If you clock in on a work item, and then walk away from your computer—perhaps to take a phone call—you often need to “resolve” the time you were away by either subtracting it from the current clock, or applying it to another one.
By customizing the variable
org-clock-idle-time to some integer, such
as 10 or 15, Emacs can alert you when you get back to your computer after
being idle for that many minutes1, and ask what you want to do with the idle time.
There will be a question waiting for you when you get back, indicating how
much idle time has passed (constantly updated with the current amount), as
well as a set of choices to correct the discrepancy:
What if you subtracted those away minutes from the current clock, and now want to apply them to a new clock? Simply clock in to any task immediately after the subtraction. Org will notice that you have subtracted time “on the books”, so to speak, and will ask if you want to apply those minutes to the next task you clock in on.
There is one other instance when this clock resolution magic occurs. Say you were clocked in and hacking away, and suddenly your cat chased a mouse who scared a hamster that crashed into your UPS's power button! You suddenly lose all your buffers, but thanks to auto-save you still have your recent Org mode changes, including your last clock in.
If you restart Emacs and clock into any task, Org will notice that you have a dangling clock which was never clocked out from your last session. Using that clock's starting time as the beginning of the unaccounted-for period, Org will ask how you want to resolve that time. The logic and behavior is identical to dealing with away time due to idleness; it is just happening due to a recovery event rather than a set amount of idle time.
You can also check all the files visited by your Org agenda for dangling clocks at any time using M-x org-resolve-clocks RET (or C-c C-x C-z).
You may want to start clocking from the time when you clocked out the
previous task. To enable this systematically, set
t. Each time you clock in, Org retrieves the clock-out time of the
last clocked entry for this session, and start the new clock from there.
If you only want this from time to time, use three universal prefix arguments
org-clock-in and two C-u C-u with
 On computers using Mac OS X,
idleness is based on actual user idleness, not just Emacs' idle time. For
X11, you can install a utility program x11idle.c, available in the
contrib/scripts directory of the Org git distribution, or install the
xprintidle package and set it to the variable
org-clock-x11idle-program-name if you are running Debian, to get the
same general treatment of idleness. On other systems, idle time refers to
Emacs idle time only.