Q:

how to define step definitions location for cucumber in intelliJ 12

I have my feature files in src/resources/com/features and my step definitions in src/main/java/com/step_definitions
My tests all run correctly, but intelliJ refuses to see where the step defs are, even if I ask it to create a new one.  Where is this configured?

A:

I was just tearing my hair out with exactly the same problem (for the record my background is Java, Ruby, Cucumber and RubyMine but I'm completely new to IntelliJ and Cucumber-JVM).
In the Cucumber-JVM run configuration you must specify the package where the step definitions are stored in the glue field as mentioned in the IntelliJ documentation. IntelliJ - for me at least - does not seem to provide a default value.
To elaborate further, a very basic project looks like this:
Example
└───src
    ├───main
    │   └───java
    └───test
        ├───java
        │   └───com
        │       └───bensnape
        │           └───example
        │                   MyStepdefs.java
        └───resources
                example.feature

The glue value here would be com.bensnape.example.
Update
After playing with IntelliJ some more this morning, it seems that it does provide the glue value for you if you adhere to the Cucumber-JVM conventions - i.e. the features must live under src/test/resources/<package> and similarly, the steps must live under src/test/java/<package>.
Example project tree:
Example
└───src
    ├───main
    │   └───java
    └───test
        ├───java
        │   └───com
        │       └───bensnape
        │           └───example
        │                   MyStepdefs.java
        │
        └───resources
            └───com
                └───bensnape
                    └───example
                            example.feature

A:

If you mark the folder as a (test) source root (right click folder -> Mark directory as -> (Test) Source Root) it will work as well.
My grails project is set up like this:
        test
        ├───cucumber
        │   └───steps
        │   └───support
        │   └───features
        └───unit

Unit was marked as test source root, after also marking cucumber as one the step definitions were parsed correctly.

A:

The default convention is to have step definitions defined in a step_definitions sub-folder under the features directory. The name of the sub-folder isn't important; it will work the same whatever the name is. 
My guess is that an IDE would follow the same convention, and hence IntelliJ should execute the features correctly if the step_definitions folder is moved under features folder. 
The cucumber command takes a -r option to require files before executing the features. This option can be used to make it look for step_definitions in a non-conventional place. 
I am guessing you may have -r src/main/java/com/step_definitions on your local configuration for cucumber to see these step_definitions when invoked from commandline. 
Running cucumber --verbose shows where the command line is finding the step definition code.   

