Fix source code links moved to the scifio-tools foder

This is the same doc fixing commit as #376 rebased onto force pushed origin/dev_4_4.

Merging #376 into `dev_4_4` caused the [BIOFORMATS-docs-release-stable#22](http://hudson.openmicroscopy.org.uk/view/Docs/job/BIOFORMATS-docs-release-stable/22) job to fail. So `origin/dev_4_4` was force pushed excluding #376 and this doc fixing PR was reopened separately.

[BIOFORMATS-doc-merge-stable](http://hudson.openmicroscopy.org.uk/view/Docs/job/BIOFORMATS-docs-merge-stable/) shouldn't fail because of files moved in #368. 

DO NOT MERGE BEFORE 4.4.7 is tagged