Change -conf's help message to indicate that relative path values will be prefixed by the datadir path. This behavior probably merits clarification; it's kind of confusing when attempting to specify a configuration file in the current directory with -conf=bitcoin.conf, but instead loading the bitcoin.conf file in ~/.bitcoin datadir.
Edit
This PR has been modified to document all cases where relative path configurations are modified to be under datadir. A small refactoring has also been added which consolidates this normalization.