Using the Board Manager, it is possible to automatically download both the hardware files and any tool dependencies for a given board.
These are saved to: /Users//AppData/Roaming/Arduino15/packages/
on Windows and in a similar folder on other platforms.
The required tools, which are not already installed, are placed in the packages//tools folder.
The issue is, that the Arduino IDE appears to assume that all the tools are located in the /packages/arduino/tools folder, and so it cannot find the new tools installed for that board.
Is this the correct behaviour, or am I missing some configuration somewhere?