Merge remote-tracking branch 'upstream/main' into fix-for-issue-8729

* upstream/main: (55 commits)
  Update guidelines-for-setting-up-a-local-workspace.md
  Add link to good first issues (and fix link)
  Refine guidelines (and fix .md file linking)
  Extend ArXiv fetcher results by using data from related DOIs (JabRef#9170)
  New Crowdin updates (JabRef#9366)
  Fix token
  New translations JabRef_en.properties (Chinese Simplified) (JabRef#9364)
  Fix date field change causes an uncaught exception (JabRef#9365)
  Add date format and respective test case (JabRef#9310)
  Bump jackson-datatype-jsr310 from 2.13.4 to 2.14.0 (JabRef#9357)
  Bump jackson-dataformat-yaml from 2.13.4 to 2.14.0 (JabRef#9356)
  Bump tika-core from 2.5.0 to 2.6.0 (JabRef#9358)
  Refine guideline "Set up a local workspace" (JabRef#9355)
  Adds missing "requires" statement (JabRef#9354)
  Bind "Find unlinked files" default directory to the current library (JabRef#9290)
  Rename "Remote" to "Tele" (JabRef#9270)
  Fixed display of file field adjusting for the dark theme (JabRef#9343)
  Update sorting of entries in maintable by special fields immediately (JabRef#9338)
  New translations JabRef_en.properties (German) (JabRef#9336)
  Fix Abbreviation for Escaped Ampersand (JabRef#9288)
  ...

# Conflicts:
#	CHANGELOG.md
#	src/main/java/org/jabref/preferences/AppearancePreferences.java
#	src/main/java/org/jabref/preferences/JabRefPreferences.java
#	src/test/java/org/jabref/gui/theme/ThemeManagerTest.java

Author: Siedlerchr

.github/workflows/GreetingFirstTimeCodeContribution.yml

@@ -0,0 +1,22 @@
+name: GreetingFirstTimeCodeContribution
+
+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@v2
+      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/automerge.yml

@@ -16,12 +16,12 @@ jobs:
         env:
           GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
       - name: Auto approve
-        uses: hmarr/auto-approve-action@v3.0.0
+        uses: hmarr/auto-approve-action@v3.1.0
         if: steps.waitforstatuschecks.outputs.status == 'success'
         with:
           github-token: "${{ secrets.GITHUB_TOKEN }}"
       - name: Merge pull requests
-        uses: pascalgn/[email protected].3
+        uses: pascalgn/[email protected].5
         if: steps.waitforstatuschecks.outputs.status == 'success'
         env:
           MERGE_METHOD: "merge"

.github/workflows/deployment.yml

@@ -31,7 +31,6 @@ concurrency:
   group: ${{ github.ref }}
   cancel-in-progress: true
 
-
 jobs:
   build:
     strategy:
@@ -51,45 +50,58 @@ jobs:
     runs-on: ${{ matrix.os }}
     name: Create installer and portable version for ${{ matrix.displayName }}
     steps:
+      - name: Check secrets presence
+        id: checksecrets
+        shell: bash
+        run: |
+          if [ "$BUILDJABREFPRIVATEKEY" == "" ]; then
+            echo ::set-output name=secretspresent::false
+          else
+            echo ::set-output name=secretspresent::true
+          fi
+        env:
+          BUILDJABREFPRIVATEKEY: ${{ secrets.buildJabRefPrivateKey }}
       - name: Fetch all history for all tags and branches
         uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].14
+        uses: gittools/actions/gitversion/[email protected].15
         with:
           versionSpec: "5.x"
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].14
+        uses: gittools/actions/gitversion/[email protected].15
       - name: Set up JDK
         uses: actions/setup-java@v3
         with:
           java-version: 18
           distribution: 'temurin'
           cache: 'gradle'
       - name: Setup OSX key chain on OSX
-        if: matrix.os == 'macos-latest'
+        if: (matrix.os == 'macos-latest') && steps.checksecrets.outputs.secretspresent
         uses: apple-actions/import-codesign-certs@v1
         with:
           p12-file-base64: ${{ secrets.OSX_SIGNING_CERT }}
           p12-password: ${{ secrets.OSX_CERT_PWD }}
           keychain-password: jabref
       - name: Setup OSX key chain on OSX for app id cert
-        if: matrix.os == 'macos-latest'
+        if: (matrix.os == 'macos-latest') && steps.checksecrets.outputs.secretspresent
         uses: apple-actions/import-codesign-certs@v1
         with:
           p12-file-base64: ${{ secrets.OSX_SIGNING_CERT_APPLICATION }}
           p12-password: ${{ secrets.OSX_CERT_PWD }}
           create-keychain: false
           keychain-password: jabref
       - name: Build runtime image
+        if: (matrix.os != 'macos-latest') || steps.checksecrets.outputs.secretspresent
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jlinkZip
       - name: Build installer
+        if: (matrix.os != 'macos-latest') || steps.checksecrets.outputs.secretspresent
         run: ./gradlew -i -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jpackage
         shell: bash
       - name: Resign app image for OSX and build dmg
-        if: matrix.os == 'macos-latest'
+        if: (matrix.os == 'macos-latest') && steps.checksecrets.outputs.secretspresent
         shell: bash
         run: |
           codesign --entitlements buildres/mac/jabref.entitlements --options runtime -vvv -f --sign "Developer ID Application: JabRef e.V. (6792V39SK3)" build/distribution/JabRef.app/Contents/runtime/Contents/MacOS/libjli.dylib
@@ -100,7 +112,7 @@ jobs:
           jpackage --type pkg --dest build/distribution --name JabRef --mac-package-identifier JabRef --app-version "${{ 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 }}.${{ steps.gitversion.outputs.Minor }}-signed.pkg"
       - name: Notarize dmg and pkg installer
-        if: matrix.os == 'macos-latest' && startsWith(github.ref, 'refs/tags/')
+        if: (matrix.os == 'macos-latest') && startsWith(github.ref, 'refs/tags/') && steps.checksecrets.outputs.secretspresent
         shell: bash
         run: |
           REQUEST_UUID_DMG=$(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}')
@@ -157,12 +169,12 @@ jobs:
       - name: Fetch all history for all tags and branches
         run: git fetch --prune --unshallow
       - name: Install GitVersion
-        uses: gittools/actions/gitversion/[email protected].14
+        uses: gittools/actions/gitversion/[email protected].15
         with:
           versionSpec: '5.x'
       - name: Run GitVersion
         id: gitversion
-        uses: gittools/actions/gitversion/[email protected].14
+        uses: gittools/actions/gitversion/[email protected].15
       - name: Get linux binaries
         uses: actions/download-artifact@master
         with:

