The Java files are compiled to the source tree, making it difficult to
restart a build. Fix this by passing the output directory to javac.

cd secp256k1
./autogen.sh
mkdir build && cd build
../configure --enable-jni --enable-experimental --enable-module-ecdh
make check-java

Check the .class files are located under the build directory
(build/src/java/org/bitcoin/*.class).

make clean

Check the .class files are deleted.