tools: .gitignore: Add libfdt related files

Some files are generated during libfdt build. Ignore them.

This was wrongly put in the .gitignore in the root directory before.
Now let's remove entries there and put them in the right place.

Fixes: 34e2c285 ("gitignore: add intermediates from libfdt build")
Signed-off-by: Bin Meng <bmeng.cn@gmail.com>