Merge remote-tracking branch 'upstream/master' into jdk9

* upstream/master: (229 commits)
  Try to fix not on FX thread for search and autocomplete (#4618)
  Convert DuplicateResolverDialog to javafx (#4601)
  Fix for BibTex source tab parsing issue if field contains {} (#4581)
  Convert OO/LO SidePanel to javafx (#4341)
  Convert "Customize importer" dialog to JavaFX (#4608)
  Convert "From Aux file" dialog to JavaFX (#4607)
  Convert "Show preferences" dialog to JavaFX (#4605)
  Fix not on FX thread exception
  Force javafx to run thread (#4604)
  Convert new version dialog to JavaFX (#4602)
  Add a variable to track the change in preview style (#4587)
  Solution for submitting dialog with Ctrl + Enter (#4496) (#4592)
  Bump mysql-connector-java from 8.0.13 to 8.0.14 (#4599)
  Fix overlapping font in id entry type (#4595)
  update jfoenix and gradle plugins Replace outdated transformer log4j2 with official new one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)
  ...

# Conflicts:
#	build.gradle
#	src/main/java/org/jabref/gui/FindUnlinkedFilesDialog.java
#	src/main/java/org/jabref/gui/JabRefFrame.java
#	src/main/java/org/jabref/gui/fieldeditors/EditorTextArea.java
#	src/main/java/org/jabref/gui/fieldeditors/EditorTextField.java
#	src/main/java/org/jabref/gui/openoffice/CitationManager.java
#	src/main/java/org/jabref/gui/openoffice/OOBibBase.java
#	src/main/java/org/jabref/gui/openoffice/OpenOfficePanel.java
#	src/main/java/org/jabref/gui/openoffice/OpenOfficeSidePanel.java

Author: Siedlerchr

.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.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/bug_report.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/feature_request.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/question.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.

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

@@ -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

.gitmodules

@@ -48,7 +48,7 @@ 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 jacocoTestReport; bash <(curl -s https://codecov.io/bash); fi
@@ -72,3 +72,4 @@ cache:
   directories:
     - $HOME/.gradle/caches/
     - $HOME/.gradle/wrapper/
+

.travis.yml

@@ -13,6 +13,7 @@ Alexsandro Lauber
 Ali Ayan
 Alick Zhao
 Ambrogio Oliva
+Amish Shah
 Andreas Amann
 Andreas Buhr
 Andreas Rudert

