Merge remote-tracking branch 'upstream/main' into improve-DOI-import-…

…failure-dialog

* upstream/main: (76 commits)
  New Crowdin updates (#8972)
  New Crowdin updates (#8969)
  Fix .bat errorlevel handling with pwsh.exe check (#8965)
  revert jsoup version upgrade
  Fix charset detection with utf16 and others (#8947)
  Bump classgraph from 4.8.147 to 4.8.149 (#8968)
  Bump jsoup from 1.15.1 to 1.15.2 (#8967)
  Keep UTF-8 encoding header if present (#8964)
  Cleanup index when opening a library (#8962)
  Refactor context menu entry types changing (#8957)
  Improvement on check for missing commas when importing or opening a .bib file (#8840)
  Disable ResearchGateTest on CI (#8955)
  Bump checkstyle from 10.1 to 10.3.1 (#8950)
  Bump checkstyle from 10.1 to 10.3.1 (#8950)
  Bump mariadb-java-client from 2.7.5 to 2.7.6 (#8953)
  Add notification when adding previous entries to new group configuration (#8919)
  Remember Sidepane width after restart (#8936)
  move "Warn about duplicates on import" preferences option (#8937)
  Fix theme switching exception (#8939)
  fix merge conflict
  ...

# Conflicts:
#	src/main/resources/l10n/JabRef_en.properties

.github/workflows/automerge.yml

@@ -21,7 +21,7 @@ jobs:
         with:
           github-token: "${{ secrets.GITHUB_TOKEN }}"
       - name: Merge pull requests
-        uses: pascalgn/automerge-action@v0.15.2
+        uses: pascalgn/automerge-action@v0.15.3
         if: steps.waitforstatuschecks.outputs.status == 'success'
         env:
           MERGE_METHOD: "merge"

.github/workflows/tests.yml

@@ -37,9 +37,10 @@ jobs:
       - 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: '10.1'
+          checkstyle_version: '10.3'
       - name: Run checkstyle gradle
         run: ./gradlew checkstyleMain checkstyleTest checkstyleJmh
       - name: Run markdown-lint

.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

CHANGELOG.md

@@ -13,27 +13,51 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 - We added a fetcher for [Biodiversity Heritage Library](https://www.biodiversitylibrary.org/). [8539](https://github.com/JabRef/jabref/issues/8539)
 - We added support for multiple messages in the snackbar. [#7340](https://github.com/JabRef/jabref/issues/7340)
+- We added an extra option in the 'Find Unlinked Files' dialog view to ignore unnecessary files like Thumbs.db, DS_Store, etc. [koppor#373](https://github.com/koppor/jabref/issues/373)
 - JabRef now writes log files. Linux: `$home/.cache/jabref/logs/version`, Windows: `%APPDATA%\..\Local\harawata\jabref\version\logs`, Mac: `Users/.../Library/Logs/jabref/version`
+- We added an importer for Citavi backup files, support ".ctv5bak" and ".ctv6bak" file formats. [#8322](https://github.com/JabRef/jabref/issues/8322)
 
 ### Changed
 
+- The file column in the main table now shows the corresponding defined icon for the linked file [8930](https://github.com/JabRef/jabref/issues/8930).
+- We improved the color of the selected entries and the color of the summary in the Import Entries Dialog in the dark theme. [#7927](https://github.com/JabRef/jabref/issues/7927)
+- We upgraded to Lucene 9.2 for the fulltext search.
+  Thus, the now created search index cannot be read from older versions of JabRef anylonger.
+  ⚠️ JabRef will recreate the index in a new folder for new files and this will take a long time for a huge library.
+  Moreover, switching back and forth JabRef versions and meanwhile adding PDFs also requires rebuilding the index now and then.
+  [#8868](https://github.com/JabRef/jabref/pull/8868)
 - We improved the Latex2Unicode conversion [#8639](https://github.com/JabRef/jabref/pull/8639)
 - Writing BibTeX data into a PDF (XMP) removes braces. [#8452](https://github.com/JabRef/jabref/issues/8452)
 - Writing BibTeX data into a PDF (XMP) does not write the `file` field.
 - Writing BibTeX data into a PDF (XMP) considers the configured keyword separator (and does not use "," as default any more)
 - The Medline/Pubmed search now also supports the [default fields and operators for searching](https://docs.jabref.org/collect/import-using-online-bibliographic-database#search-syntax). [forum#3554](https://discourse.jabref.org/t/native-pubmed-search/3354)
 - We improved group expansion arrow that prevent it from activating group when expanding or collapsing. [#7982](https://github.com/JabRef/jabref/issues/7982), [#3176](https://github.com/JabRef/jabref/issues/3176)
+- When configured SSL certificates changed, JabRef warns the user to restart to apply the configuration.
+- We improved the appearances and logic of the "Manage field names & content" dialog, and renamed it to "Automatic field editor". [#6536](https://github.com/JabRef/jabref/issues/6536)
+- We improved the message explaining the options when modifying an automatic keyword group [#8911](https://github.com/JabRef/jabref/issues/8911)
+- We moved the preferences option "Warn about duplicates on import" option from the tab "File" to the tab "Import and Export". [koppor#570](https://github.com/koppor/jabref/issues/570)
+- When JabRef encounters `% Encoding: UTF-8` header, it is kept during writing (and not removed). [#8964](https://github.com/JabRef/jabref/pull/8964)
+- We replace characters which cannot be decoded using the specified encoding by a (probably another) valid character. This happens if JabRef detects the wrong charset (e.g., UTF-8 instead of Windows 1252). One can use the [Integrity Check](https://docs.jabref.org/finding-sorting-and-cleaning-entries/checkintegrity) to find those characters.
 
