diff --git a/.run/pytest.run.xml b/.run/pytests.run.xml
similarity index 94%
rename from .run/pytest.run.xml
rename to .run/pytests.run.xml
index b923b9b..07542e6 100644
--- a/.run/pytest.run.xml
+++ b/.run/pytests.run.xml
@@ -1,5 +1,5 @@
 <component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="pytest" type="tests" factoryName="py.test">
+  <configuration default="false" name="pytests" type="tests" factoryName="py.test">
     <module name="docforge" />
     <option name="ENV_FILES" value="" />
     <option name="INTERPRETER_OPTIONS" value="" />
diff --git a/docforge.nav.yml b/docforge.nav.yml
index 9d484b5..c152294 100644
--- a/docforge.nav.yml
+++ b/docforge.nav.yml
@@ -1,26 +1,26 @@
-home: docforge/index.md
+home: index.md
 groups:
   Loaders:
-    - docforge/loaders/index.md
-    - docforge/loaders/griffe_loader.md
+    - loaders/index.md
+    - loaders/griffe_loader.md
   Models:
-    - docforge/models/index.md
-    - docforge/models/module.md
-    - docforge/models/object.md
-    - docforge/models/project.md
+    - models/index.md
+    - models/module.md
+    - models/object.md
+    - models/project.md
   Navigation:
-    - docforge/nav/index.md
-    - docforge/nav/spec.md
-    - docforge/nav/resolver.md
-    - docforge/nav/mkdocs.md
+    - nav/index.md
+    - nav/spec.md
+    - nav/resolver.md
+    - nav/mkdocs.md
   Renderers:
-    - docforge/renderers/index.md
-    - docforge/renderers/base.md
-    - docforge/renderers/mkdocs_renderer.md
-    - docforge/renderers/mcp_renderer.md
+    - renderers/index.md
+    - renderers/base.md
+    - renderers/mkdocs_renderer.md
+    - renderers/mcp_renderer.md
   CLI:
-    - docforge/cli/index.md
-    - docforge/cli/main.md
-    - docforge/cli/commands.md
-    - docforge/cli/mcp_utils.md
-    - docforge/cli/mkdocs_utils.md
+    - cli/index.md
+    - cli/main.md
+    - cli/commands.md
+    - cli/mcp_utils.md
+    - cli/mkdocs_utils.md
diff --git a/docforge/cli/commands.py b/docforge/cli/commands.py
index 335f818..12305a4 100644
--- a/docforge/cli/commands.py
+++ b/docforge/cli/commands.py
@@ -18,6 +18,7 @@ def cli() -> None:
 @cli.command()
 @click.option("--mcp", is_flag=True, help="Build MCP resources")
 @click.option("--mkdocs", is_flag=True, help="Build MkDocs site")
+@click.option("--module-is-source", is_flag=True, help="Module is source folder and to be treated as root folder")
 @click.option("--module", help="Python module to document")
 @click.option("--project-name", help="Project name override")
 # MkDocs specific
@@ -32,6 +33,7 @@ def cli() -> None:
 def build(
     mcp: bool,
     mkdocs: bool,
+    module_is_source: bool,
     module: Optional[str],
     project_name: Optional[str],
     site_name: Optional[str],
@@ -52,7 +54,8 @@ def build(
     Args:
         mcp: Use the MCP documentation builder.
         mkdocs: Use the MkDocs documentation builder.
-        module: The dotted path of the module to document.
+        module_is_source: Module is the source folder and to be treated as the root folder.
+        module: The dotted path of the module to the document.
         project_name: Optional override for the project name.
         site_name: (MkDocs) The site display name. Defaults to module name.
         docs_dir: (MkDocs) Target directory for Markdown sources.
@@ -71,7 +74,12 @@ def build(
             site_name = module
 
         click.echo(f"Generating MkDocs sources in {docs_dir}...")
-        mkdocs_utils.generate_sources(module, project_name, docs_dir)
+        mkdocs_utils.generate_sources(
+            module,
+            docs_dir,
+            project_name,
+            module_is_source,
+        )
 
