Speed up logical overwrites by pruning manifests in `Snapshot._manifests`

[gabeiglio]

Feature Request / Improvement

We’ve observed a large performance gap between the Python and Java implementations for logical overwrites (metadata-only). Profiling shows most time is spent in snapshot.py (_manifests), where we are not pruning manifests when computing _existing_manifests and _deleted_entries.

After adding manifest pruning, we see the following benchmark results (100 overwrite iterations):

Scenario	Avg (s)	Min (s)	Max (s)
Current PyIceberg – same partition	1.15	0.78	1.51
Current PyIceberg – random partitions	0.96	0.77	1.26
Pruning PyIceberg – same partition	0.50	0.28	0.78
Pruning PyIceberg – random partitions	0.38	0.27	0.49

Benchmark script: https://gist.github.com/gabeiglio/0092970c144228ef6d333a873dc1d316

Here is the PR for the optimization

[gabeiglio]

Resolved!