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Fixes multiple problems (see #12 ) and warnings that the build outputted.
The structure wasn't cohesive anymore and now it's fixed.
I tried splitting into multiple commits but this is all that I could manage.
@sjib I tried to keep the structure you implemented but there were some duplicates that I had to remove.
The documentation builds now but there are 5 images ( see #12) that are linked in the docs but not pushed.
Also, there were some duplicated labels. E.g. the
.. _Admin Guide:
and_QGEP User Guide
labels were pointing at multiple chapters which breaks the conventions as one link cannot go to multiple chapters.