Improved directory setup, scan processing, and reporting output.

Changes proposed in this pull request:

Improved directory setup logic in setup_dirs.
Enhanced scan collection and processing.
Integrated reporting output for various scan types (Log4J, Daemons, CSV, Summary).

For any logging statements, is there any chance that they could be logging sensitive data?
Are log statements using a logging library with a logging level set? Setting a logging level means that log statements "below" that level will not be written to the output. For example, if the logging level is set to INFO and debugging statements are written with log.debug or similar, then they won't be written to the otput, which can prevent unintentional leaks of sensitive data.

improved security reporting.