.github/workflows/pages.yml

@@ -1,6 +1,10 @@
 name: Deploy Jekyll site to Pages
 
 on:
+  pull_request:
+    paths:
+      - 'docs/**'
+      - '.github/workflows/pages.yml'
   push:
     paths:
       - 'docs/**'
@@ -27,19 +31,21 @@ jobs:
       - name: Setup Ruby
         uses: ruby/setup-ruby@v1
         with:
-          ruby-version: '3.0' # Not needed with a .ruby-version file
+          ruby-version: '2.7' # Not needed with a .ruby-version file
           bundler-cache: true # runs 'bundle install' and caches installed gems automatically
-          cache-version: 0 # Increment this number if you need to re-download cached gems
+          cache-version: 1 # Increment this number if you need to re-download cached gems
+          working-directory: docs/
       - name: Setup Pages
         id: pages
         uses: actions/configure-pages@v2
       - name: Build with Jekyll
-        uses: actions/jekyll-build-pages@v1
-        with:
-          source: docs/
-          destination: ./_site
+        run: |
+          cd docs
+          bundle exec jekyll build
       - name: Upload artifact
         uses: actions/upload-pages-artifact@v1
+        with:
+          path: docs/_site/
 
   deploy:
     if: github.ref == 'refs/heads/main'

.github/workflows/tests-fetchers.yml

@@ -11,10 +11,8 @@ on:
       - 'build.gradle'
   pull_request:
     paths:
-      - 'src/main/java/org/jabref/logic/**'
-      - 'src/test/java/org/jabref/logic/**'
-      - 'src/main/java/org/jabref/model/**'
-      - 'src/test/java/org/jabref/model/**'
+      - 'src/main/java/org/jabref/logic/importer/fetcher/**'
+      - 'src/test/java/org/jabref/logic/importer/fetcher/**'
       - '.github/workflows/tests-fetchers.yml'
       - 'build.gradle'
   schedule:

.idea/runConfigurations/JabRef_Main.xml

@@ -20,10 +20,12 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - An SLR can now be started from the SLR itself. [#9131](https://github.com/JabRef/jabref/pull/9131), [koppor#601](https://github.com/koppor/jabref/issues/601)
 - Implement a new ISBN Fetcher ([doi-to-bibtex-converter.herokuapp.com](http://doi-to-bibtex-converter.herokuapp.com) as source). [#9145](https://github.com/JabRef/jabref/pull/9145)
 - We added support for the Ukrainian and Arabic languages. [#9236](https://github.com/JabRef/jabref/pull/9236), [#9243](https://github.com/JabRef/jabref/pull/9243)
+- The default file directory of a library is used as default directory for [unlinked file lookup](https://docs.jabref.org/collect/findunlinkedfiles#link-the-pdfs-to-your-bib-library). [koppor#546](https://github.com/koppor/jabref/issues/546)
 - JabRef UI theme now changes depending on OS system preferences [#9263](https://github.com/JabRef/jabref/pull/9263)
 
