Suppose I do this in my Ammonite script:
"com.lihaoyi" %% "ammonite-ops" % "0.7.7"
One solution is to create a module that holds the scripts.
I create a new module by defining a project in SBT and adding the dependencies necessary:
projectDependencies ++= Seq( "com.lihaoyi" %% "ammonite-ops" % "0.7.7" )
Then I have to reimport the SBT project into IDEA. The process is a little slow, but voilà, I can have autocompletion in my scritps.
I've created also an issue in IDEA for 1st class support of Ammonite. https://youtrack.jetbrains.com/issue/SCL-10752