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

* upstream/master: (583 commits)
  update jfoenix and gradle plugins Replace outdated transformer log4j2 with official new one
  Update journalList.txt
  Fix for Issue #4437 - Some bugs in preference->Entry table columns (#4546)
  Don't set column sort type at startup (#4577)
  Add uncaught exception message (#4565)
  Converts integrity check dialog to JavaFX (#4559)
  Do not extract file ending from Urls (#4547)
  Bump checkstyle from 8.15 to 8.16 (#4562)
  Bump xmpbox from 2.0.12 to 2.0.13 (#4561)
  Delete the deprecated BibEntry Constructor (#4560)
  Refactor BibEntry deprecated method (#4554)
  Added extra stats to be sent with MrDLib recommendations (#4452)
  improve styling of preferences side menu (#4556)
  Cleanup interfaces (#4553)
  Bump fontbox from 2.0.12 to 2.0.13 (#4552)
  Bump pdfbox from 2.0.12 to 2.0.13 (#4551)
  Bump wiremock from 2.19.0 to 2.20.0 (#4550)
  Fixes that renaming a group did not change the group name in the interface (#4549)
  Bump applicationinsights-logging-log4j2 from 2.2.1 to 2.3.0 (#4540)
  Bump antlr4-runtime from 4.7.1 to 4.7.2 (#4542)
  ...

# Conflicts:
#	src/main/java/org/jabref/gui/JabRefFrame.java
#	src/main/java/org/jabref/model/entry/BibtexString.java

.circleci/config.yml

@@ -0,0 +1,85 @@
+version: 2
+
+jobs:
+  downloadinstall4j:
+    docker:
+      - image: circleci/openjdk:8-jdk
+    steps:
+      - checkout
+      - run: git submodule sync
+      - run: git submodule update --init
+      - restore_cache:
+          keys:
+            - install4j-{{ checksum "scripts/extract-install4j.sh" }}
+      - run: scripts/download-install4j-and-jres.sh
+      - save_cache:
+          key: install4j-{{ checksum "scripts/extract-install4j.sh" }}
+          paths:
+            - "~/downloads"
+            - "~/.install4j7"
+    filters:
+      tags:
+        only: /.*/
+
+  buildDev:
+    docker:
+      - image: circleci/openjdk:8-jdk
+    steps:
+      - restore_cache:
+          key: dependency-cache
+      - checkout
+      - run: git submodule sync
+      - run: git submodule update --init
+      - restore_cache:
+          key: install4j-{{ checksum "scripts/extract-install4j.sh" }}
+      - run: scripts/extract-install4j.sh
+      - run: install4j7/bin/install4jc --verbose --license=$INSTALL4J_KEY
+      - run: ./gradlew -Pdev=true -Pinstall4jDir="install4j7" release --stacktrace
+      - save_cache:
+          key: dependency-cache
+          paths:
+            - "~/.gradle"
+      - store_artifacts:
+          path: build/releases
+          destination: build
+      - run: scripts/upload-to-builds.jabref.org.sh
+
+  buildRelease:
+    docker:
+      - image: circleci/openjdk:8-jdk
+    steps:
+      - restore_cache:
+          key: dependency-cache
+      - checkout
+      - run: git submodule sync
+      - run: git submodule update --init
+      - restore_cache:
+          key: install4j-{{ checksum "scripts/extract-install4j.sh" }}
+      - run: scripts/extract-install4j.sh
+      - run: install4j7/bin/install4jc --verbose --license=$INSTALL4J_KEY
+      - run: ./gradlew -Pinstall4jDir="install4j7" release --stacktrace
+      - store_artifacts:
+          path: build/releases
+          destination: release
+      - run: scripts/upload-to-builds.jabref.org.sh
+    filters:
+      tags:
+        only: /.*/
+
+workflows:
+  version: 2
+  build:
+    jobs:
+      - downloadinstall4j
+      - buildDev:
+          requires:
+            - downloadinstall4j
+      - buildRelease:
+          requires:
+            - downloadinstall4j
+          filters:
+            branches:
+              ignore: /.*/
+            tags:
+              only: /.*/
+

