Skip auto-navigation population when template defines explicit sections

When a MintlifyTemplate specifies Tabs, Anchors, Dropdowns, or Products
directly in the <Navigation> XML, the renderer was still calling
PopulateNavigationFromPath which unconditionally initialized Pages and
auto-discovered MDX files from disk. This produced a spurious
"navigation.pages" block alongside the explicit "navigation.tabs" in the
output docs.json.

Fix by checking for explicit navigation sections after loading the
template config and skipping both PopulateNavigationFromPath and
BuildNavigationStructure when they are present. The NavigationType-based
auto-generation path (where Pages are discovered then moved to a Tab by
ApplyNavigationType) is unaffected.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: robertmclaws

src/CloudNimble.DotNetDocs.Mintlify/MintlifyRenderer.cs

@@ -136,14 +136,27 @@ public async Task RenderAsync(DocAssembly? model)
                     .Where(d => !string.IsNullOrWhiteSpace(d))
                     .ToArray();
 
-                // First: Discover existing MDX files in documentation root, preserving template navigation
-                // Exclude DocumentationReference output directories to prevent them from being treated as conceptual docs
-                _docsJsonManager.PopulateNavigationFromPath(Context.DocumentationRootPath, new[] { ".mdx" }, includeApiReference: false, preserveExisting: true, excludeDirectories: excludeDirectories);
-
-                // Second: Add API reference content to existing navigation ONLY if model exists
-                if (model is not null)
-                {
-                    BuildNavigationStructure(_docsJsonManager.Configuration!, model);
+                // Determine whether the template already defines explicit navigation sections.
+                // When Tabs, Anchors, Dropdowns, or Products are present, all navigation is
+                // managed by the template — auto-discovery into Pages would produce a spurious
+                // parallel "pages" block alongside the explicit sections.
+                var templateNav = _docsJsonManager.Configuration?.Navigation;
+                var hasExplicitSections = templateNav?.Tabs is not null
+                    || templateNav?.Anchors is not null
+                    || templateNav?.Dropdowns is not null
+                    || templateNav?.Products is not null;
+
+                if (!hasExplicitSections)
+                {
+                    // First: Discover existing MDX files in documentation root, preserving template navigation
+                    // Exclude DocumentationReference output directories to prevent them from being treated as conceptual docs
+                    _docsJsonManager.PopulateNavigationFromPath(Context.DocumentationRootPath, new[] { ".mdx" }, includeApiReference: false, preserveExisting: true, excludeDirectories: excludeDirectories);
+
+                    // Second: Add API reference content to existing navigation ONLY if model exists
+                    if (model is not null)
+                    {
+                        BuildNavigationStructure(_docsJsonManager.Configuration!, model);
+                    }
                 }
 
                 // Third: Apply NavigationType from template to move root content to Tabs/Products if configured