Fix failure in case of missing index.yaml, cleanup

Fix failure in case of missing index.yaml, cleanup

If the index.yaml was not present in data directory, update-sources
command would fail with an IOError. Fix this by handling this case. Now,
if sources are updated on a new data directory, there is an info message
"Adding all sources in the log".

Modularize the current structure to make it more readable and perform
one thing per function. Sort the imports and clean them.