Refactors miniCA script to add ca_instances
Refactors ca_init function to chdir into ca directory.

This is in preparation for intermediate CAs.
Run tests with shorter key lengths
Adds intermediate

This commit adds basic intermediate operation.

For an issue with intermediate validation see #2.
Minor improvements

- move the MINICA_TEST_MODE setting to testhelper.inc
- make sure non-set values default to "" where applicable
- improve openssl command logging.
Updates README.md