layoutStore spatial index silently drops nodes outside ±10000

## Summary
`layoutStore`'s node spatial index cannot hold a node whose bounds fall outside a fixed ±10000 box, and drops it without any signal. Real workflows outgrow that box, so `queryNodesInBounds` and every hit-test built on it return incomplete results.

## Detail
- `layoutStore` constructs `SpatialIndexManager` with no bounds argument (`layoutStore.ts`), so it defaults to `QUADTREE_CONFIG.DEFAULT_BOUNDS` — `{x: -10000, y: -10000, width: 20000, height: 20000}` (`constants.ts`).
- `QuadNode.insert` returns `false` for anything not fully contained (`QuadTree.ts`), and `SpatialIndexManager.insert` discards that return value.
- `QuadTree.update` early-returns for an id not in `itemMap`, so a node dropped once is never recovered — even if it later moves back inside the box.

A 3000-node workflow built by tiling the default graph spans roughly 48,000 units, so the majority of its nodes are absent from the index.

## Impact
Anything reading the shared index gets silently partial results. Today that is hit-testing and selection paths; it would also have made viewport culling render far-flung nodes permanently invisible, which is why #15030 uses a private index sized to the graph extent rather than the shared one.

## Suggested fix
Size the root to the actual graph extent (rebuilding on outgrow), or keep an overflow list for out-of-bounds items. Either way, stop discarding `insert`'s return value.

Found during review of #15030 by @christian-byrne.

Start with layoutStore.ts, constants.ts, and QuadTree.ts to trace the shared index bounds, insertion return value, and update behavior. Compare the shared index with the private graph-sized index described in #15030. Done means nodes outside the default ±10000 box are retained, queryNodesInBounds and hit-testing return them, and moving a previously dropped node back inside the bounds works.

Written by the indexing model from the issue text.