         click.echo(f"Generating MkDocs config {mkdocs_yml}...")
         mkdocs_utils.generate_config(docs_dir, nav_file, template, mkdocs_yml, site_name)
diff --git a/docforge/cli/commands.pyi b/docforge/cli/commands.pyi
index df4f535..a38d851 100644
--- a/docforge/cli/commands.pyi
+++ b/docforge/cli/commands.pyi
@@ -7,6 +7,7 @@ cli: Group
 def build(
     mcp: bool,
     mkdocs: bool,
+    module_is_source: bool,
     module: Optional[str],
     project_name: Optional[str],
     site_name: Optional[str],
diff --git a/docforge/cli/mkdocs_utils.py b/docforge/cli/mkdocs_utils.py
index 5f9f68e..1c135bd 100644
--- a/docforge/cli/mkdocs_utils.py
+++ b/docforge/cli/mkdocs_utils.py
@@ -6,7 +6,12 @@ from docforge.loaders import GriffeLoader, discover_module_paths
 from docforge.renderers import MkDocsRenderer
 from docforge.nav import load_nav_spec, resolve_nav, MkDocsNavEmitter
 
-def generate_sources(module: str, project_name: str | None, docs_dir: Path) -> None:
+def generate_sources(
+    module: str,
+    docs_dir: Path,
+    project_name: str | None = None,
+    module_is_source: bool | None = None,
+) -> None:
     """
     Generate Markdown source files for the specified module.
 
@@ -14,13 +19,18 @@ def generate_sources(module: str, project_name: str | None, docs_dir: Path) -> N
         module: The dotted path of the primary module to document.
         project_name: Optional override for the project name.
         docs_dir: Directory where the generated Markdown files will be written.
+        module_is_source: Module is the source folder and to be treated as the root folder.
     """
     loader = GriffeLoader()
     discovered_paths = discover_module_paths(module)
     project = loader.load_project(discovered_paths, project_name)
 
     renderer = MkDocsRenderer()
-    renderer.generate_sources(project, docs_dir)
+    renderer.generate_sources(
+        project,
+        docs_dir,
+        module_is_source,
+    )
 
 def generate_config(docs_dir: Path, nav_file: Path, template: Path | None, out: Path, site_name: str) -> None:
     """
diff --git a/docforge/cli/mkdocs_utils.pyi b/docforge/cli/mkdocs_utils.pyi
index fc23e03..052bee9 100644
--- a/docforge/cli/mkdocs_utils.pyi
+++ b/docforge/cli/mkdocs_utils.pyi
@@ -1,6 +1,11 @@
 from pathlib import Path
 
-def generate_sources(module: str, project_name: str | None, docs_dir: Path) -> None: ...
+def generate_sources(
+    module: str,
+    docs_dir: Path,
+    project_name: str | None = None,
+    module_is_source: bool | None = None,
+) -> None: ...
 def generate_config(docs_dir: Path, nav_file: Path, template: Path | None, out: Path, site_name: str) -> None: ...
 def build(mkdocs_yml: Path) -> None: ...
 def serve(mkdocs_yml: Path) -> None: ...
diff --git a/docforge/renderers/mkdocs_renderer.py b/docforge/renderers/mkdocs_renderer.py
index 8edd3d1..b851812 100644
--- a/docforge/renderers/mkdocs_renderer.py
+++ b/docforge/renderers/mkdocs_renderer.py
@@ -1,11 +1,16 @@
 """
-This module implements the MkDocsRenderer, which generates Markdown source files
-compatible with the MkDocs 'material' theme and 'mkdocstrings' extension.
+MkDocsRenderer
+
+Generates Markdown source files compatible with MkDocs Material
+and mkdocstrings, ensuring:
+
+- Root index.md always exists
+- Parent package indexes are created automatically
+- Child modules are linked in parent index files
 """
 
 from pathlib import Path
-
-from docforge.models import Project
+from docforge.models import Project, Module
 
 
 class MkDocsRenderer:
@@ -16,7 +21,15 @@ class MkDocsRenderer:
 
     name = "mkdocs"
 
