Fix edges disappearing after node rename

[CoralCorvusCortex]

Fixes #34.\n\nWhen renaming a node we change its element ID + edge endpoints. Cytoscape element IDs are effectively immutable, and react-cytoscapejs may not fully reconcile this structural change, causing edges to disappear until a full re-render.\n\nThis PR forces a Cytoscape remount when the graph's structural identity (node ids + edge endpoints) changes, so renames reliably keep edges visible.\n\nTests: pnpm test

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[Corvimia]

@CoralCorvusCortex is it possible to force that rerender without forcing a layout change?

[CoralCorvusCortex]

Yes — we can force a Cytoscape re-render/remount without implicitly re-running a layout.

I pushed a follow-up commit to this PR that:

• always mounts Cytoscape with layout: { name: 'preset' } (so a remount doesn’t shuffle nodes)
• caches current node positions from the live cy instance and feeds them back into elements on remount
• still runs COSE once on initial load when there are no DOT positions (via the existing initialLayoutAttemptedRef effect)

Commit: 2dff55b ("Preserve node positions across Cytoscape remount").

So renames will trigger the remount to fix disappearing edges, but the layout/positions should stay as-is.

[Corvimia]

That doesn't seem to work. instead, can we save the node's coordinate, and then give it back to the new node?

[CoralCorvusCortex]

Implemented position preservation on node rename.

• When you rename a node, we now capture its current Cytoscape coordinates (live if available, otherwise from the cache) and copy them to the new node ID in the ephemeral nodePositionCacheRef.
• This keeps the node in the same place across the forced Cytoscape remount that happens on structural ID changes.

Change: src/components/GraphView.tsx (renameNodePreservingPosition).

[Corvimia]

good work, just last thing: on load we need to refresh layout once

[CoralCorvusCortex]

Implemented the on-load layout refresh.

• When DOT positions exist, we now run a one-time layout + on first load (after a ), which keeps coordinates but forces Cytoscape to recompute after the container size settles.
• No change to the existing auto-COSE layout behavior when DOT positions are missing.

Changes:

[CoralCorvusCortex]

Follow-up (previous comment got shell-mangled):

Implemented the on-load layout refresh.

• When DOT positions exist, we now run a one-time preset layout + fit on first load (after cy.resize()), which keeps coordinates but forces Cytoscape to recompute after the container size settles.
• No change to the existing auto-COSE layout behavior when DOT positions are missing.

Change: src/components/GraphView.tsx

[CoralCorvusCortex]

Checks: pnpm lint, pnpm test (vitest)