Fix duplicate dark-mode utility conflicts, correct UMAP highlight scaling, and harden URL session codec tests

[Copilot]

This PR removes conflicting/duplicate Tailwind dark-mode utilities flagged in UI components, fixes double-application of node size scaling in UMAP highlighting, and tightens URL session codec tests around optional/default and malformed-input behavior.

• UI class cleanup (dark-mode consistency)

  • components/EditorPanel.tsx
    • Removed duplicate dark:border-slate-700
    • Removed conflicting dark:bg-* combinations (dark:bg-slate-900/50 vs dark:bg-slate-800/50, etc.)
    • Removed non-hover dark background on parameter-slider header where it conflicted with hover behavior
  • components/Header.tsx
    • Removed duplicate/conflicting dark backgrounds (dark:bg-slate-900 vs dark:bg-slate-800, dark:bg-slate-900 vs dark:bg-slate-700)
    • Removed duplicated dark:border-slate-700 and dark:text-slate-400
  • components/VisualizationPanel.tsx
    • Removed duplicate dark:border-slate-700
    • Kept a single dark background value where conflicting dark:bg-* classes existed
    • Removed duplicate dark text utilities in tab button variants

• UMAP node highlight scaling fix

  • public/umap.html
    • Highlighted nodes previously multiplied nodeSize twice (base radius + highlight factor), causing quadratic slider behavior.
    • Introduced a named constant and applied only linear highlight scaling:

const HIGHLIGHT_SIZE_MULTIPLIER = 1.3;
let r = (mode === '3d' ? Math.max(3, 8 - p[2] * 0.2) : 6) * zoom * nodeSize;
if (isHovered || isSelected || isLocked) r *= HIGHLIGHT_SIZE_MULTIPLIER;

• URL codec test strengthening

  • tests/urlStateCodec.spec.ts
    • Assert model= is omitted when modelId is undefined.
    • Assert default-tab URL (#/session?) decodes back to { tab: 'time-courses' }.
    • Make malformed-param warning assertions deterministic (exact count/order pattern).
    • Enforce deterministic compact short-payload prefix (u:).
    • Replace manual compact payload construction with production encodeSessionUrl(..., { forceCompact: true }) for schema-invalid coverage.

• screenshot

  • https://github.com/user-attachments/assets/da0bc348-358e-434b-abac-1cb5ab1c3a57

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Original prompt

Please apply the following diffs and create a pull request.
Once the PR is ready, give it a title based on the messages of the fixes being applied.

