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

# By dependabot-preview[bot] (18) and others
# Via GitHub (17) and others
* upstream/master: (77 commits)
  Reenable caching of gradle
  Refactor BibtexKeyPatternPreferences (#6489)
  Update CHANGELOG.md
  Add changelog entry and remove unnecessary code
  EasyBind revision part two
  Fix Drag and Drop on empty database
  Truncates DOIs and URLs in the column "Linked identifiers" in main table, if too long (#6498)
  Bump flexmark-ext-gfm-tasklist from 0.61.26 to 0.61.30
  Bump flexmark from 0.61.26 to 0.61.30
  Bump xmlunit-matchers from 2.6.4 to 2.7.0
  Bump java-string-similarity from 1.2.1 to 2.0.0
  Bump flexmark-ext-gfm-strikethrough from 0.61.26 to 0.61.30
  Bump xmlunit-core from 2.6.4 to 2.7.0
  Truncates the link and/or the link description in the column "linked files" in main table, if too long (#6179)
  Keep group pane size when resizing window (#6180) (#6423)
  Changelog: Fix missing citation for biblatex-mla
  Update AUTHORS
  Check duplicate DOI (#6333)
  Fix missing citation for biblatex-mla
  Change EasyBind dependency (#6480)
  ...

# Conflicts:
#	src/main/java/org/jabref/gui/actions/ActionHelper.java
#	src/main/java/org/jabref/gui/customentrytypes/CustomEntryTypeDialogViewModel.java
#	src/main/java/org/jabref/gui/customentrytypes/CustomizeEntryTypeDialogView.java
#	src/main/java/org/jabref/model/entry/field/FieldFactory.java

.editorconfig

@@ -5,3 +5,6 @@ charset = utf-8
 indent_style = space
 insert_final_newline = true
 trim_trailing_whitespace = true
+
+[*.md]
+trim_trailing_whitespace = false

.github/ISSUE_TEMPLATE/bug_report.md

@@ -20,7 +20,7 @@ JabRef version <!-- version as shown in the about box --> on <!-- Windows 10|Ubu
       Please make a backup of your library before you try out this version.
       If you already use a development version, ensure that you use the latest one.
  -->
-- [ ] I have tested the latest development version from http://builds.jabref.org/master/ and the problem persists
+- [ ] **Mandatory**: I have tested the latest development version from http://builds.jabref.org/master/ and the problem persists
 
 <!-- Add a clear and concise description of what the bug is. -->
 

.github/outdatedDependencies.md

@@ -1,5 +1,5 @@
 ---
 title: Outdated dependencies
-labels: t: dependencies
+labels: type: dependencies
 ---
 [There are outdated dependencies!](https://github.com/JabRef/jabref/actions?query=is%3Afailure+workflow%3A%22Check+dependencies%22) 

.github/workflows/deployment.yml

@@ -54,6 +54,13 @@ jobs:
         uses: actions/setup-java@v1
         with:
           java-version: 14
+      - name: Restore gradle cache
+        uses: actions/cache@master
+        with:
+          path: ~/.gradle/caches
+          key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle*') }}
+          restore-keys: |
+            ${{ runner.os }}-gradle-
       - name: Build runtime image
         run: ./gradlew -PprojVersion="${{ steps.gitversion.outputs.AssemblySemVer }}" -PprojVersionInfo="${{ steps.gitversion.outputs.InformationalVersion }}" jlinkZip
       - name: Build installer

.gitignore

@@ -2,6 +2,9 @@
 src/main/gen/
 src/main/generated/
 
+# the journal list cache
+*.mv
+
 # private data
 /buildres/jabref-cert-2016.p12
 

