Problems with detecting and linking in module invokes

Migrated issue

Reported by: jhodgdon

I noticed today that at least some module invocations are not being recognized and/or displayed on api.drupal.org.

Examples:
https://api.drupal.org/api/drupal/modules%21aggregator%21aggregator.api.php/function/hook_aggregator_parse/7.x

This shows 1 invocation, but there's another one that isn't displayed in
https://api.drupal.org/api/drupal/modules%21aggregator%21aggregator.module/function/aggregator_refresh/7.x
You can see that the call to
module_invoke($parser, 'aggregator_parse', $feed)
makes aggregator_parse into a link to the hook, but on the hook page, it isn't shown as an invocation.

Also in Drupal 8.x branches, if you look up various hooks, you cannot see where they are invoked, even though they definitely are being invoked.

So, this needs to be investigated.

Related issue: Issue #2217105