.coveragerc: fix reporting of coverage to match what is run

Without this change, the HTML report will show all lines specified in
run.omit. As they have 0% coverage, this will negatively impact the overall
coverage percentage calculated in the report.

Note: at this moment, we have an overall 74% test coverage.
Test by installing pytest-cov and running:
py.test --cov=kallithea --cov-config=.coveragerc --cov-report html
and opening htmlcov/index.html in a browser.