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This will save your open windows to a file (~/.windows).
To start those applications:
cat ~/.windows | while read line; do $line &; done
Should work on any EWMH/NetWM compatible X Window Manager.
If you use DWM or another Window Manager not using EWMH or NetWM try this:
xwininfo -root -children | grep '^ ' | grep -v children | grep -v '<unknown>' | sed -n 's/^ *\(0x[0-9a-f]*\) .*/\1/p' | uniq | while read line; do xprop -id $line _NET_WM_PID | sed -n 's/.* = \([0-9]*\)$/\1/p'; done | uniq -u | grep -v '^$' | while read line; do ps -o cmd= $line; done > ~/.windows
There are 2 alternatives - vote for the best!
If you can do better, submit your command here.
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wmctrl -l -p | while read line; do ps -o cmd= "$(echo "$line" | awk '$0=$3')"; done
Okay, thanks that works better if you have a two character desktop number (-1 or 10).