fix #12552: include extra annotations in disk usage calculation

Adds to the disk usage request described in #2919 (see that for basic testing instructions) coverage of the extra annotations introduced in #2412 which may of course be file annotations. Cc: @ximenesuk regarding #3009 which may also be useful for testing. Also now includes pyramid lock files in disk usage count.

Fixes http://trac.openmicroscopy.org.uk/ome/ticket/12552.
--no-rebase