Please note that the latest upstream patch for this issue requires special 
buildparameters (--with-xss or something) which links the binary agains libxss 
(X screen saver idle detection).
AFAIK this is not done in Debian because they don't want a command line client 
depending on a X library (a system without GUI does not suffer from this issue 
though). A solution to this would be to deliver a special "boinc" binary with 
the boinc-manager package.

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https://bugs.launchpad.net/bugs/128357

Title:
  boinc does not idle with mouse movement

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