From its inception, PmWiki has been designed so that WikiAdministrators can greatly customize the way PmWiki displays pages and the markup sequences used to generate pages. (This is even mentioned explicitly in PmWikiPhilosophy #4.) As a result, the core pmwiki.php script makes extensive use of PmWiki.Variables to determine how markup sequences will be processed and what each individual page will output. Thus, a WikiAdministrator can make a lot of customizations simply by setting variables in the config.php file.
The bulk of this page describes how customizations work in general, see PmWiki.DocumentationIndex for specific customizations that are commonly performed at many PmWiki installations, including:
The scripts/ subdirectory (below the directory holding the pmwiki.php script) and the PmWiki Cookbook contain many example customizations that you can include in your config.php site configuration. The first few lines of each of these scripts generally contain instructions about how to enable (and use) the feature provided by the script--for most scripts, simply adding a line like:
include_once("scripts/scriptfile.php");
somewhere in the config.php file will enable it. Some of the scripts are automatically enabled for you via the scripts/stdconfig.php script unless you disable it by setting $EnableStdConfig=0; in local/config.php.
Note that you should strongly resist the temptation to directly modify the pmwiki.php script or the files in the scripts/ subdirectory. Any modifications you make to these files will probably be overwritten whenever you perform a PmWiki.Upgrade. Instead, look at some of the sample scripts for examples of customizations that can be performed from config.php. You can even create your own script to do a customization and use include_once(...) to include it from config.php. If you do make your own customization script, you can safely put it in the cookbook/ subdirectory--it won't get overwritten by an upgrade there. You might also want to submit your customization to the pmwiki-users mailing list or the Cookbook so that others can benefit from your effort and so that it can perhaps be included in future releases of PmWiki.