-    def generate_sources(self, project: Project, out_dir: Path) -> None:
+    # -------------------------
+    # Public API
+    # -------------------------
+    def generate_sources(
+        self,
+        project: Project,
+        out_dir: Path,
+        module_is_source: bool | None = None,
+    ) -> None:
         """
         Produce a set of Markdown files in the output directory based on the
         provided Project models.
@@ -24,7 +37,11 @@ class MkDocsRenderer:
         Args:
             project: The project models to render.
             out_dir: Target directory for documentation files.
+            module_is_source: Module is the source folder and to be treated as the root folder.
         """
+        out_dir.mkdir(parents=True, exist_ok=True)
+        self._ensure_root_index(project, out_dir)
+
         modules = list(project.get_all_modules())
         paths = {m.path for m in modules}
 
@@ -35,12 +52,23 @@ class MkDocsRenderer:
         }
 
         for module in modules:
-            self._write_module(module, packages, out_dir)
+            self._write_module(
+                module,
+                packages,
+                out_dir,
+                module_is_source,
+            )
 
     # -------------------------
     # Internal helpers
     # -------------------------
-    def _write_module(self, module, packages: set[str], out_dir: Path) -> None:
+    def _write_module(
+        self,
+        module: Module,
+        packages: set[str],
+        out_dir: Path,
+        module_is_source: bool | None = None,
+    ) -> None:
         """
         Write a single module's documentation file. Packages are written as
         'index.md' inside their respective directories.
@@ -49,30 +77,36 @@ class MkDocsRenderer:
             module: The module to write.
             packages: A set of module paths that are identified as packages.
             out_dir: The base output directory.
+            module_is_source: Module is the source folder and to be treated as the root folder.
         """
         parts = module.path.split(".")
 
+        if module_is_source:
+            module_name, parts = parts[0], parts[1:]
+        else:
+            module_name, parts = parts[0], parts
+
         if module.path in packages:
-            # package → index.md
+            # Package → directory/index.md
             dir_path = out_dir.joinpath(*parts)
             dir_path.mkdir(parents=True, exist_ok=True)
-
             md_path = dir_path / "index.md"
-            title = parts[-1].replace("_", " ").title()
+            link_target = f"{parts[-1]}/" if parts else None
         else:
-            # leaf module → <name>.md
+            # Leaf module → parent_dir/<name>.md
             dir_path = out_dir.joinpath(*parts[:-1])
             dir_path.mkdir(parents=True, exist_ok=True)
-
             md_path = dir_path / f"{parts[-1]}.md"
-            title = parts[-1].replace("_", " ").title()
+            link_target = f"{parts[-1]}.md" if parts else None
 
+        title = parts[-1].replace("_", " ").title() if parts else module_name
         content = self._render_markdown(title, module.path)
 
-        if md_path.exists() and md_path.read_text(encoding="utf-8") == content:
-            return
+        if not md_path.exists() or md_path.read_text(encoding="utf-8") != content:
+            md_path.write_text(content, encoding="utf-8")
 
-        md_path.write_text(content, encoding="utf-8")
+        if not module_is_source:
+            self._ensure_parent_index(parts, out_dir, link_target, title)
 
     def _render_markdown(self, title: str, module_path: str) -> str:
         """
@@ -89,3 +123,46 @@ class MkDocsRenderer:
             f"# {title}\n\n"
             f"::: {module_path}\n"
         )
+
+    def _ensure_root_index(
+        self,
+        project: Project,
+        out_dir: Path
+    ) -> None:
+        root_index = out_dir / "index.md"
+
+        if not root_index.exists():
+            root_index.write_text(
+                f"# {project.name}\n\n"
+                "## Modules\n\n",
+                encoding="utf-8",
+            )
+
+    def _ensure_parent_index(
+        self,
+        parts: list[str],
+        out_dir: Path,
+        link_target: str,
+        title: str,
+    ) -> None:
+        if len(parts) == 1:
+            parent_index = out_dir / "index.md"
+            link = f"- [{title}]({link_target})\n"
+        else:
+            parent_dir = out_dir.joinpath(*parts[:-1])
+            parent_dir.mkdir(parents=True, exist_ok=True)
+            parent_index = parent_dir / "index.md"
+
+            link = f"- [{title}]({link_target})\n"
+
+            if not parent_index.exists():
+                parent_title = parts[-2].replace("_", " ").title()
+                parent_index.write_text(
+                    f"# {parent_title}\n\n",
+                    encoding="utf-8",
+                )
+
+        content = parent_index.read_text(encoding="utf-8")
+
+        if link not in content:
+            parent_index.write_text(content + link, encoding="utf-8")
diff --git a/docforge/renderers/mkdocs_renderer.pyi b/docforge/renderers/mkdocs_renderer.pyi
index b3f3f7c..130e4dc 100644
--- a/docforge/renderers/mkdocs_renderer.pyi
+++ b/docforge/renderers/mkdocs_renderer.pyi
@@ -1,17 +1,27 @@
 from pathlib import Path
-from typing import Set
-
 from docforge.models import Project, Module
 
