When running
puppet-summary prune
with any command-line flag, the command returns
Error pruning: database is locked
and pruning does not occur. The -verbose flag did not provide more information.
-auto-prune is also affected, judging from the ever-increasing space occupied by reports. (Edit: Actually, it doesn't seem to be affected; my bad.)
I was able to reproduce the issue on multiple clean Vagrant boxes running Debian Stretch.
To reproduce:

• Install puppet-summary, using the binary release, go get installation or building it manually from source.
• Start puppet-summary directly with puppet-summary serve
• (Import some data)
• Execute puppet-summary prune with any option/flag combination

I was able to resolve my issue by modifying SetupDB code & rebuilding:

@@ -84,7 +84,7 @@ func SetupDB(path string) error {
        //
        // Return if the database already exists.
        //
-       db, err = sql.Open("sqlite3", path)
+  db, err = sql.Open("sqlite3", "file:"+path+"?_journal_mode=WAL")
        if err != nil {
                return err
        }

I was "inspired" to try this after reading mattn/go-sqlite3#607 (among many other related issues), but I'm not particularly suggesting my fix -- I'll gladly admit that I'm out of my depth.