Properties parsing 5.0.3-rc1 fixes

Fixes some minor issues during configuration parsing:

- fixes the multiline parsing logic, see the default values for `omero.search.excludes/includes`
- fixes indentation in the list, see e.g. `omero.checksum.supported`
- restores lost search properties text and adds some security properties text
- moves hyperlinks to the unparsed headers in `omero.properties`
- use/fixes markup in `omero.properties`
- removes whitespaces/extra linebreaks
- fixes the name of the `Ice` section

To test this PR check the auto-generated content by snoopycrimecop on https://github.com/snoopycrimecop/ome-documentation/tree/dev_5_0/merge/autogen and compare all the whitelisted values/description from `omero.properties` are properly included.
I'd add a `##` here.