Node Replacement for Pure Subgraph (.json files)

### What problem are you experiencing?

The Auto Node Replacement feature (which updates deprecated or missing nodes) is currently inactive for Pure Subgraph JSON files. While the replacement logic triggers correctly when a subgraph is part of a larger workflow, standalone subgraph files do not benefit from this automation. This creates a maintenance gap where modular subgraph libraries become outdated and require manual node-by-node updates, defeating the purpose of the auto-replacement system.

### When does this problem occur?

This occurs specifically when opening or editing a Pure Subgraph (.json) file directly.

- Case A (Working): Adding a subgraph node into an existing workflow - the replacement logic triggers for the internal nodes of that subgraph.
- Case B (Broken): Opening the raw subgraph JSON file to edit its definition - the replacement logic is ignored, leaving deprecated or missing nodes as-is without a prompt to update.

### How often do you encounter this problem?

Weekly

### How much does this problem affect your workflow?

Significantly slows down my work

### Current workarounds

The only current workaround is to manually delete and replace deprecated nodes, or to import the subgraph into a "dummy" workflow, allow the replacement to happen there, and then attempt to re-save the logic back into a subgraph file. This is prone to error and significantly slows down the maintenance of custom nodes.

### Ideas for solutions (Optional)

_No response_

### Additional context

_No response_

┆Issue is synchronized with this [Notion page](https://www.notion.so/Issue-11565-Node-Replacement-for-Pure-Subgraph-json-files-34b6d73d36508124a2faf92156a430ba) by [Unito](https://www.unito.io)