Move flags to persistent setup so hyprctl reload doesn't reset them

install/config/all.sh

@@ -22,6 +22,7 @@ run_logged $OMARCHY_INSTALL/config/unmount-fuse.sh
 run_logged $OMARCHY_INSTALL/config/sudoless-asdcontrol.sh
 run_logged $OMARCHY_INSTALL/config/input-group.sh
 run_logged $OMARCHY_INSTALL/config/omarchy-ai-skill.sh
+run_logged $OMARCHY_INSTALL/config/omarchy-config-flags.sh
 run_logged $OMARCHY_INSTALL/config/kernel-modules-hook.sh
 run_logged $OMARCHY_INSTALL/config/powerprofilesctl-rules.sh
 run_logged $OMARCHY_INSTALL/config/wifi-powersave-rules.sh

install/config/omarchy-config-flags.sh

@@ -0,0 +1,3 @@
+# Flags are used to toggle certain features on/off in a persistent way
+mkdir -p ~/.local/state/omarchy/flags/hypr
+cp $OMARCHY_PATH/default/hypr/flags/flags.conf ~/.local/state/omarchy/flags/hypr/