 
 class MkDocsRenderer:
     name: str
 
-    def generate_sources(self, project: Project, out_dir: Path) -> None: ...
+    def generate_sources(
+        self,
+        project: Project,
+        out_dir: Path,
+        module_is_source: bool | None = None,
+    ) -> None: ...
+
     def _write_module(
         self,
         module: Module,
-        packages: Set[str],
+        packages: set[str],
         out_dir: Path,
+        module_is_source: bool | None = None,
     ) -> None: ...
+
     def _render_markdown(self, title: str, module_path: str) -> str: ...
+
+    def _ensure_root_index(self, project, out_dir) -> None: ...
+
+    def _ensure_parent_index(self, parts, out_dir, link_target, title) -> None: ...
diff --git a/docs/docforge/cli/commands.md b/docs/cli/commands.md
similarity index 100%
rename from docs/docforge/cli/commands.md
rename to docs/cli/commands.md
diff --git a/docs/docforge/cli/index.md b/docs/cli/index.md
similarity index 100%
rename from docs/docforge/cli/index.md
rename to docs/cli/index.md
diff --git a/docs/docforge/cli/main.md b/docs/cli/main.md
similarity index 100%
rename from docs/docforge/cli/main.md
rename to docs/cli/main.md
diff --git a/docs/docforge/cli/mcp_utils.md b/docs/cli/mcp_utils.md
similarity index 100%
rename from docs/docforge/cli/mcp_utils.md
rename to docs/cli/mcp_utils.md
diff --git a/docs/docforge/cli/mkdocs_utils.md b/docs/cli/mkdocs_utils.md
similarity index 100%
rename from docs/docforge/cli/mkdocs_utils.md
rename to docs/cli/mkdocs_utils.md
diff --git a/docs/docforge/index.md b/docs/index.md
similarity index 56%
rename from docs/docforge/index.md
rename to docs/index.md
index 86fda32..96e8919 100644
--- a/docs/docforge/index.md
+++ b/docs/index.md
@@ -1,3 +1,3 @@
-# Docforge
+# docforge
 
