I get the following exception when I copy the Red_And_Blue.java plugin included with ImageJ into Fiji.app/plugins and try to compile it in Fiji using Plugins>Compile and Run. Plugins>Compile and Run works as expected in ImageJ 1.49p.

ImageJ (Fiji Is Just) ImageJ 2.0.0-rc-24/1.49p; Java 1.8.0_25 [64-bit]; Mac OS X 10.10.1; 52MB of 6983MB (<1%)
 
java.lang.Exception: Could not compile /Applications/Fiji.app/plugins//Red_And_Blue.java:
/Applications/Fiji.app/plugins/Red_And_Blue.java:8: cannot access java.lang.Object
bad class file: ZipFileIndexFileObject[/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Object.class)]
class file has wrong version 52.0, should be 50.0
Please remove or make sure it appears in the correct subdirectory of the classpath.
public class Red_And_Blue implements PlugIn {
       ^

	at fiji.scripting.java.Refresh_Javas.compile(Refresh_Javas.java:369)
	at fiji.scripting.java.Refresh_Javas.compile(Refresh_Javas.java:320)
	at fiji.scripting.java.Refresh_Javas.compile(Refresh_Javas.java:313)
	at fiji.scripting.java.Refresh_Javas.compileAndRun(Refresh_Javas.java:105)
	at fiji.scripting.java.Refresh_Javas.runScript(Refresh_Javas.java:71)
	at common.RefreshScripts.run(RefreshScripts.java:287)
	at fiji.scripting.java.Refresh_Javas.run(Refresh_Javas.java:61)
	at ij.IJ.runUserPlugIn(IJ.java:199)
	at ij.IJ.runPlugIn(IJ.java:163)
	at ij.IJ.runPlugIn(IJ.java:152)
	at fiji.Compile_and_Run.run(Compile_and_Run.java:23)
	at ij.IJ.runUserPlugIn(IJ.java:199)
	at ij.IJ.runPlugIn(IJ.java:163)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:745)

I get this exception if I open Red_And_Blue.java in the Script Editor and try to compile and run by clicking on the "Run" button:

Started Red_And_Blue.java at Sun Mar 01 08:56:17 EST 2015
Compiling 1 file in /var/folders/sj/hs9p4kxn1z9brlkf83ycm4qr0000gn/T/java4446364991685643541
/var/folders/sj/hs9p4kxn1z9brlkf83ycm4qr0000gn/T/java4446364991685643541/src/main/java/Red_And_Blue.java:8: cannot access java.lang.Object
bad class file: ZipFileIndexFileObject[/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Object.class)]
class file has wrong version 52.0, should be 50.0
Please remove or make sure it appears in the correct subdirectory of the classpath.
public class Red_And_Blue implements PlugIn {
       ^
org.scijava.minimaven.JavaCompiler$CompileError: Compile error: 1
	at org.scijava.minimaven.JavaCompiler.call(JavaCompiler.java:80)
	at org.scijava.minimaven.MavenProject.build(MavenProject.java:477)
	at org.scijava.minimaven.MavenProject.build(MavenProject.java:406)
	at org.scijava.minimaven.MavenProject.build(MavenProject.java:391)
	at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:154)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:175)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)

To complement my initial posting. The message I get when I press the "Compile and Run" is:

' The "Compile and Run" command is not currently supported. We recommend using the Script Editor or an IDE such as Eclipse for plugin development. '

I apologize for my previous one line comment. Wayne, thanks for expanding the bug report.

All best,
Andrés

I updated Fiji and now also get the message

"The "Compile and Run" command is not currently supported. We recommend using the Script Editor or an IDE such as Eclipse for plugin development."

when I try to use the Plugins>Compile and Run Command. I am using Fiji 2.0.0-rc-25/1.49p and Java 1.8.0_25 [64-bit] on OS X 10.10.1.

When I open the "Red_And_Blue.java" file in the Script Editor and click "Run" I get this exception:

Started Red_And_Blue.java at Sun Mar 01 16:33:21 EST 2015
Compiling 1 file in /var/folders/sj/hs9p4kxn1z9brlkf83ycm4qr0000gn/T/java218593696282971329
/var/folders/sj/hs9p4kxn1z9brlkf83ycm4qr0000gn/T/java218593696282971329/src/main/java/Red_And_Blue.java:8: cannot access java.lang.Object
bad class file: ZipFileIndexFileObject[/Library/Java/JavaVirtualMachines/jdk1.8.0_25.jdk/Contents/Home/lib/ct.sym(META-INF/sym/rt.jar/java/lang/Object.class)]
class file has wrong version 52.0, should be 50.0
Please remove or make sure it appears in the correct subdirectory of the classpath.
public class Red_And_Blue implements PlugIn {
       ^
org.scijava.minimaven.JavaCompiler$CompileError: Compile error: 1
	at org.scijava.minimaven.JavaCompiler.call(JavaCompiler.java:80)
	at org.scijava.minimaven.MavenProject.build(MavenProject.java:477)
	at org.scijava.minimaven.MavenProject.build(MavenProject.java:406)
	at org.scijava.minimaven.MavenProject.build(MavenProject.java:391)
	at org.scijava.plugins.scripting.java.JavaEngine.eval(JavaEngine.java:154)
	at org.scijava.script.ScriptModule.run(ScriptModule.java:175)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
	at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)

We do not currently have the resources to make "Compile and Run" work as expected in ImageJ2. For those curious why, some related technical details can be seen here:

  https://github.com/imagej/ij1-patcher/issues/31#issuecomment-52185528

The "cannot access java.lang.Object bad class file" error is a different problem that is new to me. I filed an issue for it here:

  https://github.com/scijava/scripting-java/issues/7

When testing this myself, I received a different error, also new to me, which I filed at:

  https://github.com/scijava/scripting-java/issues/6

Even before these bugs cropped up, using Java in the Script Editor suffered from another very serious bug:

   https://github.com/scijava/scripting-java/issues/5

So I would definitely recommend using a dedicated tool such as Eclipse to develop one's ImageJ plugins. (The Script Editor is best for scripts and macros.)

Plugin authors should distribute their plugins using an update site (http://imagej.net/Update_Sites), or at least as a .jar or .class file, rather than as a .java file.

If you feel you have a compelling use case for the Compile and Run command that would justify the substantial amount of time required to make it work in ImageJ2, I invite you to start a discussion about it on the imagej-devel mailing list:

  http://imagej.net/Mailing_Lists