Added command line option handling
Fixed typo
Added CLI args to init
Added java_exec option
Updated changelog and todo
Corrected default output_file. Updated TODO
Revert "Corrected default output_file. Updated TODO"

This reverts commit 82fbbfc5a3a3a7d55cc5ff8bb258a1c215c25d06.
Restored part of commit
Merge branch 'dev2' into dev

Conflicts:
	CHANGELOG.md
Bumped version