 ::: docforge
diff --git a/docs/docforge/loaders/griffe_loader.md b/docs/loaders/griffe_loader.md
similarity index 100%
rename from docs/docforge/loaders/griffe_loader.md
rename to docs/loaders/griffe_loader.md
diff --git a/docs/docforge/loaders/index.md b/docs/loaders/index.md
similarity index 100%
rename from docs/docforge/loaders/index.md
rename to docs/loaders/index.md
diff --git a/docs/docforge/models/index.md b/docs/models/index.md
similarity index 100%
rename from docs/docforge/models/index.md
rename to docs/models/index.md
diff --git a/docs/docforge/models/module.md b/docs/models/module.md
similarity index 100%
rename from docs/docforge/models/module.md
rename to docs/models/module.md
diff --git a/docs/docforge/models/object.md b/docs/models/object.md
similarity index 100%
rename from docs/docforge/models/object.md
rename to docs/models/object.md
diff --git a/docs/docforge/models/project.md b/docs/models/project.md
similarity index 100%
rename from docs/docforge/models/project.md
rename to docs/models/project.md
diff --git a/docs/docforge/nav/index.md b/docs/nav/index.md
similarity index 100%
rename from docs/docforge/nav/index.md
rename to docs/nav/index.md
diff --git a/docs/docforge/nav/mkdocs.md b/docs/nav/mkdocs.md
similarity index 100%
rename from docs/docforge/nav/mkdocs.md
rename to docs/nav/mkdocs.md
diff --git a/docs/docforge/nav/resolver.md b/docs/nav/resolver.md
similarity index 100%
rename from docs/docforge/nav/resolver.md
rename to docs/nav/resolver.md
diff --git a/docs/docforge/nav/spec.md b/docs/nav/spec.md
similarity index 100%
rename from docs/docforge/nav/spec.md
rename to docs/nav/spec.md
diff --git a/docs/docforge/renderers/base.md b/docs/renderers/base.md
similarity index 100%
rename from docs/docforge/renderers/base.md
rename to docs/renderers/base.md
diff --git a/docs/docforge/renderers/index.md b/docs/renderers/index.md
similarity index 100%
rename from docs/docforge/renderers/index.md
rename to docs/renderers/index.md
diff --git a/docs/docforge/renderers/mcp_renderer.md b/docs/renderers/mcp_renderer.md
similarity index 100%
rename from docs/docforge/renderers/mcp_renderer.md
rename to docs/renderers/mcp_renderer.md
diff --git a/docs/docforge/renderers/mkdocs_renderer.md b/docs/renderers/mkdocs_renderer.md
similarity index 100%
rename from docs/docforge/renderers/mkdocs_renderer.md
rename to docs/renderers/mkdocs_renderer.md
diff --git a/docs/docforge/servers/index.md b/docs/servers/index.md
similarity index 100%
rename from docs/docforge/servers/index.md
rename to docs/servers/index.md
diff --git a/docs/docforge/servers/mcp_server.md b/docs/servers/mcp_server.md
similarity index 100%
rename from docs/docforge/servers/mcp_server.md
rename to docs/servers/mcp_server.md
diff --git a/mcp_docs/modules/docforge.cli.commands.json b/mcp_docs/modules/docforge.cli.commands.json
index 3bf3e1e..1d5d04d 100644
--- a/mcp_docs/modules/docforge.cli.commands.json
+++ b/mcp_docs/modules/docforge.cli.commands.json
@@ -139,7 +139,7 @@
                 "kind": "function",
                 "path": "docforge.cli.commands.mkdocs_utils.MkDocsRenderer.generate_sources",
                 "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources')>",
-                "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files."
+                "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files.\n    module_is_source: Module is the source folder and to be treated as the root folder."
               }
             }
           },
@@ -178,7 +178,7 @@
             "kind": "function",
             "path": "docforge.cli.commands.mkdocs_utils.generate_sources",
             "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.cli.mkdocs_utils.generate_sources')>",
-            "docstring": "Generate Markdown source files for the specified module.\n\nArgs:\n    module: The dotted path of the primary module to document.\n    project_name: Optional override for the project name.\n    docs_dir: Directory where the generated Markdown files will be written."
+            "docstring": "Generate Markdown source files for the specified module.\n\nArgs:\n    module: The dotted path of the primary module to document.\n    project_name: Optional override for the project name.\n    docs_dir: Directory where the generated Markdown files will be written.\n    module_is_source: Module is the source folder and to be treated as the root folder."
           },
           "generate_config": {
             "name": "generate_config",
@@ -319,7 +319,7 @@
             "kind": "function",
             "path": "docforge.cli.commands.mcp_utils.serve",
             "signature": "<bound method Alias.signature of Alias('serve', 'docforge.cli.mcp_utils.serve')>",
