[MySQL] Separate integration from publishing checkpoints

[AlCutter]

This PR disconnects the act of integrating new entries into a tree, from the act of publishing a new checkpoint which publicly commits to that new tree state for the MySQL storage implementation.

See #323 for more details on the rationale.

Helps with #309 and #198.

[roger2hk]

Shall we align the wrapped error? Some of them are wrapped %w while some of them are not %v.

[AlCutter]

Shall we align the wrapped error? Some of them are wrapped %w while some of them are not %v.

No, don't use %w without a reason - only do it when you're explicitly making the decision to allow callers of the func to be able to be aware of implementation details (https://go.dev/wiki/ErrorValueFAQ#i-am-already-using-fmterrorf-with-v-or-s-to-provide-context-for-an-error-when-should-i-switch-to-w).

[roger2hk]

Shall we align the wrapped error? Some of them are wrapped %w while some of them are not %v.

No, don't use %w without a reason - only do it when you're explicitly making the decision to allow callers of the func to be able to be aware of implementation details (https://go.dev/wiki/ErrorValueFAQ#i-am-already-using-fmterrorf-with-v-or-s-to-provide-context-for-an-error-when-should-i-switch-to-w).

Right, I see some of the error messages are using %w. Shall we convert them back to %v in a follow up PR?

[AlCutter]

Shall we align the wrapped error? Some of them are wrapped %w while some of them are not %v.

No, don't use %w without a reason - only do it when you're explicitly making the decision to allow callers of the func to be able to be aware of implementation details (https://go.dev/wiki/ErrorValueFAQ#i-am-already-using-fmterrorf-with-v-or-s-to-provide-context-for-an-error-when-should-i-switch-to-w).

Right, I see some of the error messages are using %w. Shall we convert them back to %v in a follow up PR?

Yeah, there seems to be a mix throughout the file so probably needs some time to think about why they were added.