Fixed --save-prefs regression

Also removed deprecated Prefences.save() method.

Fix #6067

app/src/processing/app/Base.java

@@ -277,7 +277,9 @@ public class Base {
     // Save the preferences. For GUI mode, this happens in the quit
     // handler, but for other modes we should also make sure to save
     // them.
-    PreferencesData.save();
+    if (parser.isForceSavePrefs()) {
+      PreferencesData.save();
+    }
 
     if (parser.isInstallBoard()) {
       ContributionsIndexer indexer = new ContributionsIndexer(

app/src/processing/app/Preferences.java

@@ -75,11 +75,6 @@ public class Preferences {
 
   static final int GUI_SMALL = 6;
 
-  @Deprecated
-  protected static void save() {
-    PreferencesData.save();
-  }
-
   @Deprecated
   public static String get(String attribute) {
     return PreferencesData.get(attribute);

build/shared/revisions.txt

@@ -2,6 +2,7 @@ ARDUINO 1.8.2
 
 [ide]
 * Fix command line: works again with relative paths (regression)
+* Fix command line: "--save-prefs" works again (regression)
 * AVR toolchain has been updated with a tentative fix for the ld-returned-5-exit-status bug
 * Update arduino-builder to 1.3.25
   - avoid name clashing for libraries