## Summary
Fix workflow loading for nested subgraphs with duplicate node IDs by
configuring subgraph definitions in topological (leaf-first) order.
## Changes
- **What**: Three pre-existing bugs that surface when loading nested
subgraphs with colliding node IDs:
1. Subgraph definitions configured in serialization order — a parent
subgraph's `SubgraphNode.configure` would run before its referenced
child subgraph was populated, causing link/widget resolution failures.
2. `_resolveLegacyEntry` returned `undefined` when `input._widget`
wasn't set yet, instead of falling back to `resolveSubgraphInputTarget`.
3. `_removeDuplicateLinks` removed duplicate links without updating
`SubgraphOutput.linkIds`, leaving stale references that broke prompt
execution.
- **What (housekeeping)**: Moved `subgraphDeduplication.ts` from
`utils/` to `subgraph/` directory where it belongs.
## Review Focus
- Topological sort correctness: Kahn's algorithm with edges from
dependency→dependent ensures leaves configure first. Cycle fallback
returns original order.
- IO slot link repair: `_repairIOSlotLinkIds` runs after
`_configureSubgraph` creates IO slots, patching any `linkIds` that point
to links removed by `_removeDuplicateLinks` during `super.configure()`.
┆Issue is synchronized with this [Notion
page](https://www.notion.so/PR-10314-fix-configure-nested-subgraph-definitions-in-dependency-order-3286d73d36508171b149e238b8de84c2)
by [Unito](https://www.unito.io)
---------
Co-authored-by: Amp <amp@ampcode.com>
