Add the folloing to your product.conf:
AddVMOption -Xdebug
AddVMoption -Xrunjdwp:transport=dt_socket,address=8998,server=y,suspend=n
See user.conf property in the Properties tab of SQL Developer's About dialog for the exact location of your product.conf file.
The option suspend=y would suspend SQL Developer during startup until the debugger connects. You do not want this, unless when debugging the startup process itself. suspend=n will allow to start SQL Developer normally. The debugger can connect and disconnect antime while SQL Developer is running. This is much more convenient and leads to less misunderstandings, because e.g. the SQL Developer does not seem to start because it is waiting for a debugging session.
See JDPA Connection and Invocation Details for more information about the -Xrunjdwp option.
Add the following debug configuration for your extension project. The port number has to match the one entered in product.conf.
Start SQL Developer.
Set a breakpoint in your Java code and start the previously configured Debug Configuration.
The debuger will suspend the process when it reaches a breakpoint.
Disconnect from SQL Developer after debugging.
Stop the SQL Developer in the normal way. Do not press the Terminate button in the debugger to avoid data loss.
Delete or comment out the two previously added AddVMOption entries.
However, if you debug frequently, it is more convenient to keep SQL Developer ready for incoming debugging connections.