set jar manifest with main class and dependencies

The Jar was missing a manifest which denoted the location of the main
class and class paths of its dependencies. Now it is more convenient to
execute it from a shell
allow compiling whole directories from commandline

The first command line option has been extended to accept a directory.
All .java files in this directory and all subdirectories recursively are
compiled. The directory structure of the input directory is preserved
for the generated AS3 files.