Core: Simplify save as

Fixes #197
Core: Simplify logs cleaning
Core: Simplify code
Core: Use a separate FileDB object

Addresses #174
Core: Use FileDB

Addresses #174
Core: Use FileDB

Addresses #174
Core: Use FileDB

Addresses #174
Core: Remove unused code
Core: Use FileDB

Addresses #174
Core: Use FileDB

Addresses #174
Core: Move database validity tests to FileDB class