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Root cause (proven via live lag-triage capture + deterministic PTY repro): fish latches feature flags from its startup env before config.fish runs, so the existing no-query-term settings never applied to zellij-spawned shells. With query-term on, fish queries the terminal after every command; one reply zellij fails to relay permanently degrades that fish process's reader. Subshells were immune (inherited the exported var), which is why the lag always 'disappeared' when tested in a new shell. Also adds the lag-triage/unlag/term-probe diagnostic toolkit used to find this, and upstream_repro.py for filing the fish-shell bug.
Documentation
Reference documents for some of the more complicated services and maintenance tasks.