Even with innodb_file_per_table enabled, individual table files on disk don't normally shrink.
For most tables, like maniphest_task, this is fine, since the data in the table normally never shrinks, or only shinks a tiny amount.
However, some tables (like the "worker" and "daemon" tables) grow very large during a huge import but most of the data is later deleted by garbage collection. In these cases, this lost space can be reclaimed by running OPTIMIZE TABLE on the tables.
Add a script to OPTIMIZE TABLE every table.
My primary goal here is just to reduce storage pressure on db001 since there are a couple of "import the linux kernel" installs on that host wasting a bunch of space. We're not in any trouble, but this should buy us a good chunk of headroom.