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

* upstream/main: (387 commits)
  Show a warning in the merge dialog when authors are the same but formatted differently (#9088)
  Fix subdatabase from aux on cli (#9117)
  Visual improvements to LinkedFilesEditor (#9114)
  SLR Remove "last-search-date" (#9116)
  Hide diffs when one of the field values is blank a.k.a no conflict (#9110)
  Squashed 'buildres/csl/csl-locales/' changes from e637746677..b2afeb4d87
  Squashed 'buildres/csl/csl-styles/' changes from c750b6e..8d69f16
  Fix title case capitalization after en-dash characters (#9102)
  Update journal abbrev list (#9109)
  Fix CSL rendering in case of article (#8607)
  [WIP][GSOC22] - C - Improve the external changes resolver dialog (#9021)
  Bump jsoup from 1.15.1 to 1.15.3 (#9103)
  Bump checkstyle from 10.3.2 to 10.3.3 (#9104)
  Bump postgresql from 42.4.2 to 42.5.0 (#9105)
  Bump unirest-java from 3.13.10 to 3.13.11 (#9106)
  Include check for TimeStamp (#9089)
  Close OO connection on JabRef exit (#9076)
  Bump slf4j-tinylog from 2.4.1 to 2.5.0 (#9085)
  Bump bcprov-jdk18on from 1.71 to 1.71.1 (#9079)
  Bump tinylog-impl from 2.4.1 to 2.5.0 (#9086)
  ...

# Conflicts:
#	src/main/java/org/jabref/gui/shared/SharedDatabaseUIManager.java
#	src/main/java/org/jabref/gui/util/DefaultTaskExecutor.java
#	src/main/java/org/jabref/logic/shared/DBMSSynchronizer.java

.editorconfig

@@ -6,5 +6,8 @@ indent_style = space
 insert_final_newline = true
 trim_trailing_whitespace = true
 
+[*.{fxml,java,properties,sh}]
+end_of_line = lf
+
 [*.md]
 trim_trailing_whitespace = false

.gitattributes

@@ -5,12 +5,17 @@ gradlew text eol=lf
 # windows line endings at windows files
 *.bat text eol=crlf
 
-# ensure that line endings of *.java, and *.properties are normalized
-*.java text
-*.properties text
+# ensure that line endings of *.fxml, *.java, and *.properties are normalized
+*.fxml text eol=lf
+*.java text eol=lf
+*.properties text eol=lf
 
 # .bib files have to be written using OS specific line endings to enable our tests working
 *.bib text !eol
 
-# disable after a release
-CHANGELOG.md merge=union
+# Citavi needs to be LF line ending
+# This overwrites the setting of "*.bib"
+Citavi*.bib eol=lf
+
+# disable after a release (otherwise, duplicate CHANGELOG.md entries will be generated)
+# CHANGELOG.md merge=union

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -12,7 +12,7 @@ body:
     attributes:
       label: JabRef version
       options:
-        - "5.5 (latest release)"
+        - "5.7 (latest release)"
         - "3.8.2"
         - Latest development branch build (please note build date below)
         - Other (please describe below)

.github/PULL_REQUEST_TEMPLATE.md

@@ -15,4 +15,5 @@ The title of the PR must not reference an issue, because GitHub does not support
 - [ ] Tests created for changes (if applicable)
 - [ ] Manually tested changed features in running JabRef (always required)
 - [ ] Screenshots added in PR description (for UI changes)
+- [ ] [Checked developer's documentation](https://devdocs.jabref.org/): Is the information available and up to date? If not, I outlined it in this pull request.
 - [ ] [Checked documentation](https://docs.jabref.org/): Is the information available and up to date? If not, I created an issue at <https://github.com/JabRef/user-documentation/issues> or, even better, I submitted a pull request to the documentation repository.

