Remove notations for bi_bare and bi_persistently.

(□ P) now means (bi_bare (bi_persistently P)).

This is motivated by the fact that these two modalities are rarely
used separately.

In the case of an affine BI, we keep the □ notation. This means that a
bi_bare is inserted each time we use □. Hence, a few adaptations need
to be done in the proof mode class instances.