Breathe Inline fixes

[Robert-Morgowicz]

Ran into some complications when trying to use this builder for a document set that was previously hosted in html. Mostly this was to do with directives generated by the breathe extension for interfacing doxygen with sphinx (I was getting empty headings where function definitions sourced from the C should be), but I also noticed images weren't copying into the document output and some broken links within documents I fixed as well.

Only tested these changes on my local so further vetting required here