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Used the simplest strategy: double-checked locking with synchronized. Since this task is meant to be run manually by the user, it’s totally OK. It’s a simple and robust solution that doesn’t affect performance, so in my opinion this is a good approach.
If you disagree or have a better idea, I’m happy to hear it!

One more corner case related to parallel execution: the current solution prevents parallel file modification within a single JVM process.
However, if a user runs Gradle in multiple consoles at the same time, we could end up with parallel creation/editing of the same file with a few Gradle processes...
That could be handled using a file lock on the OS level with Java's FileChannel, but I’m not sure we need to worry about this case — it’s very unlikely to happen in practice.
What do you think?