Minor fixes and increasing consistency in sysadmin docs.
Further dependency name updates after sbesson's review.
Additional capitalization suggested in review.
Conversion for File Formats from Plone
Reorganise files to make
Fixing most of the warnings
Adding local copies of images
Adding mac folder hidden file to ignore list
Fixing missing images and broken tables
Fixing files that would not convert
Updating Compliant Specification to 2012-06
Updating for schema 2012 docs in sync with Plone

Some linked samples need work
./downloads/sample-files.txt - Linked samples and associated text need updated
./working-with-ome-xml/6d-7d-and-8d-storage.txt - Linked sample needs updated
./ome-tiff/ome-tiff-specification.txt - BRANCH DONE - PLONE DONE  - Linked samples and fragments need updated
./working-with-ome-xml/spim-initial-support.txt - BRANCH DONE - PLONE DONE - Linked sample needs updated
./from-trac/DataModel.txt - BRANCH DONE - NOT ON PLONE- Linked page needs updated
./schemas/specifications/compliant-file-specification.txt - BRANCH DONE - PLONE DONE
./schemas/specifications/compliant-hcs-specification.txt - BRANCH DONE - PLONE DONE
./schemas/specifications/minimum-specification.txt - BRANCH DONE - PLONE DONE
./schemas/versions/version-information.txt - BRANCH DONE - PLONE DONE
./working-with-ome-xml/using-ome-xml-in-your-work.txt - BRANCH DONE - PLONE DONE
./working-with-ome-xml/tiled-images.txt - BRANCH DONE - PLONE DONE
Fixing typos.
Fix Typo and add TODO
Update links for Samples and Schemas
Turning on build of formats directory
Delete unused files saving some text for editing
Structuring ome-tiff section & link formatting
Organising versions & specifications
Starting developer section edits