The content index, also called the search index, supports Confluence's search functionality. It is also used for a number of related functions such as building email threads in the mail archive.
When searches are not performing as expected, or macros that depend on the index are performing unpredictably, that's when admins run the re-index manually. It runs automatically by default, so under typical circumstances it does not need to be run manually.
We have a great article on the subject: Content Index Administration
Like JIRA, it is also wise to re-index Confluence after upgrading or installing add-ons.
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