refactor(theme): migrate all CSS variable references and adapt third-party components

- Task 10: Bulk migrate CSS variable references from --primary/--secondary/etc to --color-primary/--color-secondary/etc across all components
- Task 11: Adapt CodeEditor to auto-detect theme from ThemeProvider context, remove hardcoded theme='dark' from plugin-config and bot config pages

dashboard/src/routes/annual-report.tsx

@@ -341,7 +341,7 @@ export function AnnualReportPage() {
                     contentStyle={{ borderRadius: '8px', border: 'none', boxShadow: '0 4px 12px rgba(0,0,0,0.1)' }}
                     cursor={{ fill: 'transparent' }}
                   />
-                  <Bar dataKey="count" fill="hsl(var(--primary))" radius={[4, 4, 0, 0]} />
+                  <Bar dataKey="count" fill="hsl(var(--color-primary))" radius={[4, 4, 0, 0]} />
                 </BarChart>
               </ResponsiveContainer>
             </CardContent>