 ### Fixed
 
+- We fixed an issue that caused JabRef to sometimes open multiple instances when "Remote Operation" is enabled. [#8653](https://github.com/JabRef/jabref/issues/8653)
+- We fixed an issue where linked files with the filetype "application/pdf" in an entry were not shown with the correct PDF-Icon in the main table [8930](https://github.com/JabRef/jabref/issues/8930)
+- We fixed an issue where "open folder" for linked files did not open the folder and did not select the file unter certain Linux desktop environments [#8679](https://github.com/JabRef/jabref/issues/8679), [#8849](https://github.com/JabRef/jabref/issues/8849)
 - We fixed an issue where the content of a big shared database library is not shown [#8788](https://github.com/JabRef/jabref/issues/8788)
 - We fixed the unnecessary horizontal scroll bar in group panel [#8467](https://github.com/JabRef/jabref/issues/8467)
 - We fixed an issue where the notification bar message, icon and actions appeared to be invisible. [#8761](https://github.com/JabRef/jabref/issues/8761)
 - We fixed an issue where deprecated fields tab is shown when the fields don't contain any values. [#8396](https://github.com/JabRef/jabref/issues/8396)
-- We fixed an issue where an exxception for DOI search occured when the DOI contained urlencoded characters. [#8787](https://github.com/JabRef/jabref/issues/8787)
+- We fixed an issue where an exception for DOI search occurred when the DOI contained urlencoded characters. [#8787](https://github.com/JabRef/jabref/issues/8787)
 - We fixed an issue which allow us to select and open identifiers from a popup list in the maintable [#8758](https://github.com/JabRef/jabref/issues/8758), [8802](https://github.com/JabRef/jabref/issues/8802)
 - We fixed an issue where the escape button had no functionality within the "Filter groups" textfield. [koppor#562](https://github.com/koppor/jabref/issues/562)
-- We fixed an issue where right clicking a group and choose "remove selected entries from this group" leads to error when Bibtex source tab is selected. [#8012](https://github.com/JabRef/jabref/issues/8012)
+- We fixed an issue where the exception that there are invalid characters in filename. [#8786](https://github.com/JabRef/jabref/issues/8786)
+- When the proxy configuration removed the proxy user/password, this change is applied immediately.
+- We fixed an issue where removing several groups deletes only one of them. [#8390](https://github.com/JabRef/jabref/issues/8390)
+- We fixed an issue where the Sidepane (groups, web search and open office) width is not remembered after restarting JabRef. [#8907](https://github.com/JabRef/jabref/issues/8907)
+- We fixed a bug where switching between themes will cause an error/exception. [#8939](https://github.com/JabRef/jabref/pull/8939)
+- We fixed a bug where files that were deleted in the source bibtex file were kept in the index. [#8962](https://github.com/JabRef/jabref/pull/8962)
+- We fixed "Error while sending to JabRef" when the browser extension interacts with JabRef. [JabRef-Browser-Extension#479](https://github.com/JabRef/JabRef-Browser-Extension/issues/479)
 
