JABREF_MACHINE_PR_APPROVE}}
+      - name: Merge PR
+        run: gh pr merge --auto --squash "$PR_URL"
         env:
-          MERGE_METHOD: "merge"
-          MERGE_LABELS: ""
-          GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
+          PR_URL: ${{github.event.pull_request.html_url}}
+          GITHUB_TOKEN: ${{secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER}}

.github/workflows/check-links.yaml

@@ -1,11 +1,6 @@
 name: Check external href links in the documentation
 
 on:
-  push:
-    paths:
-      - '**.md'
-    paths-ignore:
-      - 'CHANGELOG.md'
   schedule:
     # Run on the first of each month at 9:00 AM (See https://pubs.opengroup.org/onlinepubs/9699919799/utilities/crontab.html#tag_20_25_07)
     - cron: "0 9 1 * *"
@@ -15,11 +10,13 @@ jobs:
   markdown-link-check:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+        with:
+          show-progress: 'false'
       - uses: gaurav-nelson/github-action-markdown-link-check@v1
         with:
           use-quiet-mode: 'yes'
           use-verbose-mode: 'no'
           config-file: 'mlc_config.json'
           folder-path: 'docs/'
-          file-path: './CHANGELOG.md, ./README.md'
+          file-path: './README.md'

.github/workflows/cleanup-pr.yml

@@ -0,0 +1,42 @@
+name: Cleanup after PR
+
+on:
+  pull_request:
+    types: [closed]
+
+jobs:
+  cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Cancel deployment run
+        uses: styfle/cancel-workflow-action@0.12.0
+        with:
+          ignore_sha: true
+          workflow_id: 9813 # workflow "Deployment"
+      - name: Check secrets presence
+        id: checksecrets
+        shell: bash
+        run: |
+          if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
+            echo "secretspresent=NO" >> $GITHUB_OUTPUT
+          else
+            echo "secretspresent=YES" >> $GITHUB_OUTPUT
+          fi
+        env:
+          BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
+      - name: Delete folder on builds.jabref.org
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
+        uses: appleboy/ssh-action@v1.0.0
+        with:
+          script: rm -rf /var/www/builds.jabref.org/www/pull/${{ github.event.pull_request.number }} || true
+          host: build-upload.jabref.org
+          port: 9922
+          username: jrrsync
+          key: ${{ secrets.buildJabRefPrivateKey }}
+      - name: Update PR comment
+        if: steps.checksecrets.outputs.secretspresent == 'YES'
+        uses: thollander/actions-comment-pull-request@v2
+        with:
+          comment_tag: download-link
+          message: The build for this PR is no longer available. Please visit <https://builds.jabref.org/main/> for the latest build.
+          mode: upsert