The following fails under GNU/Linux:
gradle -PBUILD_JAVADOC=true -PCOMPILE_WEBKIT=true all

      [jar] Building jar: /home/bothner/JWebPane/jfx/deploy/javafx-deploy-samples/dist/mediaplayer.jar
      [jar] adding directory META-INF/
      [jar] adding entry META-INF/MANIFEST.MF
      [jar] adding directory mediaplayer/
      [jar] adding entry mediaplayer/PlayerApp.class
      [jar] No Implementation-Title set.No Implementation-Version set.No Implementation-Vendor set.
      [jar] Location: /home/bothner/JWebPane/jfx/deploy/javafx-deploy-samples/build.xml:166:
      [ant] Exiting /home/bothner/JWebPane/jfx/deploy/javafx-deploy-samples/build.xml.
      [ant] Exiting /home/bothner/JWebPane/jfx/deploy/build.xml.
  [antcall] Exiting /home/bothner/JWebPane/jfx/build.xml.

BUILD FAILED
/home/bothner/JWebPane/jfx/build-src/build-components.xml:338: The following error occurred while executing this line:
/home/bothner/JWebPane/jfx/build-src/build-components.xml:220: The following error occurred while executing this line:
/home/bothner/JWebPane/jfx/build/xml_generated/build-deploy.xml:71: The following error occurred while executing this line:
/home/bothner/JWebPane/jfx/build-src/build-components.xml:77: The following error occurred while executing this line:
/home/bothner/JWebPane/jfx/deploy/build.xml:281: The following error occurred while executing this line:
/home/bothner/JWebPane/jfx/deploy/javafx-deploy-samples/build.xml:171: Error: Failed to create jar file dist/mediaplayer.jar
        at com.sun.javafx.tools.ant.FXJar.execute(FXJar.java:154)
Caused by: com.sun.javafx.tools.packager.PackagerException: Error: Failed to create jar file dist/mediaplayer.jar
        at com.sun.javafx.tools.packager.PackagerLib.packageAsJar(PackagerLib.java:326)
        at com.sun.javafx.tools.ant.FXJar.execute(FXJar.java:152)
        ... 81 more
Caused by: java.io.FileNotFoundException: /tmp/tempcopy6433419252498180291.jar (No such file or directory)
        at java.util.zip.ZipFile.open(Native Method)
        at java.util.zip.ZipFile.<init>(ZipFile.java:220)
        at java.util.zip.ZipFile.<init>(ZipFile.java:150)
        at java.util.jar.JarFile.<init>(JarFile.java:160)
        at java.util.jar.JarFile.<init>(JarFile.java:124)
        at com.sun.javafx.tools.packager.PackagerLib.copyFromOtherJar(PackagerLib.java:1458)
        at com.sun.javafx.tools.packager.PackagerLib.jar(PackagerLib.java:1400)
        at com.sun.javafx.tools.packager.PackagerLib.packageAsJar(PackagerLib.java:322)
        ... 82 more

Total time: 15 seconds
:appsLinux FAILED

The failure is because of a bug in
modules/fxpackager/src/main/java/com/sun/javafx/tools/packager/PackagerLib.java
The problem is line 28:
    jarToUpdate.renameTo(newInputJar);
This will typically fail under Unix-like systems, because newInputJar is in the /tmp filesystem, while jarToUpdate may be on some other file-system, such as /home.

The fix is to use java.nio.file.Files#move. Patch follows.