 ### Removed
 
@@ -65,7 +89,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 ### Changed
 
 - We upgraded to Lucene 9.1 for the fulltext search.
-  Thus, the now created search index cannot be read from older versions of JabRef anylonger.
+  Thus, the now created search index cannot be read from older versions of JabRef any longer.
   ⚠️ JabRef will recreate the index in a new folder for new files and this will take a long time for a huge library.
   Moreover, switching back and forth JabRef versions and meanwhile adding PDFs also requires rebuilding the index now and then.
   [#8362](https://github.com/JabRef/jabref/pull/8362)
@@ -92,7 +116,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where "Copy DOI url" in the right-click menu of the Entry List would just copy the DOI and not the DOI url. [#8389](https://github.com/JabRef/jabref/issues/8389)
 - We fixed an issue where opening the console from the drop-down menu would cause an exception. [#8466](https://github.com/JabRef/jabref/issues/8466)
 - We fixed an issue when reading non-UTF-8 encoded. When no encoding header is present, the encoding is now detected from the file content (and the preference option is disregarded). [#8417](https://github.com/JabRef/jabref/issues/8417)
-- We fixed an issue where pasting a URL was replacing + signs by spaces making the URL unreachable. [#8448](https://github.com/JabRef/jabref/issues/8448)
+- We fixed an issue where pasting a URL was replacing `+` signs by spaces making the URL unreachable. [#8448](https://github.com/JabRef/jabref/issues/8448)
 - We fixed an issue where creating subsidiary files from aux files created with some versions of biblatex would produce incorrect results. [#8513](https://github.com/JabRef/jabref/issues/8513)
 - We fixed an issue where opening the changelog from withing JabRef led to a 404 error. [#8563](https://github.com/JabRef/jabref/issues/8563)
 - We fixed an issue where not all found unlinked local files were imported correctly due to some race condition. [#8444](https://github.com/JabRef/jabref/issues/8444)
@@ -101,6 +125,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where no citationkey was generated on import, pasting a doi or an entry on the main table. [8406](https://github.com/JabRef/jabref/issues/8406), [koppor#553](https://github.com/koppor/jabref/issues/553)
 - We fixed an issue where accent search does not perform consistently. [#6815](https://github.com/JabRef/jabref/issues/6815)
 - We fixed an issue where the incorrect entry was selected when "New Article" is pressed while search filters are active. [#8674](https://github.com/JabRef/jabref/issues/8674)
+- We fixed an issue where "Write BibTeXEntry metadata to PDF" button remains enabled while writing to PDF is in-progress. [#8691](https://github.com/JabRef/jabref/issues/8691)
 
 ### Removed
 

README.md

@@ -71,7 +71,7 @@ An explanation of donation possibilities and usage of donations is available at
 [![OpenHub](https://www.openhub.net/p/jabref/widgets/project_thin_badge.gif)](https://www.openhub.net/p/jabref)
 [![Deployment Status](https://github.com/JabRef/jabref/workflows/Deployment/badge.svg)](https://github.com/JabRef/jabref/actions?query=workflow%3ADeployment)
 [![Test Status](https://github.com/JabRef/jabref/workflows/Tests/badge.svg)](https://github.com/JabRef/jabref/actions?query=workflow%3ATests)
-[![codecov.io](https://codecov.io/github/JabRef/jabref/coverage.svg?branch=master)](https://codecov.io/github/JabRef/jabref?branch=master)
+[![codecov.io](https://codecov.io/github/JabRef/jabref/coverage.svg?branch=master)](https://codecov.io/github/JabRef/jabref?branch=main)
 
 Want to be part of a free and open-source project that tens of thousands of scientists use every day?
 Check out the ways you can contribute, below:
@@ -84,7 +84,7 @@ Check out the ways you can contribute, below:
 
 We view pull requests as a collaborative process.
 Submit a pull request early to get feedback from the team on work in progress.
-We will discuss improvements with you and agree to merge them once the [developers](https://github.com/JabRef/jabref/blob/main/MAINTAINERS) approve.
+We will discuss improvements with you and agree to merge them once the [developers](https://github.com/JabRef/jabref/blob/main/MAINTAINERS) approve. Please also remember to discuss bigger changes early with the core developers to avoid a waste of time and work. Some fundamental design decisions can be found within our list of [Architectural Decision Records](https://devdocs.jabref.org/adr.html).
 
 If you want a step-by-step walk-through on how to set-up your workspace, please check [this guideline](https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace).