Merge remote-tracking branch 'upstream/master' into sharelatex

* upstream/master: (217 commits)
  Fix handling of URL in file field (JabRef#7347)
  Fix expansion of bracketed expressions in RegExpBasedFileFinder (JabRef#7338)
  Refactor unlinked files (JabRef#7209)
  Add pressing enter when the search field is focused as a way to trigger search (JabRef#7377)
  Upgrade citeproc to 3.x snapshot without graal (JabRef#7370)
  Fix Exception if no AzureInstrumentationKey is available (JabRef#7373)
  Update snapcraft source url (JabRef#7372)
  Fix checkstyle and adjust language
  GitBook: [master] 3 pages and 32 assets modified
  Add migration to special field (JabRef#7368)
  GitBook: [master] 5 pages and 29 assets modified
  Modify message at the duplicates found dialog (JabRef#7231)
  Fixes miss-parsed names in `AutomaticPersonsGroup` (JabRef#7228)
  Fix an issue where the password for a shared SQL database was only remembered if it was the same as the username (JabRef#7364)
  Fix harvard exporter by changing AuthorsFormatter (JabRef#7355)
  Bump styfle/cancel-workflow-action from 0.6.0 to 0.7.0 (JabRef#7363)
  Bump mockito-core from 3.7.0 to 3.7.7 (JabRef#7360)
  Bump org.beryx.jlink from 2.23.1 to 2.23.2 (JabRef#7361)
  Bump libreoffice from 7.0.3 to 7.0.4 (JabRef#7362)
  Export full month name instead of number in ms office (JabRef#7358)
  ...

# Conflicts:
#	external-libraries.md
#	src/main/java/module-info.java
#	src/main/java/org/jabref/gui/shared/SharedDatabaseLoginDialogViewModel.java

.gitattributes

@@ -5,9 +5,6 @@ gradlew text eol=lf
 # windows line endings at windows files
 *.bat text eol=crlf
 
-# required for proper releasing
-AUTHORS text eol=lf
-
 # ensure that line endings of *.java, and *.properties are normalized
 *.java text
 *.properties text

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,8 @@
+blank_issues_enabled: false
+contact_links:
+  - name: Help
+    url: https://discourse.jabref.org/c/help/
+    about: Questions and requests for help are handled at https://discourse.jabref.org
+  - name: Feature requests
+    url: https://discourse.jabref.org/c/features/
+    about: If you are missing an important feature? Let us know!

.github/workflows/automerge.yml

@@ -9,14 +9,14 @@ jobs:
     steps:
       - name: 'Wait for status checks'
         id: waitforstatuschecks
-        uses: "WyriHaximus/github-action-wait-for-status@v1.2"
+        uses: "WyriHaximus/github-action-wait-for-status@v1.3"
         with:
           ignoreActions: Automerge Dependabot
           checkInterval: 13
         env:
           GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
       - name: Merge pull requests
-        uses: pascalgn/automerge-action@v0.12.0
+        uses: pascalgn/automerge-action@v0.13.0
         if: steps.waitforstatuschecks.outputs.status == 'success'
         env:
           MERGE_METHOD: "squash"

.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: ${{ steps.checksecrets.outputs.secretspresent }}
-        uses: appleboy/[email protected].3
+        uses: appleboy/[email protected].4
         with:
           script: rm -rf /var/www/builds.jabref.org/www/${{ steps.extract_branch.outputs.branch }} || true
           host: build-upload.jabref.org

