Add unified API landing page and fix footer layout

- Add docs/api/ Doxygen target with a landing page linking to
  Pre-Process, Simulation, and Post-Process API docs
- Consolidate sidebar from 4 links to 2: "User Guide" and
  "API Documentation" (highlights for all API sub-projects)
- Unify browser tab title to "MFC" across all Doxygen targets
- Fix footer blank space caused by missing #nav-path element
  that navtree.js needs for content height calculation

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

Author: sbryngelson

CMakeLists.txt

@@ -803,9 +803,10 @@ if (MFC_DOCUMENTATION)
          \"${CMAKE_CURRENT_SOURCE_DIR}/docs/custom.css\"")
 
     # > Generate Documentation & Landing Page
-    GEN_DOCS(pre_process   "MFC: Pre-Process")
-    GEN_DOCS(simulation    "MFC: Simulation")
-    GEN_DOCS(post_process  "MFC: Post-Process")
+    GEN_DOCS(pre_process   "MFC")
+    GEN_DOCS(simulation    "MFC")
+    GEN_DOCS(post_process  "MFC")
+    GEN_DOCS(api           "MFC")
     GEN_DOCS(documentation "MFC")
 
     # Generate API landing pages for pre_process, simulation, post_process.
@@ -826,6 +827,7 @@ if (MFC_DOCUMENTATION)
     add_dependencies(pre_process_doxygen gen_api_landing)
     add_dependencies(simulation_doxygen gen_api_landing)
     add_dependencies(post_process_doxygen gen_api_landing)
+    add_dependencies(api_doxygen gen_api_landing)
 
     # Fix @file/@brief headers to match actual module/program declarations.
     # Handles mixed-case Fortran names and catches stale module renames.

docs/api/readme.md

@@ -0,0 +1,17 @@
+@mainpage API Documentation
+
+MFC's source code is organized into three components that form a complete simulation pipeline. Each component has full module-level API documentation.
+
+### [Pre-Process](../pre_process/index.html)
+
+The pre-process component generates initial conditions and computational meshes for MFC simulations. It supports patch-based geometry construction, multi-component material initialization, and immersed boundary geometry.
+
+### [Simulation](../simulation/index.html)
+
+The simulation component is the core flow solver. It advances the governing equations in time using high-order finite-volume methods on structured grids with GPU acceleration via OpenACC/OpenMP offloading.
+
+### [Post-Process](../post_process/index.html)
+
+The post-process component reads raw simulation output and computes derived quantities for visualization. It produces silo/HDF5 files compatible with VisIt, ParaView, and other visualization tools.
+
+All three components share a set of **common modules** for MPI communication, variable conversion, derived types, and utility functions. These are documented within each component's API reference.

docs/custom.css

@@ -3,6 +3,12 @@
  * Overrides for doxygen-awesome theme
  */
 
+/* Hide empty nav-path footer (kept for navtree.js height calculation) */
+#nav-path {
+    height: 0;
+    overflow: hidden;
+}
+
 /* Cross-navigation panel at top of sidebar */
 #mfc-nav {
     display: flex;

docs/footer.html

@@ -1,6 +1,9 @@
 <!-- HTML footer for doxygen 1.9.1-->
 <!-- start footer part -->
 <!--BEGIN GENERATE_TREEVIEW-->
+<div id="nav-path" class="navpath">
+  <ul></ul>
+</div>
 <!--END GENERATE_TREEVIEW-->
 <!--BEGIN !GENERATE_TREEVIEW-->
 <!--END !GENERATE_TREEVIEW-->

docs/gen_api_landing.py

@@ -1,11 +1,12 @@
 #!/usr/bin/env python3
-"""Generate API landing pages for pre_process, simulation, and post_process.
+"""Generate API landing pages for MFC documentation.
 
 Usage: python3 gen_api_landing.py [source_dir]
   source_dir defaults to current directory.
 
 Scans src/{target}/*.fpp,*.f90 and src/common/*.fpp,*.f90 to produce module
-tables in docs/{target}/readme.md. Intro text is defined below per target.
+tables in docs/{target}/readme.md. Also generates a unified API landing page
+at docs/api/readme.md that links to all three sub-project APIs.
 """
 
 from __future__ import annotations
@@ -149,3 +150,31 @@ def get_modules(directory: Path) -> list[tuple[str, str]]:
     out.parent.mkdir(parents=True, exist_ok=True)
     out.write_text("\n".join(lines), encoding="utf-8")
     print(f"Generated {out}")
+
+# --- Unified API landing page ---
+api_lines = [
+    "@mainpage API Documentation",
+    "",
+    "MFC's source code is organized into three components that form a complete "
+    "simulation pipeline. Each component has full module-level API documentation.",
+    "",
+]
+
+for target, info in TARGETS.items():
+    label = info["title"].replace("MFC ", "")
+    api_lines.append(f"### [{label}](../{target}/index.html)")
+    api_lines.append("")
+    api_lines.append(info["intro"])
+    api_lines.append("")
+
+api_lines.append(
+    "All three components share a set of **common modules** for MPI communication, "
+    "variable conversion, derived types, and utility functions. "
+    "These are documented within each component's API reference."
+)
+api_lines.append("")
+
+api_out = src_dir / "docs" / "api" / "readme.md"
+api_out.parent.mkdir(parents=True, exist_ok=True)
+api_out.write_text("\n".join(api_lines), encoding="utf-8")
+print(f"Generated {api_out}")

docs/header.html

@@ -73,16 +73,21 @@
   nav.id = 'mfc-nav';
   var items = [
     ['../documentation/index.html', 'documentation', 'User Guide'],
-    ['../pre_process/index.html',   'pre_process',   'Pre-Process API'],
-    ['../simulation/index.html',    'simulation',    'Simulation API'],
-    ['../post_process/index.html',  'post_process',  'Post-Process API']
+    ['../api/index.html',           'api',           'API Documentation']
   ];
   var path = window.location.pathname;
+  var apiPaths = ['/api/', '/pre_process/', '/simulation/', '/post_process/'];
   for (var i = 0; i < items.length; i++) {
     var a = document.createElement('a');
     a.href = items[i][0];
     a.textContent = items[i][2];
-    if (path.indexOf('/' + items[i][1] + '/') !== -1) a.className = 'active';
+    if (items[i][1] === 'api') {
+      for (var j = 0; j < apiPaths.length; j++) {
+        if (path.indexOf(apiPaths[j]) !== -1) { a.className = 'active'; break; }
+      }
+    } else {
+      if (path.indexOf('/' + items[i][1] + '/') !== -1) a.className = 'active';
+    }
     nav.appendChild(a);
   }
   var sideNav = document.getElementById('side-nav');