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,40 @@
+---
+name: Bug report
+about: Create a report to help us improve
+
+---
+
+<!-- 
+Note: Please use the GitHub issue tracker only for bug reports. 
+Feature requests, questions and general feedback is now handled at http://discourse.jabref.org.
+Thanks! 
+--> 
+
+JabRef version <!-- version as shown in the about box --> on <!-- Windows 10|Ubuntu 14.04|Mac OS X 10.8|... -->
+
+<!-- IMPORTANT NOTE ->
+<!-- 
+      Please always test if the bug is still reproducible in the latest development version.
+      We are constantly improving JabRef and some bugs may already be fixed.
+      You can download the development version at: http://builds.jabref.org/master/
+      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
+
+<!-- Add a clear and concise description of what the bug is. -->
+
+Steps to reproduce the behavior:
+1. ...
+2. ...
+3. ...
+
+<!-- If applicable, add excerpt of the bibliography file, screenshot, and excerpt of log (available in the error console) -->
+
+<details>
+  <summary>Log File</summary>
+
+  ```
+  Paste an excerpt of your log file here
+  ```
+</details>

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,9 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+
+---
+
+Please use the GitHub issue tracker only for bug reports and suggestions for improvements.
+Feature requests, questions and general feedback is now handled at http://discourse.jabref.org.
+Thanks!

.github/ISSUE_TEMPLATE/question.md

@@ -0,0 +1,9 @@
+---
+name: Question
+about: Ask a question about JabRef
+
+---
+
+Please use the GitHub issue tracker only for bug reports and suggestions for improvements.
+Feature requests, questions and general feedback is now handled at http://discourse.jabref.org.
+Thanks!

.github/ISSUE_TEMPLATE/suggestion-for-improvement.md

@@ -0,0 +1,20 @@
+---
+name: Suggestion for improvement
+about: Suggest an enhancement
+
+---
+
+<!--
+Please use the GitHub issue tracker only for bug reports and smaller suggestions for improvements.
+Requests for completely new features, questions and general feedback is now handled at http://discourse.jabref.org.
+Thanks!
+-->
+
+**Is your suggestion for improvement related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.gitmodules

@@ -0,0 +1,6 @@
+[submodule "src/main/resources/csl-styles"]
+	path = src/main/resources/csl-styles
+	url = https://github.com/citation-style-language/styles.git
+[submodule "src/main/resources/csl-locales"]
+	path = src/main/resources/csl-locales
+	url = https://github.com/citation-style-language/locales.git

.mailmap

@@ -117,7 +117,7 @@ Daniel Mair <[email protected]> <[email protected]>
 Sven Jäger <[email protected]>
 Tim van Rossum <[email protected]>
 Saulius Gražulis <[email protected]>
-Rolf Starre <[email protected]> <[email protected]>
+Rolf Starre <[email protected]>
 Owen Huang <[email protected]>
 Anita Armbruster <[email protected]>
 Fabian Bauer <[email protected]>
@@ -140,3 +140,6 @@ Mattia Bunel <[email protected]>
 Waida Fan <[email protected]>
 Johannes Manner <[email protected]>
 Dominik Traczyk <[email protected]>
+Cerrianne Santos <[email protected]>
+Stefan Scheffel <[email protected]>
+Stefan Gerzmann <[email protected]>