-            "docstring": "Serve MCP documentation from a pre-built bundle.\n\nArgs:\n    mcp_root: Path to the directory containing index.json, nav.json, and modules/."
+            "docstring": "Serve MCP documentation from a pre-built bundle.\n\nArgs:\n    module: The dotted path of the primary module to serve.\n    mcp_root: Path to the directory containing index.json, nav.json, and modules/."
           }
         }
       },
@@ -334,22 +334,22 @@
         "name": "build",
         "kind": "function",
         "path": "docforge.cli.commands.build",
-        "signature": "<bound method Function.signature of Function('build', 18, 89)>",
-        "docstring": "Build documentation (MkDocs site or MCP resources).\n\nThis command orchestrates the full build process:\n1. Introspects the code (Griffe)\n2. Renders sources (MkDocs Markdown or MCP JSON)\n3. (MkDocs only) Generates config and runs the final site build.\n\nArgs:\n    mcp: Use the MCP documentation builder.\n    mkdocs: Use the MkDocs documentation builder.\n    module: The dotted path of the module to document.\n    project_name: Optional override for the project name.\n    site_name: (MkDocs) The site display name. Defaults to module name.\n    docs_dir: (MkDocs) Target directory for Markdown sources.\n    nav_file: (MkDocs) Path to the docforge.nav.yml specification.\n    template: (MkDocs) Optional custom mkdocs.yml template.\n    mkdocs_yml: (MkDocs) Target path for the generated mkdocs.yml.\n    out_dir: (MCP) Target directory for MCP JSON resources."
+        "signature": "<bound method Function.signature of Function('build', 18, 97)>",
+        "docstring": "Build documentation (MkDocs site or MCP resources).\n\nThis command orchestrates the full build process:\n1. Introspects the code (Griffe)\n2. Renders sources (MkDocs Markdown or MCP JSON)\n3. (MkDocs only) Generates config and runs the final site build.\n\nArgs:\n    mcp: Use the MCP documentation builder.\n    mkdocs: Use the MkDocs documentation builder.\n    module_is_source: Module is the source folder and to be treated as the root folder.\n    module: The dotted path of the module to the document.\n    project_name: Optional override for the project name.\n    site_name: (MkDocs) The site display name. Defaults to module name.\n    docs_dir: (MkDocs) Target directory for Markdown sources.\n    nav_file: (MkDocs) Path to the docforge.nav.yml specification.\n    template: (MkDocs) Optional custom mkdocs.yml template.\n    mkdocs_yml: (MkDocs) Target path for the generated mkdocs.yml.\n    out_dir: (MCP) Target directory for MCP JSON resources."
       },
       "serve": {
         "name": "serve",
         "kind": "function",
         "path": "docforge.cli.commands.serve",
-        "signature": "<bound method Function.signature of Function('serve', 92, 120)>",
-        "docstring": "Serve documentation (MkDocs or MCP).\n\nArgs:\n    mcp: Serve MCP resources via an MCP server.\n    mkdocs: Serve the MkDocs site using the built-in development server.\n    mkdocs_yml: (MkDocs) Path to the mkdocs.yml configuration.\n    out_dir: (MCP) Path to the mcp_docs/ directory."
+        "signature": "<bound method Function.signature of Function('serve', 100, 133)>",
+        "docstring": "Serve documentation (MkDocs or MCP).\n\nArgs:\n    mcp: Serve MCP resources via an MCP server.\n    mkdocs: Serve the MkDocs site using the built-in development server.\n    module: The dotted path of the module to serve.\n    mkdocs_yml: (MkDocs) Path to the mkdocs.yml configuration.\n    out_dir: (MCP) Path to the mcp_docs/ directory."
       },
       "tree": {
         "name": "tree",
         "kind": "function",
         "path": "docforge.cli.commands.tree",
-        "signature": "<bound method Function.signature of Function('tree', 123, 153)>",
-        "docstring": "Visualize the project structure in the terminal.\n\nArgs:\n    modules: List of module import paths to recursively introspect.\n    project_name: Optional override for the project name shown at the root."
+        "signature": "<bound method Function.signature of Function('tree', 136, 165)>",
+        "docstring": "Visualize the project structure in the terminal.\n\nArgs:\n    module: The module import path to recursively introspect.\n    project_name: Optional override for the project name shown at the root."
       },
       "Group": {
         "name": "Group",
diff --git a/mcp_docs/modules/docforge.cli.json b/mcp_docs/modules/docforge.cli.json
index 0b3ab64..51c5aad 100644
--- a/mcp_docs/modules/docforge.cli.json
+++ b/mcp_docs/modules/docforge.cli.json
@@ -169,7 +169,7 @@
                     "kind": "function",
                     "path": "docforge.cli.commands.mkdocs_utils.MkDocsRenderer.generate_sources",
                     "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources')>",
