Limit commit object finalization strip-off

[miloszm]

Summary

After finalization, commit objects need to be stripped-off off the finalized inidices(by index we mean
an element, i.e., a subtree of memory pages for a given contract), otherwise commit grow in size
like snow balls (since a new commit is always created off of a base commit). Sometimes yet such strip-off
is too aggressive, as sometimes this information is still needed. In such case, a check needs to be done
if a given element is in main, and if it is, it should be recalled back.

Possible solution design or implementation

Check if missing element is in main, and if it is, bring it back into the commit.

Additional context

This feature is critical for correct root calculations in cases when root is called after finalization and a given element has already beed stripped-off from the commit object.