.github/workflows/automerge.yml

@@ -9,19 +9,19 @@ jobs:
     steps:
       - name: 'Wait for status checks'
         id: waitforstatuschecks
-        uses: "WyriHaximus/github-action-wait-for-status@v1.4"
+        uses: "WyriHaximus/github-action-wait-for-status@v1.6"
         with:
           ignoreActions: Automerge Dependabot,Code coverage,Create snapcraft image,Deploy binaries on builds.jabref.org,codecov/project,markdown-link-check
           checkInterval: 13
         env:
           GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
       - name: Auto approve
-        uses: hmarr/auto-approve-action@v2.1.0
+        uses: hmarr/auto-approve-action@v2.4.0
         if: steps.waitforstatuschecks.outputs.status == 'success'
         with:
           github-token: "${{ secrets.GITHUB_TOKEN }}"
       - name: Merge pull requests
-        uses: pascalgn/automerge-action@v0.14.3
+        uses: pascalgn/automerge-action@v0.15.3
         if: steps.waitforstatuschecks.outputs.status == 'success'
         env:
           MERGE_METHOD: "merge"

.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/cleanup_pr.yml

@@ -27,7 +27,7 @@ jobs:
           echo "##[set-output name=branch;]$(echo ${{ github.event.pull_request.head.ref }})"
       - name: Delete folder on builds.jabref.org
         if: ${{ steps.checksecrets.outputs.secretspresent }}
-        uses: appleboy/ssh-action@v0.1.4
+        uses: appleboy/ssh-action@v0.1.5
         with:
           script: rm -rf /var/www/builds.jabref.org/www/${{ steps.extract_branch.outputs.branch }} || true
           host: build-upload.jabref.org

.github/workflows/deployment.yml

@@ -22,6 +22,7 @@ env:
   SpringerNatureAPIKey: ${{ secrets.SpringerNatureAPIKey }}
   AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey }}
   IEEEAPIKey: ${{ secrets.IEEEAPIKey }}
+  BiodiversityHeritageApiKey: ${{ secrets.BiodiversityHeritageApiKey}}
   OSXCERT: ${{ secrets.OSX_SIGNING_CERT }}
   GRADLE_OPTS: -Xmx4g -Dorg.gradle.daemon=false -Dorg.gradle.vfs.watch=false
   JAVA_OPTS: -Xmx4g
@@ -51,20 +52,20 @@ 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
-        uses: gittools/actions/gitversion/setup@v0.9.11
+        uses: gittools/actions/gitversion/setup@v0.9.13
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.9.11
+        uses: gittools/actions/gitversion/execute@v0.9.13
       - name: Set up JDK
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
-          java-version: 17
+          java-version: 18
           distribution: 'temurin'
           cache: 'gradle'
       - name: Setup OSX key chain on OSX
@@ -152,16 +153,16 @@ 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
-        uses: gittools/actions/gitversion/setup@v0.9.11
+        uses: gittools/actions/gitversion/setup@v0.9.13
         with:
           versionSpec: '5.x'
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/execute@v0.9.11
+        uses: gittools/actions/gitversion/execute@v0.9.13
       - name: Get linux binaries
         uses: actions/download-artifact@master
         with:

.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

@@ -6,14 +6,17 @@ on:
     - cron: '1 2 1,15 * *'
   workflow_dispatch:
 
+permissions:
+  contents: read
+
 jobs:
   publish:
     name: Refresh Citation Style Language Files
     runs-on: ubuntu-latest
     if: github.repository == 'JabRef/jabref'
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           ref: main
           fetch-depth: 0
@@ -42,7 +45,7 @@ jobs:
           cp buildres/csl/csl-locales/locales-en-US.xml src/main/resources/csl-locales/
           git add .
           git commit -m"Refresh example styles" || true
-      - uses: peter-evans/create-pull-request@v3
+      - uses: peter-evans/create-pull-request@v4
         with:
           token: ${{ secrets.GH_TOKEN_UPDATE_GRADLE_WRAPPER }}
           branch: refresh-csl

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

@@ -4,21 +4,27 @@ on:
   workflow_dispatch:
     # Allow to run manually
 
+permissions:
+  contents: read
+
 jobs:
   publish:
+    permissions:
+      contents: write  # for peter-evans/create-pull-request to create branch
+      pull-requests: write  # for peter-evans/create-pull-request to create a PR
     name: Refresh Journal List Files
     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
           fetch-depth: 0
       - name: Set up JDK
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
-          java-version: 17
+          java-version: 18
           distribution: 'temurin'
           cache: 'gradle'
       - name: Update journal lists
@@ -46,7 +52,7 @@ jobs:
           # create .mv file
           cd $GITHUB_WORKSPACE
           ./gradlew generateJournalAbbreviationList
-      - uses: peter-evans/create-pull-request@v3
+      - uses: peter-evans/create-pull-request@v4
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           branch: update-journallist

