While auditing composer dependencies to try to exclude them from phan's analyzed files, I came across nikic/php-parser, which is only used by maintenance/findDeprecated.php. What this script does is iterate all files in includes and, for each file, make a list of deprecated methods (via wfDeprecated and/or @deprecated). Then, it prints the list, order by the MW version in which the methods were deprecated.
This is something that can probably be done using phan, so that we don't have to add another dependency. Moreover, we could think of moving the script to another library (e.g. mediawiki/tools/phan) and make it configurable, e.g. add a directory parameter to use instead of includes.