_project.py: Add fatal-warnings configuration item

This allows for users to configure fatal-warnings to be either a list of
warnings or simply True to consider all warnings as errors.

This commit deprecates the use of fail-on-overlap within project.conf,
this will now use the fatal-warnings configuration item.

tests: This modifys the tests/frontend/overlaps.py tests to support the
new fatal-warnings configuration. Backwards compatibility is also
tested for `fail-on-overlap`

_versions.py: BST_FORMAT_VERSION bumped to 12 for fatal-warnings

Fixes: #526