Isn't compiler support integrated with Java6 (JSR199)?

Yes, it is now. JSR199 in the end brought the official java compiler tools that now come with Java 6. Progress on this had stalled for many years. This is how JCI was born. JCI provided what was missing from the JDK. And it still provides it also for earlier versions. The main author of JCI has later on joined the EG and will make sure there is a bridge to the JSR199 API.

Doesn't JSR199 already deprecate JCI?

Well, as said before ...there are no backports so far. And if you give the the final java tools API in Java 6 a try you might well come back and enjoy JCI :)

How well tested is the code?

Well, there are a couple of projects out there using this code already for quite some time in production. Drools and Cocoon to name just a few well known Open Source projects. Code coverage is not bad at all ...but there still a few things on the TODO list and contributions are always welcome.

Will the ... compiler be supported?

There is always room for new implementations. And if the compiler supports compilation to java bytecode, there is also a good chance it can be added. There are currently already a few potential candidates out there. But it all comes down to the need and the time to implement.