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This covers a very convoluted use-case that may be reproduce this way: 1. Using an previous version of the IDE, a new AVR core is installed using the board manager. 2. The IDE is then updated so the core installed in 1. is now also the bundled one 3. The AVR core installed 1. is now removed using the board manager 4. The board manager will uninstall the (presumably) no longer used tools, from the built-in folder leaving, in fact, the IDE without the bundled tools that are supposed to be read-only. This commit fix this bug by actually making the built-in tool read-only