.mailmap

@@ -193,3 +193,10 @@ Christoph Treude <ctreude@gmail.com>
 Goutam Lavudiya <gtam25@gmail.com>
 Shikun Xiong <53288073+ShikunXiong@users.noreply.github.com>
 Fabiani Giovanni <fabiani.giovanni@gmail.com>
+Dimitra Karadima <44123133+dimitra-karadima@users.noreply.github.com>
+Dimitra Karadima <44123133+dimitra-karadima@users.noreply.github.com> <t8170038@aueb.gr>
+Cai Zhichun <54977532+braincident@users.noreply.github.com>
+Gennadiy Stakhovskiy <GennadiyStakhovskiy@gmail.com>
+Mootez Saad <34676841+MootezSaaD@users.noreply.github.com>
+Mootez Saad <34676841+MootezSaaD@users.noreply.github.com> <mootez.saad@medtech.tn>
+Chen Yuheng <pass@chenyuheng.cn>

AUTHORS

@@ -41,6 +41,7 @@ Ayachi Nene
 Bartosz J. Kaczkowski
 Bartłomiej Dach
 Behrouz Javanmardi
+Benedikt Tutzer
 Benjamin Köhler
 Berk Gureken
 Bernd Kalbfuss
@@ -51,15 +52,18 @@ Bherwani Ayush
 Bitor Tonixa Biriato Balença
 Brian Quistorff
 Brian Van Essen
+Cai Zhichun
 captain123
 Carl Christian Snethlage
 carlg0ransson
 Carlos Morales
 Carlos Silla
 Carlos Silva
+Catarina Gomes
 Cerrianne Santos
 Chamod Shehanka
 Chelsey Ong
+Chen Yuheng
 Chris Brown
 Christian Bartsch
 Christian Kopf
@@ -88,6 +92,7 @@ Dennis Tschechlov
 DevSiroukane
 Dilan Coss
 dima
+Dimitra Karadima
 Domenico Cufalo
 Dominik Schrempf
 Dominik Traczyk
@@ -126,15 +131,20 @@ frasca80
 Fred Stevens
 Frédéric Darboux
 Galileo Sartor
+Gennadiy Stakhovskiy
 Geoffrey Taerim Kim
 Gert Renckens
 Goutam Lavudiya
 Gregor Herrmann
+Grzegorz Popiel
 guenesaydin
 Guillaume Gardey
 Hakan Duran
 Hannes Restel
 Harinda Samarasekara
+HifeFish
+hrandrianasolo
+Hussain Arif
 Igor Chernyavsky
 Igor Steinmacher
 Illes Solt
@@ -146,6 +156,7 @@ Jan Schäfer
 Janosch Kutscherauer
 Jason Pickering
 Javier Muñoz Ferrara
+jcampbell11245
 Jeff Kerr
 Jeff Miller
 Jeffrey Kuhn
@@ -158,6 +169,7 @@ John David
 John Relph
 John Zedlewski
 Jonas Lähnemann
+Jonas Moosmann
 Jonathan Powell
 Jong-Ho Shinn
 Jorge Tornero
@@ -173,6 +185,7 @@ Jörg Wegner
 Jörg Zieren
 Jørgen Kvalsvik
 Jürgen Lange
+k3KAW8Pnf7mkmdSMPHz27
 Kai Mindermann
 Kai Takac
 Kaique Komata
@@ -213,6 +226,7 @@ Martin Stolle
 Martina Catizone
 Mathias Walter
 Matthias Geiger
+Matthias Mayr
 Matthias Mueller
 Mattia Bunel
 Mattias Ulbrich
@@ -232,6 +246,7 @@ Michel Krämer
 Mihu
 Mike Smoot
 mohamean
+Mootez Saad
 Morgan Lovato
 Moritz Ringler
 Morten Alver
@@ -312,6 +327,7 @@ Stanley Foerster
 Stefan Feyer
 Stefan Gerzmann
 Stefan Kolb
+Stefan Kufer
 Stefan Robert
 Stefan Scheffel
 Stefano Gariazzo
@@ -360,6 +376,7 @@ Yara Grassi Gouffon
 Yash Kothari
 Yichen Sun
 Yifan Peng
+Yunsheng Luo
 Yurick Honda
 zacmks
 Zeabin