AUTHORS

@@ -11,8 +11,19 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- We changed the location of some fields in the entry editor (you might need to reset your preferences for these changes to come into effect)
+  - Journal/Year/Month in biblatex mode -> Deprecated (if filled)
+  - DOI/URL: General -> Optional
+  - Internal fields like ranking, read status and priority: Other -> General
+  - Moreover, empty deprecated fields are no longer shown
+- Added server timezone parameter when connecting to a shared database.
+- We updated the dialog for setting up general fields.
+- URL field formatting is updated. All whitespace chars, located at the beginning/ending of the url, are trimmed automatically
+- We changed the behavior of the field formatting dialog such that the `bibtexkey` is not changed when formatting all fields or all text fields.
 - We added a "Move file to file directory and rename file" option for simultaneously moving and renaming of document file. [#4166](https://github.com/JabRef/jabref/issues/4166)
 - Use integrated graphics card instead of discrete on macOS [#4070](https://github.com/JabRef/jabref/issues/4070)
+- We added a cleanup operation that detects an arXiv identifier in the note, journal or url field and moves it to the `eprint` field.
+  Because of this change, the last-used cleanup operations were reset.
 - We changed the minimum required version of Java to 1.8.0_171, as this is the latest release for which the automatic Java update works.  [4093](https://github.com/JabRef/jabref/issues/4093)
 - The special fields like `Printed` and `Read status` now show gray icons when the row is hovered.
 - We added a button in the tab header which allows you to close the database with one click. https://github.com/JabRef/jabref/issues/494
@@ -25,14 +36,27 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We changed the default keyboard shortcuts for moving between entries when the entry editor is active to ̀<kbd>alt</kbd> + <kbd>up/down</kbd>.
 - Opening a new file now prompts the directory of the currently selected file, instead of the directory of the last opened file.
 - Window state is saved on close and restored on start.
+- We made the MathSciNet fetcher more reliable.
+- We added the ISBN fetcher to the list of fetcher available under "Update with bibliographic information from the web" in the entry editor toolbar.
+- Files without a defined external file type are now directly opened with the default application of the operating system
 - We streamlined the process to rename and move files by removing the confirmation dialogs.
-
-
+- We removed the redundant new lines of markings and wrapped the summary in the File annotation tab. [#3823](https://github.com/JabRef/jabref/issues/3823)
+- We add auto url formatting when user paste link to URL field in entry editor. [koppor#254](https://github.com/koppor/jabref/issues/254)
+- We added a minimal height for the entry editor so that it can no longer be hidden by accident. [#4279](https://github.com/JabRef/jabref/issues/4279)
+- We added a new keyboard shortcut so that the entry editor could be closed by <kbd>Ctrl</kbd> + <kbd>E</kbd>. [#4222] (https://github.com/JabRef/jabref/issues/4222)
+- We added an option in the preference dialog box, that allows user to pick the dark or light theme option. [#4130] (https://github.com/JabRef/jabref/issues/4130)
+- We updated updated the Related Articles tab to accept JSON from the new version of the Mr. DLib service
+- We added an option in the preference dialog box that allows user to choose behavior after dragging and dropping files in Entry Editor. [#4356](https://github.com/JabRef/jabref/issues/4356)
+- We added the ability to have an export preference where previously "File"-->"Export"/"Export selected entries" would not save the user's preference[#4495](https://github.com/JabRef/jabref/issues/4495)
+- We added the ability to add field names from the Preferences Dialog [#4546](https://github.com/JabRef/jabref/issues/4546)
+- We added the ability change the column widths directly in the main table. [#4546](https://github.com/JabRef/jabref/issues/4546)
+- We added the ability to execute default action in dialog by using with <kbd>Ctrl</kbd> + <kbd>Enter</kbd> combination [#4496](https://github.com/JabRef/jabref/issues/4496)
 
 
 
