Clean up, changes and fixes

Clean up, changes and deployment related fixes
* clean up of .github
* removed several auto generated files; no need to keep these under version control
* fixes to configure.ac for missing stdc++ and (some) stl header checks
* added a print summary to configure.ac
* added --with-jdk option to configure.ac, allows to switch of java detection
* fixed multiple memory issues (leaks, invalid references)