Changelog: update link lists to prevent duplicate link definitions

Links in the link lists have to be unique and as all issue/PR sources (this repo, Squizlabs repo, PEAR repo) use numeric issue references, there will be duplicate/overlapping numbers at some point.

To prevent this, I'm proposing the following change:
* Links to _this repo_ will continue to use simple issue number links, i.e. `[#123]`.
    This will keep things most straight forward for new content being added to the changelog.
* Links to the _Squizlabs repo_ will get a `sq` prefix in the link reference. This means the link reference will need to be added where the link is used, i.e `[#123][sq-123]`.
* Links to the _PEAR repo_ will get a `pear` prefix in the link reference. Again, this means the link reference will need to be added where the link is used, i.e `[#123][pear-123]`.

This commit makes it so for all existing issue/PR links in the changelog.

Related to 244