.travis.yml

@@ -17,8 +17,8 @@ env:
   global:
     - GRADLE_OPTS=-Dorg.gradle.daemon=false
   matrix:
-    - TEST_SUITE=checkstyle
     - TEST_SUITE=check OPTIONS=modernizer
+    - TEST_SUITE=checkstyle
     - TEST_SUITE=fetcherTest
     - TEST_SUITE=databaseTest
     - TEST_SUITE=guiTest
@@ -47,10 +47,10 @@ before_script:
 script:
   # --scan enables the Gradle build scan, which can be used to investigate the time each action consumes
   # For more information see https://gradle.com/scans/get-started
-  - if [ "$TEST_SUITE" != "guiTest" ] && [ "$TEST_SUITE" != "checkstyle" ] && [ "$TEST_SUITE" != "codecov" ]; then ./gradlew $TEST_SUITE $OPTIONS --scan; fi
+  - if [ "$TEST_SUITE" != "guiTest" ] && [ "$TEST_SUITE" != "checkstyle" ] && [ "$TEST_SUITE" != "codecov" ]; then ./gradlew $TEST_SUITE $OPTIONS -x checkstyleJmh -x checkstyleMain -x checkstyleTest --scan; fi
   - if [ "$TEST_SUITE" == "checkstyle" ]; then ./gradlew checkstyleMain checkstyleTest checkstyleJmh; fi
   - if [ "$TEST_SUITE" == "guiTest" ]; then ./buildres/gui-tests.sh; fi
-  - if [ "$TEST_SUITE" == "codecov" ]; then ./gradlew jacocoJunit5TestReport; bash <(curl -s https://codecov.io/bash); fi
+  - if [ "$TEST_SUITE" == "codecov" ]; then ./gradlew jacocoTestReport; bash <(curl -s https://codecov.io/bash); fi
   - if [ "$DEPENDENCY_UPDATES" == "check" ]; then ./gradlew -q checkOutdatedDependencies; fi
 
 after_failure:
@@ -71,3 +71,4 @@ cache:
   directories:
     - $HOME/.gradle/caches/
     - $HOME/.gradle/wrapper/
+

AUTHORS

@@ -11,7 +11,9 @@ Alex Montgomery
 Alexis Gallagher
 Alexsandro Lauber
 Ali Ayan
+Alick Zhao
 Ambrogio Oliva
+Amish Shah
 Andreas Amann
 Andreas Buhr
 Andreas Rudert
@@ -29,8 +31,8 @@ Bernd Kalbfuss
 Bernhard Tempel
 Brian Quistorff
 Brian Van Essen
-captain123
 Carlos Silla
+Cerrianne Santos
 Christian Bartsch
 Christian Kopf
 Christoph Braun
@@ -67,11 +69,11 @@ Felix Berger
 Felix Langner
 Felix Wilke
 Fernando Santagata
+Florian Beetz
 Florian Straßer
 Foivos Christoulakis
 Francois Charette
 Frank Steimle
-Fred
 Frédéric Darboux
 Gert Renckens
 Gregor Herrmann
@@ -128,9 +130,7 @@ Mathias Walter
 Matthias Geiger
 Mattia Bunel
 Mattias Ulbrich
-mcmoody
 Meltem Demirköprü
-Michael
 Michael Beckmann
 Michael Falkenthal
 Michael Lass
@@ -145,18 +145,15 @@ Nadeem Mahmood
 Nathan Dunn
 Nathan Sheffield
 Nicolas Pavillon
-nikmilpv
 Niv Ierushalmi
 Nizar N. Batada
-noravanq
 Olaf Lenz
 Oliver Beckmann
 Oliver Kopp
 Oscar Gustafsson
 Owen Huang
 Patrick Scheibe
 Paul Martin
-payload
 Peter Ansell
 Philip Johnson
 Predrag Milanovic
@@ -181,16 +178,15 @@ Seb Wills
 Shitikanth
 Simon Harrer
 Simon Rutishauser
-speed9
 Stefan Feyer
+Stefan Gerzmann
 Stefan Kolb
 Stefan Robert
 Stefano Gariazzo
 Stephan Lau
 Stephan Rave
 Stéphane Curet
 Sven Jäger
-The Gitter Badger
 Thiago Toledo
 Thomas Arildsen
 Thomas Ilsche
@@ -201,10 +197,7 @@ Tobias Boceck
 Tobias Bouschen
 Tobias Denkinger
 Tobias Diez
-tokkot
-Tony K
 Toralf Senger
-uid112001
 Ulrich Stärk
 Ulrik Stervbo
 Uwe Kuehn
@@ -213,9 +206,7 @@ Waida Fan
 Waluyo Adi Siswanto
 Ward Poelmans
 Wenbo Yang
-wuw
 Yang Zongze
 Yara Grassi Gouffon
 Yifan Peng
-zacmks
 Zhang Liang