Tools overridden via --prefs are persistent

The bug gets exposed in a very particular configuration (and is usually harmless).

Steps to reproduce:
1 - Select a board with a board manager entry (MKRWIFI1010 for example)
2 - Compile a sketch
3 - Change board with one contained in the sketchbook (one from the mbed core with openocd as programmer)
4 - Select "upload using programmer"
5 - The wrong tool version will be selected

If steps 1 and 2 are not performed the right version gets selected.
If between step 2 and 3 the user opens the board manager the correct version gets selected too.

Caused by:
These lines https://github.com/arduino/Arduino/blob/c4109e78bc62a4f344cfb9abba065f8504235e31/arduino-core/src/cc/arduino/Compiler.java#L269-L273 allow overriding the automatically discovered tools, but should be cleared when we change the target board (and they are not)