Configuration fixes

[plaffitt]

This fixes 3 issues:

• I removed flags default values in order to prevent environment variable being overwritten by them.
• I merged the user defined configuration with the default one, so one can use a config file that doesn't define all configuration entries without crashing.
• I removed some dead code.

I figured out that using confuse as proposed in the issue would require to change a lot of code since confuse doesn't allow to parse configuration into custom objects. So I came up with something lighter that doesn't need to install any additional library.

Closes #7

[obeone]

Thank you very much for this PR!

Sorry for taking so long to take care of it...