Remove magic directories from config.py.in

V1->V2:
 - Put the correct default log directory in the config file

Now that we are using autotools to build our source, we have actual
variables to indicate the proper directories for logs, config files, and
package data.  Use the provided variables so that we will run properly
if the user customizes them.

Signed-off-by: Adam Litke <agl@linux.vnet.ibm.com>