Fix the directory functionality of clan (clan.directory).
The python API interface was not able to distinguish if the directory
was set to anything other than `self.src`.
Breaking every command that relied on the clan directory, for example:
- `clan machines update`
- `clan machines update-hardware-config`
See more in #2906
This is the first step in fixing all those commands.
Individual command support and implementation will be implemented in
follow ups.
31438d6781