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The automatic update's preflight ignored mode-only changes and anything whose status line contained plugins/ or plugin-repos/, then promised "Automatic updates will not stash your changes". perform_core_update used plain git status (modes count) and ignored only 'plugins/', then ran 'git stash push -- :!plugins', which nothing ever pops. So an edit to a bundled plugin under plugin-repos/, or the installer's chmods on tracked scripts, passed the preflight and was stashed away for good. - auto_update.local_changes() is the one predicate both use: core.fileMode=false, porcelain -z, and plugins/ and plugin-repos/ excluded by leading folder rather than substring (a core file under web_interface/static/v3/js/plugins/ now counts). - Update Code's explicit stash leaves out both plugin folders; the pull's --autostash carries their edits and mode changes across and reapplies them. - The automatic updater calls perform_core_update(stash_local_changes= False), which refuses instead of stashing edits that appeared after the preflight; update_core reports that as 'blocked'. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>