Rename command clean-all -> init-pki as a better description

Since Easy-RSA 3 is designed to easily manage multiple PKIs, the notion
of "all" is slightly different. The former clean-all command is still
supported.
Fix typo in help output
Use a cert & req section for global option help output

This makes the output easier to read by grouping CLI options together by
purpose.
Move BATCH fallback below 'vars' import and improve bad value detection

Previously, the vars file wouldn't be used since the var was defined
first, and set_var() uses existing values first.

Additionally, values other than '0' or '1' issue a warning and set
BATCH=0
Prefer openssl config from PKI_DIR, falling back to EASY_RSA path

This allows specific PKI directories to have their own openssl config
file. Since this is an advanced feature, no CLI option is added. Runtime
adjustment can still be impacted with the SSL_CONFIG env-var, as before.

The vars.example file is updated to reflect this, and move SSL_CONFIG
into the advanced section; it is commented out by default to allow the
auto-detection to work.
Keep openssl .rnd file in $PKI_DIR, not $HOME

Other references to HOME in the openssl config have been removed as
unnecessary.