Manual:RefreshLinks.php

Details
refreshLinks.php file is a maint-scripts>Special:MyLanguage/Manual:Maintenance scripts|maintenance script to [re]fill , , and  tables.

You should run it if you found that categories are empty or don't show all relevant pages, if "1>Special:WhatLinksHere|What links here?" doesn't work well, or some other link-related trouble.

Additionally this script purges links that point to non-existing pages from the following tables: pagelinks, categorylinks, imagelinks,, , , , ,

Basic
 php maintenance/refreshLinks.php [starting_article]

for example, if you want the script to start with the page with id 8000:

 php maintenance/refreshLinks.php 8000

Advanced
 php refreshLinks.php [--conf|--dbpass|--dbuser|--dfn-only|--e|--globals|--help|--m|--new-only|--old-redirects-only|--quiet|--redirects-only|--wiki]

Parameters
This also supports the cmdOptions>Special:MyLanguage/Manual:Maintenance_scripts#Standard command-line options|common options as well.

Avoiding memory issues
This script may run into memory issues. To avoid this you may like to set a last page_id to refresh.

 php refreshLinks.php --e 1500

To do the next set of page_ids you enter

 php refreshLinks.php --e 3000 -- 1500

Just continue until all page ids in your wiki were refreshed.

If you forgot to set a last  to refresh and the script runs out of memory simply rerun it with the last output   as the article to start at, e.g.

 php refreshLinks.php -- 1600

Chunking refreshLinks.php to refresh all links without memory leak
Below is an example script to run refreshLinks.php against all pages but without having memory issues.