Fixes an issue reported where `spack env depfile` + `make -j` would
non-deterministically refuse to mark all environment roots explicit.
`update_explicit` had the pattern
```python
rec = self._data[key]
with self.write_transaction():
rec.explicit = explicit
```
but `write_transaction` may reinitialize `self._data`, meaning that
mutating `rec` won't mutate `self._data`, and the changes won't be
persisted.
Instead, use `mark` which has a correct implementation.
Also avoids the essentially incorrect early return in `update_explicit`
which is a pattern I don't think belongs in database.py: it branches on
possibly stale data to realize there is nothing to change, but in reality
it requires a write transaction to know that for a fact, but that would
defeat the purpose. So, leave this optimization to the call site.
e3aca49e25