I\'m trying to analyze Java source files with Clojure but I couldn\'t find a way to do that.
First, I thought using Eclipse AST plugin(by copying necessary JAR\'s to
... and it doesn't compile with latest ANTLR ...
I could not reproduce that.
Using ANTLR v3.2, I got some warnings, but no errors. Using both ANTLR v3.3 and v3.4 (latest version), I have no problems generating a parser.
You didn't mention how you're (trying) to generate a lexer/parser, but here's how it works for me:
java -cp antlr-3.4.jar org.antlr.Tool Java.g
Here's my output when running the commands:
ls wget http://www.antlr.org/download/antlr-3.4-complete.jar wget http://openjdk.java.net/projects/compiler-grammar/antlrworks/Java.g java -cp antlr-3.4-complete.jar org.antlr.Tool Java.g ls

As you can see, the .java files of the lexer and parser are properly created.
Instead of generating a parser yourself (from a grammar), you could use an existing parser like this one (Java 1.5 only AFAIK) and call it from your Clojure code.