The following may sound like a very naive suggestion, but I will make it
anyway.  Usually fsck is run routinely every 30 (or so) times a file
system is mounted.  Is there any reason why fsck can not instead be run
in the background in read-only mode every so often while the system is
running?  This will produce a number of false positive errors due to
temporary inconsistencies in the file system.  However, it should also
confirm that 99% of the file system is consistent.  Then, when fsck is
run at start up, it need only check those previously reported errors to
make sure that they have gone, which should be much faster.  This could
even be short-circuited further by comparing the errors on different
live runs and eliminating those which have disappeared since the last
run.

-- 
no visible indication that a long-running fsck is taking place in background
https://bugs.launchpad.net/bugs/38303
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