Graham Jones has a page describing how to set up BEAST2 development in IntelliJ.

Kylie Chen wrote a more recent guide.

Setting up a beast2 project in Intellij

The source code can be cloned from Github using ’git clone https://github.com/CompEvol/beast2.git and set up as a project in Intellij, named beast2.

• Menu: File => Import Project.. (NOT New Project…)
• Choose the “beast2” folder where the source code is cloned, and click “OK”
• Keep the default setting “Create project from existing sources” and click “Next”
• Accept name, location, and click “Next”
• Accept source folders, and click “Next”
• Accept libraries, and click “Next”
• Accept module structure, and click “Next”
• Accept JDK (> 1.6), and click “Next”
• click “Finish”
• Menu: Build => Make project

Setting up an add-on in Intellij

This assumes that Beast2 source code is cloned and set up as a project in Intellij, named beast2.

To set up a new Add-on to Beast 2 in Intellij

• Create new project
• Import Beast 2 as follows:

   Choose menu File/New Module
   then choose ’Import existing module’
   select the button for browsing the file to be imported.
   Then go to the Beast 2 source folder where you select Beast2.iml file.
   Press OK

• Add dependency on Beast 2 as follows:

   Choose menu File/Project structure.
   Select Modules tab
   Select your new module
   Press Add button, select Module Dependencies
   Select the Beast 2 module
   Press OK