Before this commit, only the last occurrence of this option was applied to the build context.

Now we actually can use it several times in the global section, as it was intended.

- The actual reading of 'git-repository-base' was done when constructing OptionBase from the global section of the config.
- The merging options from the constructed OptionsBase object into the BuildContext was done in setOption of BuildContext, but because it was not properly handled in OptionsBase, only the last value was appeared in BuildContext's handling.
- Now it is handled in the OptionsBase also when merging (we expect that the type of value is a hash then).
- Remove incorrect placement of 'git-repository-base' to the checking of module-set option in the Module, so our BuildContex::setOption can call its parent class Module::setOption, which then can pass this option handling to its parent class OptionsBase::setOption.

Also:
- Move endWord suggestion next to the printed message. The actual endWord does not matter when parsing, so it makes code a bit more readable when understanding how it parses
- Edit comment so it better explains why we remove some options that we read from the config
- Move the config description in docbook to the correct scope