.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

@@ -26,22 +26,26 @@ env:
   SpringerNatureAPIKey: ${{ secrets.SPRINGERNATUREAPIKEY_FOR_TESTS }}
   AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey_FOR_TESTS }}
   IEEEAPIKey: ${{ secrets.IEEEAPIKey_FOR_TESTS }}
+  BiodiversityHeritageApiKey: ${{ secrets.BiodiversityHeritageApiKey_FOR_TESTS}}
 
 concurrency:
   group: fetcher-tests-${{ github.head_ref }}
   cancel-in-progress: true
 
+permissions:
+  contents: read
+
 jobs:
   fetchertests:
     name: Fetcher tests
     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
+        uses: actions/setup-java@v3
         with:
-          java-version: 17
+          java-version: 18
           distribution: 'temurin'
           cache: 'gradle'
       - name: Run fetcher tests

.github/workflows/tests.yml

@@ -13,6 +13,7 @@ env:
   SpringerNatureAPIKey: ${{ secrets.SpringerNatureAPIKey }}
   AstrophysicsDataSystemAPIKey: ${{ secrets.AstrophysicsDataSystemAPIKey }}
   IEEEAPIKey: ${{ secrets.IEEEAPIKey }}
+  BiodiversityHeritageApiKey: ${{ secrets.BiodiversityHeritageApiKey}}
   GRADLE_OPTS: -Xmx4g
   JAVA_OPTS: -Xmx4g
 
@@ -26,18 +27,20 @@ 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
+        uses: actions/setup-java@v3
         with:
-          java-version: 17
+          java-version: 18
           distribution: 'temurin'
           cache: 'gradle'
       - name: Run check style reporter
         uses: nikitasavinov/checkstyle-action@master
         with:
-          reporter: github-pr-check
+          reporter: github-pr-review
+          github_token: ${{ secrets.GITHUB_TOKEN }}
           checkstyle_config: 'config/checkstyle/checkstyle_reviewdog.xml'
+          checkstyle_version: '10.3'
       - name: Run checkstyle gradle
         run: ./gradlew checkstyleMain checkstyleTest checkstyleJmh
       - name: Run markdown-lint
@@ -50,11 +53,11 @@ 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
+        uses: actions/setup-java@v3
         with:
-          java-version: 17
+          java-version: 18
           distribution: 'temurin'
           cache: 'gradle'
       - name: Run tests
@@ -82,11 +85,11 @@ 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
+        uses: actions/setup-java@v3
         with:
-          java-version: 17
+          java-version: 18
           distribution: 'temurin'
           cache: 'gradle'
       - name: Run tests on PostgreSQL
@@ -116,11 +119,11 @@ 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
+        uses: actions/setup-java@v3
         with:
-          java-version: 17
+          java-version: 18
           distribution: 'temurin'
           cache: 'gradle'
       - name: Run GUI tests
@@ -154,11 +157,11 @@ 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
+        uses: actions/setup-java@v3
         with:
-          java-version: 17
+          java-version: 18
           distribution: 'temurin'
           cache: 'gradle'
       - name: Update test coverage metrics
@@ -174,5 +177,5 @@ 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

.gitpod.Dockerfile

@@ -0,0 +1,8 @@
+# See https://www.gitpod.io/docs/java-in-gitpod/ for a full documentation of Java in GitPod
+
+FROM gitpod/workspace-full
+
+# All available versions can be listed using sdk ls java
+# More information about SDKMAN available at https://github.com/sdkman/sdkman-cli#sdkman-cli
+RUN bash -c ". /home/gitpod/.sdkman/bin/sdkman-init.sh \
+             && sdk install java 18.0.1.1-open"

.gitpod.yml

@@ -0,0 +1,16 @@
+image:
+  file: .gitpod.Dockerfile
+tasks:
+  - init: ./gradlew assemble
+jetbrains:
+  intellij:
+    plugins:
+      - CheckStyle-IDEA
+      - zielu.gittoolbox
+vscode:
+  extensions:
+    - redhat.java
+    - richardwillis.vscode-gradle
+    - vscjava.vscode-java-debug
+    - kiteco.kite
+    - DavidAnson.vscode-markdownlint