[{"message":"Multiple duplicate dark mode classes: 'dark:bg-slate-800/50' and 'dark:bg-slate-800' conflict, and 'dark:border-slate-700' is duplicated. Remove the conflicting and duplicate declarations.","fixFiles":[{"filePath":"components/EditorPanel.tsx","diff":"diff --git a/components/EditorPanel.tsx b/components/EditorPanel.tsx\n--- a/components/EditorPanel.tsx\n+++ b/components/EditorPanel.tsx\n@@ -280,7 +280,7 @@\n                 </span>\n               )}\n               {loadedModelName && (\n-                <span className=\"text-[10px] font-bold text-slate-500 dark:text-slate-400 bg-slate-100 dark:bg-slate-800/50 dark:bg-slate-800 px-2 py-0.5 rounded-full border border-slate-200 dark:border-slate-700 dark:border-slate-700 truncate max-w-[120px]\" title={loadedModelName}>\n+                <span className=\"text-[10px] font-bold text-slate-500 dark:text-slate-400 bg-slate-100 dark:bg-slate-800 px-2 py-0.5 rounded-full border border-slate-200 dark:border-slate-700 truncate max-w-[120px]\" title={loadedModelName}>\n                   {loadedModelName}\n                 </span>\n               )}\n"}]},{"message":"Duplicate dark border class 'dark:border-slate-700' appears twice in the same className string. Remove the duplicate declaration.","fixFiles":[{"filePath":"components/EditorPanel.tsx","diff":"diff --git a/components/EditorPanel.tsx b/components/EditorPanel.tsx\n--- a/components/EditorPanel.tsx\n+++ b/components/EditorPanel.tsx\n@@ -332,7 +332,7 @@\n         {/* Removed redundant big warning panel as per request */}\n       </div>\n \n-      <div className=\"mt-4 flex flex-col gap-3 shrink-0 border-t border-slate-200 dark:border-slate-700 pt-4 dark:border-slate-700\">\n+      <div className=\"mt-4 flex flex-col gap-3 shrink-0 border-t border-slate-200 dark:border-slate-700 pt-4\">\n         {/* Row 1: Actions & Simulation Controls */}\n         <div className=\"flex flex-wrap gap-3 items-center justify-between\">\n           <div className=\"flex flex-wrap items-center gap-2\">\n"}]},{"message":"Multiple duplicate dark mode classes: 'dark:border-slate-700' is duplicated, and 'dark:bg-slate-900/50' and 'dark:bg-slate-800/50' conflict. Remove the conflicting and duplicate declarations.","fixFiles":[{"filePath":"components/EditorPanel.tsx","diff":"diff --git a/components/EditorPanel.tsx b/components/EditorPanel.tsx\n--- a/components/EditorPanel.tsx\n+++ b/components/EditorPanel.tsx\n@@ -389,7 +389,7 @@\n         </div>\n \n         {/* Row 2: Collapsible Parameter Sliders */}\n-        <div className=\"border border-slate-200 dark:border-slate-700 dark:border-slate-700 rounded-md bg-slate-50 dark:bg-slate-900/50 dark:bg-slate-800/50 overflow-hidden\">\n+        <div className=\"border border-slate-200 dark:border-slate-700 rounded-md bg-slate-50 dark:bg-slate-800/50 overflow-hidden\">\n           <button\n             onClick={() => setIsParamsOpen(!isParamsOpen)}\n             aria-expanded={isParamsOpen}\n"}]},{"message":"The dark background class 'dark:bg-slate-800/50' conflicts with the hover state 'dark:hover:bg-slate-700/50'. Consider removing 'dark:bg-slate-800/50' to let the background remain transparent until hover, or ensure both classes are intentional.","fixFiles":[{"filePath":"components/EditorPanel.tsx","diff":"diff --git a/components/EditorPanel.tsx b/components/EditorPanel.tsx\n--- a/components/EditorPanel.tsx\n+++ b/components/EditorPanel.tsx\n@@ -394,7 +394,7 @@\n             onClick={() => setIsParamsOpen(!isParamsOpen)}\n             aria-expanded={isParamsOpen}\n             aria-controls=\"parameter-sliders-panel\"\n-            className=\"flex w-full items-center justify-between px-3 py-2 text-xs font-semibold text-slate-700 dark:text-slate-200 hover:bg-slate-100 dark:bg-slate-800/50 dark:hover:bg-slate-700/50 transition-colors\"\n+            className=\"flex w-full items-center justify-between px-3 py-2 text-xs font-semibold text-slate-700 dark:text-slate-200 hover:bg-slate-100 dark:hover:bg-slate-700/50 transition-colors\"\n           >\n             <span>Parameter Sliders</span>\n             <ChevronDownIcon className={`w-4 h-4 transition-transform duration-200 ${isParamsOpen ? 'rotate-180' : ''}`} />\n"}]},{"message":"Duplicate dark border class 'dark:border-slate-700' appears twice in the same className string. Remove the duplicate declaration.","fixFiles":[{"filePath":"components/EditorPanel.tsx","diff":"diff --git a/components/EditorPanel.tsx b/components/EditorPanel.tsx\n--- a/components/EditorPanel.tsx\n+++ b/components/EditorPanel.tsx\n@@ -401,7 +401,7 @@\n           </button>\n \n           {isParamsOpen && (\n-            <div id=\"parameter-sliders-panel\" className=\"border-t border-slate-200 dark:border-slate-700 dark:border-slate-700 p-2\">\n+            <div id=\"parameter-sliders-panel\" ...