In my fix for WT-5461, test_wt2909_checkpoint_intregrity is failing.

However, the test will pass if we disable logging.

When logging is enabled, we will replay the changes to the metadata table from the previous failed checkpoint and skip checkpointing the table if the table is clean.
In this case, we don't have the chance to bump the metadata write gen to the largest value globally.

The sequence is like this:

In the first open:
Start the first checkpoint.
Complete the first checkpoint.
Start the second checkpoint.
checkpoint a table.
update metadata through logging.
The second checkpoint crash.

Restart wiredtiger:
Open the first checkpoint.
Apply changes to metadata from the log.
Start recovery checkpoint.
Skip checkpoint all the tables.
Checkpoint the metadata table with the updates from the log.