Support CLI parameters in the configuration file

[tomzx]

Currently, no value in the configuration is a value that can be given to a command of the console.

With this change, the configuration would add values such as source-before/source-after/include-before/include-after/exclude-before/exclude-after such that it is not necessary to specify them when calling commands.

However, if a configuration file exist with specific arguments, but different arguments are given when calling the CLI, those arguments should override those set in the configuration.

See #59.

[nochso]

See #72

[tomzx]

As per #74, this is done.