OK, I have a better, but still imperfect, idea of what is happening.
Discussion below is now at
http://trac.sagemath.org/sage_trac/ticket/5459

(I'm cross-posting the contnuation of this thread from sage-support to
sage-devel).

There is a notebook configuration item indexed by 'save_interval'.
This can be set at the sage command line by instantiating a notebook
object (call it "nb") and issuing commands like nb.conf()
['save_interval'] = int(3600).   This value seems to be used by server/
notebook/twist.py to make backup copies of nb.sobj.  It seems to make
a snapshot of a worksheet as a side-effect, without any check if the
snapshot is different from previous snapshots.  This is speculation,
since I could not decipher what triggers twist.py to check and do such
a save.  Also, experimentally, I see that it happens "automatically",
even if the worksheets and notebook are left untouched.

There is also a per-user 'autosave_interval'  This can be accessed
through code like nb.user("admin")['autosave_interval'] and can also
be set from the drop-down box in the "Settings" area of the notebook
(to be 1,3,5,7,9 minutes only).  The use of this seems a bit odd.  Any
edit (but only edits) in the worksheet triggers a possible snapshot
save.  First, the time since the last save is checked against the user
autosave_interval.  If not enough time has elapsed, it exits,
otherwise it continues towards a snapshot save.  It then checks to see
if the worksheet has changed.  But it must have changed, since only
edits trigger the routine.  Then it writes a snapshot.

So in summary, a new snapshot every period given by 'save_interval'
which is not obviously user-configurable.  No check on if the snapshot
is different.  Every edit triggers a possible snapshot, it happens
only if time exceeds user's autosave_interval, which can be set by the
user to limited number of values.

This may be an imperfect understanding of the situation, but I think
it is confusing for a user and potentially filling up disk space and/
or degrading performance.  So there's some room for improvement in how
this works.

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