CHANGELOG.md

@@ -11,12 +11,19 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Added
 
+- We added a new field in the preferences in 'BibTeX key generator' for unwanted characters that can be user-specified. [#6295](https://github.com/JabRef/jabref/issues/6295)
 - We added support for searching ShortScience for an entry through the user's browser. [#6018](https://github.com/JabRef/jabref/pull/6018)
 - We updated EditionChecker to permit edition to start with a number. [#6144](https://github.com/JabRef/jabref/issues/6144)
 - We added tooltips for most fields in the entry editor containing a short description. [#5847](https://github.com/JabRef/jabref/issues/5847)
 - We added support for basic markdown in custom formatted previews [#6194](https://github.com/JabRef/jabref/issues/6194)
 - We now show the number of items found and selected to import in the online search dialog. [#6248](https://github.com/JabRef/jabref/pull/6248)
 - We created a new install screen for macOS. [#5759](https://github.com/JabRef/jabref/issues/5759)
+- We added a new integrity check for duplicate DOIs. [koppor#339](https://github.com/koppor/jabref/issues/339)
+- We implemented an option to download fulltext files while importing. [#6381](https://github.com/JabRef/jabref/pull/6381)
+- We added a progress-indicator showing the average progress of background tasks to the toolbar. Clicking it reveals a pop-over with a list of running background tasks. [6443](https://github.com/JabRef/jabref/pull/6443)
+- We fixed the bug when strike the delete key in the text field. [#6421](https://github.com/JabRef/jabref/issues/6421)
+- We added a BibTex key modifier for truncating strings. [#3915](https://github.com/JabRef/jabref/issues/3915)
+- We added support for jumping to target entry when typing letter/digit after sorting a column in maintable [#6146](https://github.com/JabRef/jabref/issues/6146)
 
 ### Changed
 
@@ -26,16 +33,23 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We changed the buttons for import/export/show all/reset of preferences to smaller icon buttons in the preferences dialog. [#6130](https://github.com/JabRef/jabref/pull/6130)
 - We moved the functionality "Manage field names & content" from the "Library" menu to the "Edit" menu, because it affects the selected entries and not the whole library
 - We merged the functionality "Append contents from a BibTeX library into the currently viewed library" into the "Import into database" functionality. Fixes [#6049](https://github.com/JabRef/jabref/issues/6049).
+- We changed the directory where fulltext downloads are stored to the directory set in the import-tab in preferences. [#6381](https://github.com/JabRef/jabref/pull/6381)
 - We improved the error message for invalid jstyles. [#6303](https://github.com/JabRef/jabref/issues/6303)
+- We changed the section name of 'Advanced' to 'Network' in the preferences and removed some obsolete options.[#6489](https://github.com/JabRef/jabref/pull/6489)
+- We improved the context menu of the column "Linked identifiers" of the main table, by truncating their texts, if they are too long. [#6499](https://github.com/JabRef/jabref/issues/6499)
 
