Make the second menu entry an action instead of a report

"Apply now" had nothing to do in the normal case. Enabling applies, the
watcher handles everything installed afterwards, and the settings and
applications screens apply on their way out - so pressing it answered
"already applied to 14 applications" and that was the whole interaction.

It is now "Re-apply everything": the state is taken back and written again
from scratch. That is the answer to the question the status block can raise
but nothing could act on - Steam showing as not patched after a client
update, an application that drifted, a flag file edited by hand.

Uninstalling an application used to leave the entry shadowing it behind, in
the user home where the package manager cannot see it, offering to start a
program that is gone. A plain apply only looks at what exists now, so the
watcher never noticed either. Those are removed on every apply now, not just
when rebuilding.

src/lib/apply.sh

@@ -110,6 +110,8 @@ mca_apply() {
 	[[ $CFG_AUTOSTART == yes ]] && mca_autostart_apply
 	[[ $CFG_SPOTIFY == yes ]] && mca_spotify_apply
 
+	mca_prune_orphans
+
 	if (( MCA_CHANGES )) && mca_have update-desktop-database; then
 		update-desktop-database "$MCA_APPDIR" 2>/dev/null || true
 	fi

src/lib/menu.sh

@@ -495,7 +495,7 @@ mca_ui_menu() {
 		mca_ui_status
 		printf '\n'
 		printf '  [1] %s\n' "$(mca_msg "Turn autoscroll on or off")"
-		printf '  [2] %s\n' "$(mca_msg "Apply now")"
+		printf '  [2] %s\n' "$(mca_msg "Re-apply everything")"
 		printf '  [3] %s\n' "$(mca_msg "Applications")"
 		printf '  [4] %s\n' "$(mca_msg "Settings")"
 		printf '  [q] %s\n' "$(mca_msg "Quit")"
@@ -519,18 +519,24 @@ mca_ui_menu() {
 				fi
 				[[ -n $MCA_UI_NEEDS_ACK ]] && mca_pause
 				;;
+			# Not a plain apply: with the watcher running there is never
+			# anything left for one to do, and a menu entry that answers
+			# "already done" every time is not an action. This is the repair -
+			# everything is taken back and written again from scratch, which is
+			# what fixes an application that drifted, a flag file somebody
+			# edited, or Steam after it restored its own script.
 			2)
-				mca_ui_cooked mca_do_apply
+				mca_ui_cooked mca_do_apply --rebuild
 				mca_pause
 				;;
 			3)
 				if mca_ui_apps; then
-					[[ $CFG_ENABLED == yes ]] && mca_ui_cooked mca_do_apply --changed
+					[[ $CFG_ENABLED == yes ]] && mca_ui_cooked mca_do_apply --rebuild
 				fi
 				;;
 			4)
 				if mca_ui_settings; then
-					[[ $CFG_ENABLED == yes ]] && mca_ui_cooked mca_do_apply --changed
+					[[ $CFG_ENABLED == yes ]] && mca_ui_cooked mca_do_apply --rebuild
 				fi
 				;;
 			q|Q) mca_ui_term_restore; trap - EXIT INT TERM; return 0 ;;

src/lib/patch.sh

@@ -418,6 +418,40 @@ mca_spotify_apply() {
 	return 0
 }
 
+# ---------------------------------------------------------------------------
+# Leftovers
+# ---------------------------------------------------------------------------
+
+# mca_prune_orphans
+# Removes generated entries whose application is gone.
+#
+# Uninstalling something deletes its entry from /usr/share/applications, but the
+# copy shadowing it is in the user's home and pacman knows nothing about it. It
+# would sit in the menu forever, offering to start a program that is no longer
+# installed - and the watcher would not notice, because a plain apply only ever
+# looks at what is there now.
+mca_prune_orphans() {
+	local kind path source line
+	local -a lines=()
+
+	[[ -f $MCA_LEDGER ]] || return 0
+	mapfile -t lines < "$MCA_LEDGER"
+
+	for line in "${lines[@]}"; do
+		IFS=$'\t' read -r kind path source <<< "$line"
+		[[ $kind == shadow && -n $source ]] || continue
+		[[ -e $source ]] && continue
+
+		# Only ever remove something still recognisably ours.
+		if [[ -f $path ]] && grep -q "^$MCA_MARK_SHADOW=" "$path" 2>/dev/null; then
+			rm -f -- "$path"
+			MCA_CHANGES=$(( MCA_CHANGES + 1 ))
+		fi
+		mca_ledger_forget "$path"
+	done
+	return 0
+}
+
 # ---------------------------------------------------------------------------
 # Undo
 # ---------------------------------------------------------------------------

src/middleclick-autoscroll

@@ -76,11 +76,11 @@ mca_do_disable() {
 }
 
 mca_do_apply() {
-	local changed=0 arg
+	local rebuild=0 arg
 
 	for arg in "$@"; do
 		case "$arg" in
-			--changed) changed=1 ;;
+			--rebuild) rebuild=1 ;;
 			--quiet)   MCA_QUIET=1 ;;
 		esac
 	done
@@ -95,17 +95,24 @@ mca_do_apply() {
 		return 1
 	fi
 
-	# A settings change can take an application out of scope as well as bring
-	# one in, and only a full undo can tell the difference, so that path starts
-	# from a clean slate. The watcher never does this: rewriting files that are
-	# already correct would make it trigger itself.
-	if (( changed )); then
+	# Start from a clean slate. Needed after a settings change, which can take
+	# an application out of scope as well as bring one in and where only a full
+	# undo can tell the difference, and it is what makes the repair a repair:
+	# whatever drifted is written again rather than left because it is "already
+	# applied".
+	#
+	# The watcher never does this. Rewriting files that are already correct
+	# would change their timestamps, and it is watching those directories.
+	if (( rebuild )); then
 		mca_revert
 	fi
 
 	mca_apply
 
-	if (( MCA_CHANGES )); then
+	if (( rebuild )); then
+		mca_ok "$(mca_msg "Applied again to %d applications." "$MCA_N_ON")"
+		mca_say "  $(mca_msg "Applications that are already running pick this up when they are restarted.")"
+	elif (( MCA_CHANGES )); then
 		mca_ok "$(mca_msg "Applied to %d applications." "$MCA_N_ON")"
 		mca_say "  $(mca_msg "Applications that are already running pick this up when they are restarted.")"
 	else
@@ -160,6 +167,7 @@ mca_do_help() {
 	  enable              $(mca_msg "Turn autoscroll on")
 	  disable             $(mca_msg "Turn it off and put everything back")
 	  apply               $(mca_msg "Apply to anything installed since the last run")
+	  apply --rebuild     $(mca_msg "Take everything back and apply it again")
 	  status              $(mca_msg "Show what is covered")
 	  list                $(mca_msg "List every application that was found")
 	  -h, --help          $(mca_msg "Show this help")