.github/workflows/deployment.yml

@@ -1,6 +1,7 @@
 name: Deployment
 
 on:
+  workflow_dispatch:
   push:
     branches:
       - master
@@ -41,20 +42,20 @@ jobs:
     name: Create installer and portable version for ${{ matrix.displayName }}
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.6.0
+        uses: styfle/cancel-workflow-action@0.7.0
         with:
           access_token: ${{ github.token }}
       - name: Fetch all history for all tags and branches
         uses: actions/checkout@v2
         with:
           fetch-depth: 0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].5
+        uses: gittools/actions/gitversion/[email protected].8
         with:
-          versionSpec: "5.3.7"
+          versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].5
+        uses: gittools/actions/gitversion/[email protected].8
       - name: Set up JDK 15 for linux and mac
         uses: actions/setup-java@v1
         with:
@@ -88,20 +89,20 @@ jobs:
           create-keychain: false
           keychain-password: jabref
       - name: Build runtime image
-        run: ./gradlew -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jlinkZip
+        run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jlinkZip
       - name: Build installer
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jpackage
         shell: bash
       - name: Resign app image for OSX and build dmg
         if: matrix.os == 'macos-latest'
         shell: bash
         run: |
-          codesign --entitlements buildres/mac/myapp.entitlements --options runtime -vvv -f --sign "Developer ID Application: Tobias Diez (W2PU6LW5U5)" build/distribution/JabRef.app/Contents/runtime/Contents/MacOS/libjli.dylib
-          codesign --entitlements buildres/mac/myapp.entitlements --options runtime -vvv -f --sign "Developer ID Application: Tobias Diez (W2PU6LW5U5)" build/distribution/JabRef.app/Contents/MacOS/JabRef
-          codesign --entitlements buildres/mac/myapp.entitlements --options runtime -vvv -f --sign "Developer ID Application: Tobias Diez (W2PU6LW5U5)" build/distribution/JabRef.app
+          codesign --entitlements buildres/mac/jabref.entitlements --options runtime -vvv -f --sign "Developer ID Application: Tobias Diez (W2PU6LW5U5)" build/distribution/JabRef.app/Contents/runtime/Contents/MacOS/libjli.dylib
+          codesign --entitlements buildres/mac/jabref.entitlements --options runtime -vvv -f --sign "Developer ID Application: Tobias Diez (W2PU6LW5U5)" build/distribution/JabRef.app/Contents/MacOS/JabRef
+          codesign --entitlements buildres/mac/jabref.entitlements --options runtime -vvv -f --sign "Developer ID Application: Tobias Diez (W2PU6LW5U5)" build/distribution/JabRef.app
           jpackage --type pkg --dest build/distribution --name JabRef --app-version "${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}" --app-image build/distribution/JabRef.app --verbose --type dmg --vendor JabRef --app-version "${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}" --file-associations buildres/mac/bibtexAssociations.properties --resource-dir buildres/mac
-          codesign -s "Developer ID Application: Tobias Diez (W2PU6LW5U5)" --options runtime --entitlements buildres/mac/myapp.entitlements -vvvv --deep "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg"
-          jpackage --type pkg --dest build/distribution --name JabRef --app-version "${{ 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 }}.${{ steps.gitversion.outputs.Minor }}" --file-associations buildres/mac/bibtexAssociations.properties --resource-dir buildres/mac
+          codesign -s "Developer ID Application: Tobias Diez (W2PU6LW5U5)" --options runtime --entitlements buildres/mac/jabref.entitlements -vvvv --deep "build/distribution/JabRef-${{ steps.gitversion.outputs.Major }}.${{ steps.gitversion.outputs.Minor }}.dmg"
+          jpackage --type pkg --dest build/distribution --name JabRef --mac-package-identifier JabRef --app-version "${{ 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 }}.${{ steps.gitversion.outputs.Minor }}" --file-associations buildres/mac/bibtexAssociations.properties --resource-dir buildres/mac
           productsign --sign "Developer ID Installer: Tobias Diez (W2PU6LW5U5)" "build/distribution/JabRef-${{ 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/master'
@@ -161,12 +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].5
+        uses: gittools/actions/gitversion/[email protected].8
         with:
-          versionSpec: '5.2.x'
+          versionSpec: '5.x'
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].5
+        uses: gittools/actions/gitversion/[email protected].8
       - name: Get linux binaries
         uses: actions/download-artifact@master
         with:

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

@@ -16,20 +16,27 @@ jobs:
         with:
           ref: master
           fetch-depth: 0
-      - name: Add csl-styles remote
-        run: git remote add -f csl-styles https://github.com/citation-style-language/styles.git
-      - name: Update csl-styles
+      - name: Initialize git
         run: |
           git checkout master
           git config --local core.editor /usr/bin/cat
           git config user.name "github actions"
           git config user.email "[email protected]"
-          git subtree pull --prefix src/main/resources/csl-styles csl-styles master --squash
+      - name: Add csl-styles remote
+        run: git remote add -f csl-styles https://github.com/citation-style-language/styles.git
+      - name: Update csl-styles
+        run: |
+          git subtree pull --prefix buildres/csl/csl-styles csl-styles master --squash
+          cp buildres/csl/csl-styles/acm-siggraph.csl src/main/resources/csl-styles/
+          cp buildres/csl/csl-styles/ieee.csl src/main/resources/csl-styles/
+          cp buildres/csl/csl-styles/turabian-author-date.csl src/main/resources/csl-styles/
       - name: Add csl-locales remote
         run: git remote add -f csl-locales https://github.com/citation-style-language/locales.git
       - name: Update csl-locales
         run: |
-          git subtree pull --prefix src/main/resources/csl-locales csl-locales master --squash
+          git subtree pull --prefix buildres/csl/csl-locales csl-locales master --squash
+          cp buildres/csl/csl-locales/locales.json src/main/resources/csl-locales/
+          cp buildres/csl/csl-locales/locales-en-US src/main/resources/csl-locales/
       - uses: ad-m/github-push-action@master
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/snap.yml