 ### Fixed
 
 - We fixed wrong button order (Apply and Cancel) in ManageProtectedTermsDialog.
+- We fixed an issue with incompatible characters at BibTeX key [#6257](https://github.com/JabRef/jabref/issues/6257)
+- We fixed an issue where dash (`-`) was reported as illegal BibTeX key [#6295](https://github.com/JabRef/jabref/issues/6295)
 - We greatly improved the performance of the overall application and many operations. [#5071](https://github.com/JabRef/jabref/issues/5071)
 - We fixed an issue where sort by priority was broken. [#6222](https://github.com/JabRef/jabref/issues/6222)
 - We fixed an issue where opening a library from the recent libraries menu was not possible. [#5939](https://github.com/JabRef/jabref/issues/5939)
 - We fixed an issue with inconsistent capitalization of file extensions when downloading files. [#6115](https://github.com/JabRef/jabref/issues/6115)
 - We fixed the display of language and encoding in the preferences dialog. [#6130](https://github.com/JabRef/jabref/pull/6130)
+- Now the link and/or the link description in the column "linked files" of the main table gets truncated or wrapped, if too long, otherwise display issues arise. [#6178](https://github.com/JabRef/jabref/issues/6178)
+- We fixed the issue that groups panel does not keep size when resizing window. [#6180](https://github.com/JabRef/jabref/issues/6180)
 - We fixed an error that sometimes occurred when using the context menu. [#6085](https://github.com/JabRef/jabref/issues/6085)
 - We fixed an issue where search full-text documents downloaded files with same name, overwriting existing files. [#6174](https://github.com/JabRef/jabref/pull/6174)
 - We fixed an issue when importing into current library an erroneous message "import cancelled" is displayed even though import is successful. [#6266](https://github.com/JabRef/jabref/issues/6266)
@@ -45,12 +59,22 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed the display of icon both in the main table and linked file editor. [#6169](https://github.com/JabRef/jabref/issues/6169)
 - We fixed the paste entry command in the menu and toolbar, that did not do anything. [#6293](https://github.com/JabRef/jabref/issues/6293)
 - We fixed an issue where the windows installer did not create an entry in the start menu [bug report in the forum](https://discourse.jabref.org/t/error-while-fetching-from-doi/2018/3)
+- We fixed an issue where only the field `abstract` and `comment` were declared as multiline fields. Other fields can now be configured in the preferences using "Do not wrap the following fields when saving" [4373](https://github.com/JabRef/jabref/issues/4373)
 - We fixed an issue where JabRef switched to discrete graphics under macOS [#5935](https://github.com/JabRef/jabref/issues/5935)
 - We fixed an issue where the Preferences entry preview will be unexpected modified leads to Value too long exception [#6198](https://github.com/JabRef/jabref/issues/6198)
 - We fixed an issue where custom jstyles for Open/LibreOffice would only be valid if a layout line for the entry type `default` was at the end of the layout section [#6303](https://github.com/JabRef/jabref/issues/6303)
+- We fixed an issue where long directory names created from patterns could create an exception. [#3915](https://github.com/JabRef/jabref/issues/3915)
+- We fixed an issue where sort on numeric cases was broken. [#6349](https://github.com/JabRef/jabref/issues/6349)
+- We fixed an issue where year and month fields were not cleared when converting to biblatex [#6224](https://github.com/JabRef/jabref/issues/6224)
+- We fixed an issue where an "Not on FX thread" exception occured when saving on linux [#6453](https://github.com/JabRef/jabref/issues/6453)
+- We fixed an issue where the library sort order was lost. [#6091](https://github.com/JabRef/jabref/issues/6091)
+- We fixed an issue where brackets in regular expressions were not working. [6469](https://github.com/JabRef/jabref/pull/6469)
+- We fixed an issue where LaTeX citations for specific commands (\autocites) of biblatex-mla were not recognized. [#6476](https://github.com/JabRef/jabref/issues/6476)
+- We fixed an issue where drag and drop was not working on empty database. [#6487](https://github.com/JabRef/jabref/issues/6487)
 
 ### Removed
 
+- We removed the option of the "enforce legal key". [#6295](https://github.com/JabRef/jabref/issues/6295)
 - We removed the obsolete `External programs / Open PDF` section in the preferences, as the default application to open PDFs is now set in the `Manage external file types` dialog. [#6130](https://github.com/JabRef/jabref/pull/6130)
 - We removed the option to configure whether a `.bib.bak` file should be generated upon save. It is now always enabled. Documentation at <https://docs.jabref.org/general/autosave>. [#6092](https://github.com/JabRef/jabref/issues/6092)
 - We removed the built-in list of IEEE journal abbreviations using BibTeX strings. If you still want to use them, you have to download them separately from <https://abbrv.jabref.org>.
@@ -102,7 +126,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where adding the addition of a new entry was not completely validated [#6370](https://github.com/JabRef/jabref/issues/6370)
 - We fixed an issue where the blue and red text colors in the Merge entries dialog were not quite visible [#6334](https://github.com/JabRef/jabref/issues/6334)
 - We fixed an issue where underscore character was removed from the file name in the Recent Libraries list in File menu [#6383](https://github.com/JabRef/jabref/issues/6383)
-
+- We fixed an issue where few keyboard shortcuts regarding new entries were missing [#6403](https://github.com/JabRef/jabref/issues/6403)
 ### Removed
 
 - Ampersands are no longer escaped by default in the `bib` file. If you want to keep the current behaviour, you can use the new "Escape Ampersands" formatter as a save action. [#5869](https://github.com/JabRef/jabref/issues/5869)