 
 ### Fixed
+- We fixed an issue where corresponding groups are sometimes not highlighted when clicking on entries [#3112](https://github.com/JabRef/jabref/issues/3112)
 - We fixed an issue where custom exports could not be selected in the 'Export (selected) entries' dialog [#4013](https://github.com/JabRef/jabref/issues/4013)
 - Italic text is now rendered correctly. https://github.com/JabRef/jabref/issues/3356
 - The entry editor no longer gets corrupted after using the source tab. https://github.com/JabRef/jabref/issues/3532 https://github.com/JabRef/jabref/issues/3608 https://github.com/JabRef/jabref/issues/3616
@@ -47,9 +71,12 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the custom file column were sorted incorrectly. https://github.com/JabRef/jabref/issues/3119
 - We fixed an issues where the entry losses focus when a field is edited and at the same time used for sorting. https://github.com/JabRef/jabref/issues/3373
 - We fixed an issue where the menu on Mac OS was not displayed in the usual Mac-specific way. https://github.com/JabRef/jabref/issues/3146
+- We improved the integrity check for page numbers. [#4113](https://github.com/JabRef/jabref/issues/4113) and [feature request in the forum](http://discourse.jabref.org/t/pages-field-allow-use-of-en-dash/1199)
 - We fixed an issue where the order of fields in customized entry types was not saved correctly. [#4033](http://github.com/JabRef/jabref/issues/4033)
+- We fixed an issue where renaming a group did not change the group name in the interface. [#3189](https://github.com/JabRef/jabref/issues/3189)
 - We fixed an issue where the groups tree of the last database was still shown even after the database was already closed.
 - We fixed an issue where the "Open file dialog" may disappear behind other windows. https://github.com/JabRef/jabref/issues/3410
+- We fixed an issue where the number of entries matched was not updated correctly upon adding or removing an entry. [#3537](https://github.com/JabRef/jabref/issues/3537)
 - We fixed an issue where the default icon of a group was not colored correctly.
 - We fixed an issue where the first field in entry editor was not focused when adding a new entry. [#4024](https://github.com/JabRef/jabref/issues/4024)
 - We reworked the "Edit file" dialog to make it resizeable and improved the workflow for adding and editing files https://github.com/JabRef/jabref/issues/2970
@@ -58,12 +85,14 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed an issue where the "Convert to BibTeX-Cleanup" moved the content of the `file` field to the `pdf` field [#4120](https://github.com/JabRef/jabref/issues/4120)
 - We fixed an issue where the preview pane in entry preview in preferences wasn't showing the citation style selected [#3849](https://github.com/JabRef/jabref/issues/3849)
 - We fixed an issue where the default entry preview style still contained the field `review`. The field `review` in the style is now replaced with comment to be consistent with the entry editor [#4098](https://github.com/JabRef/jabref/issues/4098)
-
-
-
-
-
-
+- We fixed an issue where users were vulnerable to XXE attacks during parsing [#4229](https://github.com/JabRef/jabref/issues/4229)
+- We fixed an issue where files added via the "Attach file" contextmenu of an entry were not made relative. [#4201](https://github.com/JabRef/jabref/issues/4201) and [#4241](https://github.com/JabRef/jabref/issues/4241)
+- We fixed an issue where author list parser can't generate bibtex for Chinese author. [#4169](https://github.com/JabRef/jabref/issues/4169)
+- We fixed an issue where the list of XMP Exclusion fields in the preferences was not be saved [#4072](https://github.com/JabRef/jabref/issues/4072)
+- We fixed an issue where the ArXiv Fetcher did not support HTTP URLs [koppor#328](https://github.com/koppor/jabref/issues/328)
+- We fixed an issue where only one PDF file could be imported [#4422](https://github.com/JabRef/jabref/issues/4422)
+- We fixed an issue where "Move to group" would always move the first entry in the library and not the selected [#4414](https://github.com/JabRef/jabref/issues/4414)
+- We fixed an issue where an older dialog appears when downloading full texts from the quality menu. [#4489](https://github.com/JabRef/jabref/issues/4489)
 
 
 
@@ -79,6 +108,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
   - Set/clear/append/rename fields: available through Edit menu
   - Manage keywords: available through Edit menu
   - Copy linked files to folder: available through File menu
+- We removed the option to change the column widths in the preferences dialog. [#4546](https://github.com/JabRef/jabref/issues/4546)
 
 
 
@@ -111,9 +141,9 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 
 ## Older versions
 
-The changelog of JabRef 4.x is available at the [v4.x branch](https://github.com/JabRef/jabref/blob/v4.x/CHANGELOG.md).  
-The changelog of JabRef 3.x is available at the [v3.8.2 tag](https://github.com/JabRef/jabref/blob/v3.8.2/CHANGELOG.md).  
-The changelog of JabRef 2.11 and all previous versions is available as [text file in the v2.11.1 tag](https://github.com/JabRef/jabref/blob/v2.11.1/CHANGELOG).  
+The changelog of JabRef 4.x is available at the [v4.x branch](https://github.com/JabRef/jabref/blob/v4.x/CHANGELOG.md).
+The changelog of JabRef 3.x is available at the [v3.8.2 tag](https://github.com/JabRef/jabref/blob/v3.8.2/CHANGELOG.md).
+The changelog of JabRef 2.11 and all previous versions is available as [text file in the v2.11.1 tag](https://github.com/JabRef/jabref/blob/v2.11.1/CHANGELOG).
 
 [Unreleased]: https://github.com/JabRef/jabref/compare/v4.3...HEAD
 [4.3]: https://github.com/JabRef/jabref/compare/v4.2...v4.3
@@ -125,3 +155,4 @@ The changelog of JabRef 2.11 and all previous versions is available as [text fil
 [4.0-beta]: https://github.com/JabRef/jabref/compare/v3.8.2...v4.0-beta
 [2.11.1]: https://github.com/JabRef/jabref/compare/v2.11...v2.11.1
 [JavaFX]: https://en.wikipedia.org/wiki/JavaFX
+