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

* upstream/master:
  Add preference migration for keybdingings (#3007)
  Shutdown previus AutosaveManager and BackupManager during SaveAs  (#2994)
  Run Checkstyle task after Test task (#3010)
  Mark LibraryOfCongressTest as a fetcher test (#3012)
  When browsing through the MainTable remember which EntryEditor tab was open (#3011)
  Improve performance of journal abbreviation loader (#3009)
  Update checkstyle 7.6.1 -> 8.0
  Don't abort build when there are checkstyle violations (#3006)
  Reimplement content selectors (#3003)
  Only do a back up for bigger changes or if a different field is edited (#3004)
  Listen to change events for setting dirty status of database (#3001)
  Fix #2967: MathSciNet tab works again
  Fix #2902: Tab in entry editor moves to next text area
  Fix #2946: external changes are now correctly shown in the entry editor
  Fix #2998: improve auto completion (#3002)
  Fix mac keybinding by replacing ctrl it with meta key (#3000)
  Less backups (#2995)
  [WIP] Complete rework of the auto completion (#2965)

CHANGELOG.md

@@ -21,6 +21,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
   - The buttons were changed to icons.
   - Completely new interface to add or modify linked files.
   - Removed the hidden feature that a double click in the editor inserted the current date.
+  - Complete new implementation of the the auto complete feature.
 - All authors and editors are separated using semicolons when exporting to csv. [#2762](https://github.com/JabRef/jabref/issues/2762)
 - Improved wording of "Show recommendations: into "Show 'Related Articles' tab" in the preferences
 - We added integration of the Library of Congress catalog as a fetcher based on the [LCCN identifier](https://en.wikipedia.org/wiki/Library_of_Congress_Control_Number). [Feature request 636 in the forum](http://discourse.jabref.org/t/loc-marc-mods-connection/636)
@@ -29,6 +30,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We improved the duplicate checker such that different editions of the same publication are not marked as duplicates. [2960](https://github.com/JabRef/jabref/issues/2960)
 
 ### Fixed
+- We fixed a bug that leaves .sav file after SaveAs [#2947](https://github.com/JabRef/jabref/issues/2947)
 - We fixed the function "Edit - Copy BibTeX key and link" to pass a hyperlink rather than an HTML statement.
 - We fixed the adding of a new entry from DOI which led to a connection error. The DOI resolution now uses HTTPS to protect the user's privacy.[#2879](https://github.com/JabRef/jabref/issues/2897)
 - We fixed the IEEE Xplore web search functionality [#2789](https://github.com/JabRef/jabref/issues/2789)
@@ -42,7 +44,8 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - We fixed a bug where recursive RegExpBased search found a file in a subdirectory multiple times and non-recursive RegExpBased search erroneously found files in subdirectories.
 - We fixed a bug where new groups information was not stored on save [#2932](https://github.com/JabRef/jabref/issues/2932)
 - We fixed a bug where the language files for Brazilian Portugese could not be loaded and the GUI localization remained in English [#1128](https://github.com/JabRef/jabref/issues/1182)
-
+- We fixed a bug where the database was not marked as dirty when entries or groups were changed [#2787](https://github.com/JabRef/jabref/issues/2787)
+- We restored the original functionality that when browsing through the MainTable, the Entry Editor remembers which tab was opened before [#2896](https://github.com/JabRef/jabref/issues/2896)
 ### Removed
 
 

build.gradle

@@ -398,9 +398,12 @@ task media(type: com.install4j.gradle.Install4jTask, dependsOn: "releaseJar") {
 checkstyle {
     // do not use other packages for checkstyle, excluding gen(erated) sources
     checkstyleMain.source = "src/main/java"
-    toolVersion = '7.6.1'
+    toolVersion = '8.0'
 }
 
+checkstyleMain.shouldRunAfter test
+checkstyleTest.shouldRunAfter test
+
 task release(dependsOn: ["media", "releaseJar"]) {
     group = 'JabRef - Release'
     description 'Creates a release for all target platforms.'

src/main/java/org/jabref/JabRefMain.java

@@ -76,6 +76,7 @@ private static void start(String[] args) {
         PreferencesMigrations.upgradeFaultyEncodingStrings();
         PreferencesMigrations.upgradeLabelPatternToBibtexKeyPattern();
         PreferencesMigrations.upgradeStoredCustomEntryTypes();
+        PreferencesMigrations.upgradeKeyBindingsToJavaFX();
 
         // Update handling of special fields based on preferences
         InternalBibtexFields

src/main/java/org/jabref/collab/FileUpdateMonitor.java

@@ -20,9 +20,19 @@ public class FileUpdateMonitor implements Runnable {
     private static final Log LOGGER = LogFactory.getLog(FileUpdateMonitor.class);
 
     private static final int WAIT = 4000;
-
-    private int numberOfUpdateListener;
     private final Map<String, Entry> entries = new HashMap<>();
+    private int numberOfUpdateListener;
+
+    private static synchronized Path getTempFile() {
+        Path temporaryFile = null;
+        try {
+            temporaryFile = Files.createTempFile("jabref", null);
+            temporaryFile.toFile().deleteOnExit();
+        } catch (IOException ex) {
+            LOGGER.warn("Could not create temporary file.", ex);
+        }
+        return temporaryFile;
+    }
 
     @Override
     public void run() {
@@ -119,7 +129,7 @@ public void updateTimeStamp(String key) {
      * is used for comparison with the changed on-disk version.
      * @param key String The handle for this monitor.
      * @throws IllegalArgumentException If the handle doesn't correspond to an entry.
-     * @return File The temporary file.
+     * @return Path The temporary file.
      */
     public Path getTempFile(String key) throws IllegalArgumentException {
         Entry entry = entries.get(key);
@@ -129,7 +139,6 @@ public Path getTempFile(String key) throws IllegalArgumentException {
         return entry.getTmpFile();
     }
 
-
     /**
      * A class containing the File, the FileUpdateListener and the current time stamp for one file.
      */
@@ -209,15 +218,4 @@ public void decreaseTimeStamp() {
             timeStamp--;
         }
     }
-
-    private static synchronized Path getTempFile() {
-        Path temporaryFile = null;
-        try {
-            temporaryFile = Files.createTempFile("jabref", null);
-            temporaryFile.toFile().deleteOnExit();
-        } catch (IOException ex) {
-            LOGGER.warn("Could not create temporary file.", ex);
-        }
-        return temporaryFile;
-    }
 }