README.md

@@ -1,11 +1,5 @@
 # JabRef Bibliography Management
 
-[![Deployment Status](https://github.com/JabRef/jabref/workflows/Deployment/badge.svg)](https://github.com/JabRef/jabref/actions?query=workflow%3ADeployment)
-[![Build 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)
-[![Paypal Donate](https://img.shields.io/badge/donate-paypal-00457c.svg?logo=paypal&style=flat-square)](https://paypal.me/JabRef)
-[![Crowdin](https://d322cqt584bo4o.cloudfront.net/jabref/localized.svg)](https://crowdin.com/project/jabref)
-
 JabRef is an open-source, cross-platform citation and reference management tool.
 
 Stay on top of your literature: JabRef helps you to collect and organize sources, find the paper you need and discover the latest research.
@@ -62,6 +56,7 @@ The [latest stable release is available at FossHub](https://www.fosshub.com/JabR
 ## Bug Reports, Suggestions, Other Feedback
 
 [![Donation](https://img.shields.io/badge/donate%20to-jabref-orange.svg)](https://donations.jabref.org)
+[![Paypal Donate](https://img.shields.io/badge/donate-paypal-00457c.svg?logo=paypal&style=flat-square)](https://paypal.me/JabRef)
 
 We are thankful for any bug reports or other feedback.
 If you have ideas for new features you want to be included in JabRef, [tell us in our forum](http://discourse.jabref.org/c/features)!
@@ -72,14 +67,19 @@ An explanation of donation possibilities and usage of donations is available at
 
 ## Contributing
 
+[![dev-docs](https://img.shields.io/badge/dev-docs-blue)](https://devdocs.jabref.org/)
 [![Help Contribute to Open Source](https://www.codetriage.com/jabref/jabref/badges/users.svg)](https://www.codetriage.com/jabref/jabref)
 [![Join the chat at https://gitter.im/JabRef/jabref](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/JabRef/jabref?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
 [![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)
 
-> Not a programmer? [Learn how to help.](https://contribute.jabref.org)
-
-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:
+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:
 
+- Not a programmer? Help translating JabRef at [Crowdin](https://crowdin.com/project/jabref) or learn how to help at [contribute.jabref.org](https://contribute.jabref.org)
+- Quick overview on the architecture needed? Look at our [high-level documentation](https://devdocs.jabref.org/getting-into-the-code/high-level-documentation)
 - For details on how to contribute, have a look at our [guidelines for contributing](CONTRIBUTING.md).
 - You are welcome to contribute new features. To get your code included into JabRef, just [fork](https://help.github.com/en/articles/fork-a-repo) the JabRef repository, make your changes, and create a [pull request](https://help.github.com/en/articles/about-pull-requests).
 - To work on existing JabRef issues, check out our [issue tracker](https://github.com/JabRef/jabref/issues). New to open source contributing? Look for issues with the ["good first issue"](https://github.com/JabRef/jabref/labels/good%20first%20issue) label to get started.
@@ -98,8 +98,8 @@ For IntelliJ IDEA, just import the project via a Gradle Import by pointing at th
 
 `gradlew test` executes all tests. We use [Github Actions](https://github.com/JabRef/jabref/actions) for executing the tests after each commit. For developing, it is sufficient to locally only run the associated test for the classes you changed. Github will report any other failure.
 
-  [BibTeX]: https://www.ctan.org/pkg/bibtex
-  [Biblatex]: https://www.ctan.org/pkg/biblatex
-  [install4j]: https://www.ej-technologies.com/products/install4j/overview.html
-  [JabRef]: https://www.jabref.org
-  [JavaFX]: https://en.wikipedia.org/wiki/JavaFX
+[BibTeX]: https://www.ctan.org/pkg/bibtex
+[Biblatex]: https://www.ctan.org/pkg/biblatex
+[install4j]: https://www.ej-technologies.com/products/install4j/overview.html
+[JabRef]: https://www.jabref.org
+[JavaFX]: https://en.wikipedia.org/wiki/JavaFX