 ### Changed
 
+- We disabled the "change case" menu for empty fields [#9214](https://github.com/JabRef/jabref/issues/9214)
 - We disabled the conversion menu for empty fields [#9200](https://github.com/JabRef/jabref/issues/9200)
 - We upgraded to Lucene 9.4 for the fulltext search.
   Thus, the now created search index cannot be read from older versions of JabRef anylonger.
@@ -45,9 +47,19 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where a message about changed metadata would occur on saving although nothing changed. [#9159](https://github.com/JabRef/jabref/issues/9159)
 - When adding or editing a subgroup it is placed w.r.t. to alphabetical ordering rather than at the end. [koppor#577](https://github.com/koppor/jabref/issues/577)
 - We modified the Directory of Open Access Books (DOAB) fetcher so that it will now also fetch the ISBN when possible. [#8708](https://github.com/JabRef/jabref/issues/8708)
+- ArXiv fetcher now retrieves additional data from related DOIs (both ArXiv and user-assigned). [#9170](https://github.com/JabRef/jabref/pull/9170)
+- Groups context menu now shows appropriate options depending on number of subgroups. [koppor#579](https://github.com/koppor/jabref/issues/579)
+- We changed the color of found text from red to high-contrast colors (background: yellow; font color: purple). [koppor#552](https://github.com/koppor/jabref/issues/552)
+- We modified the "Delete file" dialog and add the full file path to the dialog text. The file path in the title was changed to file name only. [koppor#534](https://github.com/koppor/jabref/issues/534)
+- Download from URL now automatically fills with URL from clipboard. [koppor#535](https://github.com/koppor/jabref/issues/535)
+- We added HTML and Markdown files to Find Unlinked Files and removed BibTeX.[koppor#547](https://github.com/koppor/jabref/issues/547)
+- We changed the messages after importing unlinked local files to past tense. [koppor#548](https://github.com/koppor/jabref/issues/548)
+- We fixed an issue where the wrong icon for a successful import of a bib entry was shown [#9308](https://github.com/JabRef/jabref/pull/9308)
 
 ### Fixed
 
+- We fixed the readability of the file field in the dark dark theme [#9340](https://github.com/JabRef/jabref/issues/9340)
+- We fixed that sorting of entries in the maintable by special fields is updated immediately [#9334](https://github.com/JabRef/jabref/issues/9334)
 - We fixed the Cleanup entries dialog is partially visible [#9223](https://github.com/JabRef/jabref/issues/9223)
 - We fixed the display of the "Customize Entry Types" dialogue title [#9198](https://github.com/JabRef/jabref/issues/9198)
 - We fixed an issue where author names with tilde accents (for example ñ) were marked as "Names are not in the standard BibTex format" [#8071](https://github.com/JabRef/jabref/issues/8071)
@@ -58,6 +70,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed a performance regression when opening large libraries [#9041](https://github.com/JabRef/jabref/issues/9041)
 - We fixed a bug where spaces are trimmed when highlighting differences in the Entries merge dialog. [koppor#371](https://github.com/koppor/jabref/issues/371)
 - We fixed some visual glitches with the linked files editor field in the entry editor and increased its height. [#8823](https://github.com/JabRef/jabref/issues/8823)
+- We fixed some visual inconsistencies (round corners of highlighted buttons). [#8806](https://github.com/JabRef/jabref/issues/8806)
 - We fixed several bugs regarding the manual and the autosave of library files that sometimes lead to exceptions or data loss. [#9067](https://github.com/JabRef/jabref/pull/9067), [#8448](https://github.com/JabRef/jabref/issues/8484), [#8746](https://github.com/JabRef/jabref/issues/8746), [#6684](https://github.com/JabRef/jabref/issues/6684), [#6644](https://github.com/JabRef/jabref/issues/6644), [#6102](https://github.com/JabRef/jabref/issues/6102), [#6002](https://github.com/JabRef/jabref/issues/6000)
 - We fixed an issue where applied save actions on saving the library file would lead to the dialog "The library has been modified by another program" popping up [#4877](https://github.com/JabRef/jabref/issues/4877)
 - We fixed issues with save actions not correctly loaded when opening the library. [#9122](https://github.com/JabRef/jabref/pull/9122)
@@ -71,6 +84,11 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where an exception was not logged correctly. [koppor#627](https://github.com/JabRef/koppor/issues/627)
 - We fixed an issue where hitting enter on the search field within the preferences dialog closed the dialog. [koppor#630](https://github.com/koppor/jabref/issues/630)
 - We fixed a typo within a connection error message. [koppor#625](https://github.com/koppor/jabref/issues/625)
+- We fixed an issue where the 'close dialog' key binding was not closing the Preferences dialog. [#8888](https://github.com/jabref/jabref/issues/8888)
+- We fixed an issue where editing entry's "date" field in library mode "biblatex" causes an uncaught exception. [#8747][https://github.com/JabRef/jabref/issues/8747]
+- We fixed an issue where journal abbreviations would not abbreviate journal titles with escaped ampersands (\\&). [#8948](https://github.com/JabRef/jabref/issues/8948)
+- We fixed an issue where font size preferences did not apply correctly to preference dialog window and the menu bar. [#8386](https://github.com/JabRef/jabref/issues/8386) and [#9279](https://github.com/JabRef/jabref/issues/9279)
+- We fixed an issue when using an unsafe character in the citation key, the auto-linking feature fails to link files. [#9267](https://github.com/JabRef/jabref/issues/9267)
 
 ### Removed