Remove the complex substitutions and add more command line flags instead.

Instead of incomprehensable URL substitutions like ${MODULE/./-|?m=%} we now
use three seperate command line flags for the top level, per-module and
per-entity source and wiki links. They are:
--source-base, --source-module, --source-entity
--comments-base, --comments-module, --comments-entity

We leave -s, --source as an alias for --source-module which is how that option
behaved previously.

The long forms of the substitutions are still available, ${FILE} ${MODULE} etc
and the only non-trivial substitution is ${MODULE/./c} to replace the '.'
characters in the module name with any other character c. eg ${MODULE/./-}

Seperating the source and wiki url flags has the added bonus that they can
be turned on or off individually. So users can have per-module links for
example without having to also have per-entity links.`