I figured out what my issue was and I think the problem is specific to me and the nature of my application. Actually I should call it a self induced issue. Let me explain the nature of events.

1. I have been using eclipse to develop and have a local install of weblogic instance. My application needs coherence cache server and I have few other JVM parameters that I pass when starting the domain. Therefore I had added a line at the start of the $DOMAIN_HOME/bin/setDomainEnv.sh file like so

   JAVA_OPTIONS="- Dtangosol.coherence.distributed.localstorage=false -Dtangosol.coherence.wka=devmachine and blah blah blah

2. I switched to intellij and started working on this project and then configured the weblogic plugin and run configuration etc.

3. I noticed that intellij adds a JAVA_OPTIONS in the startup/connection tab in Run/Debug Configurations like so

4. However the JAVA_OPTIONS that was being passed by intellij was not being used by weblogic. I believe it was overridden with what was in the setDomainEnv.sh which is why I saw the following logs.

java version "1.6.0_65" Java(TM) SE Runtime Environment (build 1.6.0_65-b14-466.1-11M4716) Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-466.1, mixed mode) Starting WLS with line: /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/bin/java -client -Xms512m -Xmx512m -XX:MaxPermSize=256m -Dweblogic.Name=AdminServer -Djava.security.policy=/Users/dparupud/omw/oracle/middleware/weblogic_10.3.6/wlserver_10.3/server/lib/weblogic.policy -Dtangosol.coherence.distributed.localstorage=false -Dtangosol.coherence.wka=devmachine blah blah blah......

5. When I went and removed the JAVA_OPTIONS from setDomainEnv.sh and restarted the server from intellij I saw the following log

starting weblogic with Java version: java version "1.6.0_65" Java(TM) SE Runtime Environment (build 1.6.0_65-b14-466.1-11M4716) Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-466.1, mixed mode) Starting WLS with line: /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/bin/java -client -Xms512m -Xmx512m -XX:MaxPermSize=256m -Dweblogic.Name=AdminServer -Djava.security.policy=/Users/dparupud/omw/oracle/middleware/weblogic_10.3.6/wlserver_10.3/server/lib/weblogic.policy - agentlib:jdwp=transport=dt_socket,address=127.0.0.1:65501,suspend=y,server=n

Now the log showed that the jdwp agent was in action. I did notice that I did not see that particular log before I asked the Question on SO but I thought maybe IntelliJ was doing something inside the covers because JAVA_OPTIONS was being passed and intellij does not allow you to mess with that ( it is readonly).

I guess I can either pass all my jvm parameters either from intellij or add the jdwp agent info in the setDomainEnv.sh.

Now I am able to debug.

Confirm. Problem was that I try to debug using maven run configuration. Switching to Application configuration type helps. I've spend half of a day on it (

Did some searching through IntelliJ Help PDF:
Help Doc pg. 431

Their documentation Describes the checkmark as "Shown at run-time when the breakpoint is recognized by the debugger as set on an executable code line."

and the regular red dot as "Shown at design-time or during the debugging session when the class with such breakpoint is not yet loaded. "

So it would seem that the line you're adding the breaking point to never gets executed. You can try stepping up line by line through the class to make sure the class is not getting hung up somewhere.

Failed import of Maven project into IntelliJ

Something went wrong with the import of the Maven project into IntelliJ.

Try again.

1. Delete .idea and myapp.iml items from project folder.
2. Re-import Maven project into IntelliJ.
3. Build project.
   Perhaps context-click in the code editor and choose Recompile MyApp.java
4. Debug.
   Click the green-bug to debug, or context-click to choose Debug 'MyApp.main()'

Then debugger works as expected, stopping on breakpoints.

Tip: Before importing a Maven project, edit the POM to specify a Java version as the compiler source & target. If omitted you get Maven's default of compiling as Java 5 (1.5) code. Per the Maven page, Setting the -source and -target of the Java Compiler inject these four lines into your POM file, a pair of tags inside a properties tag.

Here we specify Java 8 (1.8) be used by the compiler.

<project>
  [...]
  <properties>
    <maven.compiler.source>1.8</maven.compiler.source>
    <maven.compiler.target>1.8</maven.compiler.target>
  </properties>
  [...]
</project>