I noticed, however that apt-file search didn't return results.. so what had I confgured incorrectly?
answer (provided by Daviey from the Ubuntu UK Podcast).
I needed to add the following line to each distribution in conf/distributions.
Contents: .gzafter that I ran "reprepro export" to update the indices. Job done.
Now to test it.
~$ apt-file update ~$ apt-file search createdemodatabase.py openmolar-orig: /usr/lib/python2.6/dist-packages/openmolar/createdemodatabase.py openmolar-orig: /usr/lib/python2.7/dist-packages/openmolar/createdemodatabase.py openmolar-orig: /usr/share/pyshared/openmolar/createdemodatabase.py