Improve time complexity of identity node removal

[0HyperCube]

Working towards #4572.

• Reduce time complexity of remove_passthrough_node from O(n) to O(1) by using the cached list of dependants.
• Remove some unused fields and methods from OriginalLocation
• Add a test to ensure the remove_passthrough_node function works properly.
• Validate that the cached list of dependants is accurate (and fix some instances where it contained deleted node ids).

[cubic-dev-ai]

Review completed against the latest diff

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[cubic-dev-ai]

1 issue found across 3 files (changes from recent commits).

Confidence score: 3/5

• In node-graph/graph-craft/src/document.rs, nested pruning can leave a removed edge in a live upstream node’s dependant list, making graph dependency state inconsistent; rebuild the cache after pruning, clearing its buckets before repopulating them.

Prompt for AI agents (unresolved issues)

Check if these issues are valid — if so, understand the root cause of each and fix them. When an issue isn't valid or won't be fixed in this PR, reply in its thread with the reason and then resolve the thread. If appropriate, use sub-agents to investigate and fix each issue separately.


<file name="node-graph/graph-craft/src/document.rs">

<violation number="1" location="node-graph/graph-craft/src/document.rs:884">
P2: Nested pruning can remove an input from a live network node, but this cleanup leaves the removed edge in the live upstream node’s dependant list. Rebuild the cache after input pruning by clearing the buckets and calling `populate_dependants`, rather than filtering only deleted node IDs.</violation>
</file>

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Re-trigger cubic</sub>

[cubic-dev-ai]

P2: Nested pruning can remove an input from a live network node, but this cleanup leaves the removed edge in the live upstream node’s dependant list. Rebuild the cache after input pruning by clearing the buckets and calling populate_dependants, rather than filtering only deleted node IDs.

Prompt for AI agents

Check if this issue is valid — if so, understand the root cause and fix it. When an issue isn't valid or won't be fixed in this PR, reply in its thread with the reason and then resolve the thread. At node-graph/graph-craft/src/document.rs, line 884:

<comment>Nested pruning can remove an input from a live network node, but this cleanup leaves the removed edge in the live upstream node’s dependant list. Rebuild the cache after input pruning by clearing the buckets and calling `populate_dependants`, rather than filtering only deleted node IDs.</comment>

<file context>
@@ -878,13 +878,12 @@ impl NodeNetwork {
 		for node in self.nodes.values_mut() {
 			for dependants in &mut node.original_location.dependants {
-				dependants.clear();
+				dependants.retain(|dependant| !old_nodes.contains_key(dependant));
 			}
 		}
</file context>

[0HyperCube]

Nested pruning can remove an input from a live network node

Hopefully not…