I tried this and it seems to work...
public static void main(String[] args) throws IOException {
{
String privateKey = new String(Files.readAllBytes(Paths.get(PRIVATE_KEY_FILE)));
JWTEncryptionPreferences encryptionPref = new JWTEncryptionPreferences();
encryptionPref.setPublicKeyID(PUBLIC_KEY_ID);
encryptionPref.setPrivateKey(privateKey);
encryptionPref.setPrivateKeyPassword(PRIVATE_KEY_PASSWORD);
encryptionPref.setEncryptionAlgorithm(EncryptionAlgorithm.RSA_SHA_256);
IAccessTokenCache accessTokenCache = new InMemoryLRUAccessTokenCache(MAX_CACHE_ENTRIES);
BoxDeveloperEditionAPIConnection api = BoxDeveloperEditionAPIConnection.getAppEnterpriseConnection(ENTERPRISE_ID, CLIENT_ID, CLIENT_SECRET, encryptionPref, accessTokenCache);
Iterable<com.box.sdk.BoxUser.Info> users = BoxUser.getAllEnterpriseUsers(api, "App");
for (BoxUser.Info user : users) {
BoxDeveloperEditionAPIConnection userApi = BoxDeveloperEditionAPIConnection.getAppUserConnection(user.getID(), CLIENT_ID, CLIENT_SECRET, encryptionPref, accessTokenCache);
System.out.println(new BoxUser(userApi, user.getID()).getInfo().getName());
BoxFolder boxFolder = BoxFolder.getRootFolder(userApi);
Iterable<com.box.sdk.BoxItem.Info> items = boxFolder.getChildren();
for (BoxItem.Info item : items) {
System.out.println("\t" + item.getName());
}
}
}