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In your APEX application, have you tried updating the URL to include the parameter REMOTE, in order to initiate the remote debug connection? e.g.
Using the REMOTE parameter cuts out the need to specify debug code surrounding statements in the APEX PL/SQL.
The steps are as follows:
1) In SQL Developer, set break points in the the PL/SQL code, and compile using the "Compile for debug" option
2) Execute the following two grants
5) In SQL Developer, right-click on your connection and select the "Remote Debug..." context menu item. This will launch the "Listen for JPDA" dialog.
grant DEBUG CONNECT SESSION to <PARSE USER>; grant debug on <PROC> to public; <-- might not need public but just whoever the DAD is running as.
5) Run the APEX Application page containing/activating the code you wish to debug, and update its URL with REMOTE in the debug parameter of the URL, and then hit Enter.
6) Carry out the action on the page to trigger the breakpoint in your code e.g. submit the page, or click a button on the page, and you should be redirected to the breakpoint in the code in SQL Developer.
Although I'm running with the latest release of SQL Developer, version 3.2.2 (http://www.oracle.com/technetwork/developer-tools/sql-developer/downloads/index.html), and APEX 4.2, the 'REMOTE' parameter was introduced with our 3.1 release so will also be available for you to use in 4.1.