We configured a wait_timeout of 90 seconds and an interactive_timeout of 120 seconds in the MySQL server. Non of the options mentioned at https://confluence.atlassian.com/display/STASHKB/Connection+Timeout+with+MySQL+Database help to prevent that the Stash MySQL connections get closed after 90 seconds. "db.pool.idle.maxAge=1" has no effect in the latest Stash version 2.4.1 and 2.4.2.

The only solution is to host Stash on a MySQL server with wait_timeout=0.