@@ -1,6 +1,7 @@
 name: Snap
 
 on:
+  workflow_dispatch:
   push:
     branches:
       - snapcraft
@@ -28,12 +29,12 @@ jobs:
         uses: actions/checkout@v2
       # The image relies on https://builds.jabref.org/master/JabRef-5.0-portable_linux.tar.gz^
       # See snap/snapcraft.yml for details
-      - name: Build snap (1) Run build
+      - name: Run snapcraft build
         uses: snapcore/action-build@v1
         id: snapcraft
         with:
           snapcraft-args: "--debug"
-      - name: Build snap (2) Upload snap
+      - name: Upload snap
         if: ${{ steps.checksecrets.outputs.secretspresent }}
         uses: snapcore/action-publish@v1
         with:

.github/workflows/stale.yml

@@ -2,17 +2,27 @@ name: Mark stale issues and pull requests
 
 on:
   schedule:
-  - cron: "0 0 * * *"
+  - cron: "20 19 * * *"
 
 jobs:
   stale:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/stale@master
+    - uses: actions/stale@v3
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
-        stale-issue-message: 'This issue will be closed in 7 days due to inactivity :zzz: Please provide the requested information if the problem persists.'
+        days-before-stale: 180
+        days-before-close: 14
+        stale-issue-message: |
+          This issue has been inactive for half a year. Since JabRef is constantly evolving this issue may not be relevant any longer and it will be closed in two weeks if no further activity occurs.
+
+          As part of an effort to ensure that the JabRef team is focusing on important and valid issues, we would like to ask if you could update the issue if it still persists. This could be in the following form:
+
+          - If there has been a longer discussion, add a short summary of the most important points as a new comment (if not yet existing).
+          - Provide further steps or information on how to reproduce this issue.
+          - Upvote the initial post if you like to see it implemented soon. Votes are not the only metric that we use to determine the requests that are implemented, however, they do factor into our decision-making process.
+          - If all information is provided and still up-to-date, then just add a short comment that the issue is still relevant.
+
+          Thank you for your contribution!
         stale-issue-label: 'status: stale'
-        days-before-stale: 30
-        only-labels: 'status: waiting-for-customer-feedback'

.github/workflows/tests-fetchers.yml

@@ -38,7 +38,7 @@ jobs:
         with:
           java-version: 14
       - uses: actions/cache@v1
-        name: Restore gradle chache
+        name: Restore gradle cache
         with:
           path: ~/.gradle/caches
           key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}

.github/workflows/tests.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Cancel Previous Runs
-        uses: styfle/cancel-workflow-action@0.6.0
+        uses: styfle/cancel-workflow-action@0.7.0
         with:
           access_token: ${{ github.token }}
       - name: Checkout source
@@ -64,7 +64,7 @@ jobs:
         with:
           java-version: 14
       - uses: actions/cache@v1
-        name: Restore gradle chache
+        name: Restore gradle cache
         with:
           path: ~/.gradle/caches
           key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
@@ -108,7 +108,7 @@ jobs:
         with:
           java-version: 14
       - uses: actions/cache@v1
-        name: Restore gradle chache
+        name: Restore gradle cache
         with:
           path: ~/.gradle/caches
           key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
@@ -154,7 +154,7 @@ jobs:
         with:
           java-version: 14
       - uses: actions/cache@v1
-        name: Restore gradle chache
+        name: Restore gradle cache
         with:
           path: ~/.gradle/caches
           key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
@@ -204,7 +204,7 @@ jobs:
         with:
           java-version: 14
       - uses: actions/cache@v1
-        name: Restore gradle chache
+        name: Restore gradle cache
         with:
           path: ~/.gradle/caches
           key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle') }}
@@ -232,35 +232,3 @@ jobs:
     steps:
       - uses: actions/checkout@v2
       - uses: gradle/wrapper-validation-action@v1
-  checkauthors:
-    name: "Validate AUTHORS"
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-        with:
-          # full checkout needed for authors generation
-          fetch-depth: 0
-      - name: "All authors of this PR listed in AUTHORS"
-        id: authors_check
-        shell: bash
-        run: |
-          git config user.name "JabRef Author Checker [bot]"
-          git config user.email "[email protected]"
-          ./scripts/generate-authors.sh
-          set +o pipefail
-          added=$(git diff HEAD --no-ext-diff --unified=0 -a --no-prefix | egrep "^\+[^+]" | sed "s/^\+//")
-          if [ -z "$added" ]; then
-            echo "No authors added"
-            exit 0
-          fi
-          echo "Authors found in this PR not listed in the AUTHORS file."
-          echo
-          echo "The JabRef maintainers will add the following name to the AUTHORS file"
-          echo
-          echo -e "$added"
-          echo
-          echo "In case you want to use a different one, please comment here and adjust your name in your git configuration for future commits"
-          echo
-          echo "Just adding yourself into the AUHTORS file does not help as it is overwritten by our script ./scripts/generate-authors."
-          echo "Read more on the AUTHORS file at found at https://github.com/JabRef/jabref/blob/master/CONTRIBUTING.md#author-credits"
-          exit 1