Add flag to indicate that the tree sequence has passed check_integrity.

[benjeffery]

As discussed in #1899 30% of the time required to load a 1G tree sequence is spent checking its integrity. We could bypass this by recording when check integrity has passed and clearing it on any change to the data.

I've put this in C1.0 as it's an API change, but we could bump it as it would be backward compatible.