-                    "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files."
+                    "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files.\n    module_is_source: Module is the source folder and to be treated as the root folder."
                   }
                 }
               },
@@ -208,7 +208,7 @@
                 "kind": "function",
                 "path": "docforge.cli.commands.mkdocs_utils.generate_sources",
                 "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.cli.mkdocs_utils.generate_sources')>",
-                "docstring": "Generate Markdown source files for the specified module.\n\nArgs:\n    module: The dotted path of the primary module to document.\n    project_name: Optional override for the project name.\n    docs_dir: Directory where the generated Markdown files will be written."
+                "docstring": "Generate Markdown source files for the specified module.\n\nArgs:\n    module: The dotted path of the primary module to document.\n    project_name: Optional override for the project name.\n    docs_dir: Directory where the generated Markdown files will be written.\n    module_is_source: Module is the source folder and to be treated as the root folder."
               },
               "generate_config": {
                 "name": "generate_config",
@@ -349,7 +349,7 @@
                 "kind": "function",
                 "path": "docforge.cli.commands.mcp_utils.serve",
                 "signature": "<bound method Alias.signature of Alias('serve', 'docforge.cli.mcp_utils.serve')>",
-                "docstring": "Serve MCP documentation from a pre-built bundle.\n\nArgs:\n    mcp_root: Path to the directory containing index.json, nav.json, and modules/."
+                "docstring": "Serve MCP documentation from a pre-built bundle.\n\nArgs:\n    module: The dotted path of the primary module to serve.\n    mcp_root: Path to the directory containing index.json, nav.json, and modules/."
               }
             }
           },
@@ -364,22 +364,22 @@
             "name": "build",
             "kind": "function",
             "path": "docforge.cli.commands.build",
-            "signature": "<bound method Function.signature of Function('build', 18, 89)>",
-            "docstring": "Build documentation (MkDocs site or MCP resources).\n\nThis command orchestrates the full build process:\n1. Introspects the code (Griffe)\n2. Renders sources (MkDocs Markdown or MCP JSON)\n3. (MkDocs only) Generates config and runs the final site build.\n\nArgs:\n    mcp: Use the MCP documentation builder.\n    mkdocs: Use the MkDocs documentation builder.\n    module: The dotted path of the module to document.\n    project_name: Optional override for the project name.\n    site_name: (MkDocs) The site display name. Defaults to module name.\n    docs_dir: (MkDocs) Target directory for Markdown sources.\n    nav_file: (MkDocs) Path to the docforge.nav.yml specification.\n    template: (MkDocs) Optional custom mkdocs.yml template.\n    mkdocs_yml: (MkDocs) Target path for the generated mkdocs.yml.\n    out_dir: (MCP) Target directory for MCP JSON resources."
+            "signature": "<bound method Function.signature of Function('build', 18, 97)>",
+            "docstring": "Build documentation (MkDocs site or MCP resources).\n\nThis command orchestrates the full build process:\n1. Introspects the code (Griffe)\n2. Renders sources (MkDocs Markdown or MCP JSON)\n3. (MkDocs only) Generates config and runs the final site build.\n\nArgs:\n    mcp: Use the MCP documentation builder.\n    mkdocs: Use the MkDocs documentation builder.\n    module_is_source: Module is the source folder and to be treated as the root folder.\n    module: The dotted path of the module to the document.\n    project_name: Optional override for the project name.\n    site_name: (MkDocs) The site display name. Defaults to module name.\n    docs_dir: (MkDocs) Target directory for Markdown sources.\n    nav_file: (MkDocs) Path to the docforge.nav.yml specification.\n    template: (MkDocs) Optional custom mkdocs.yml template.\n    mkdocs_yml: (MkDocs) Target path for the generated mkdocs.yml.\n    out_dir: (MCP) Target directory for MCP JSON resources."
           },
           "serve": {
             "name": "serve",
             "kind": "function",
             "path": "docforge.cli.commands.serve",
-            "signature": "<bound method Function.signature of Function('serve', 92, 120)>",
-            "docstring": "Serve documentation (MkDocs or MCP).\n\nArgs:\n    mcp: Serve MCP resources via an MCP server.\n    mkdocs: Serve the MkDocs site using the built-in development server.\n    mkdocs_yml: (MkDocs) Path to the mkdocs.yml configuration.\n    out_dir: (MCP) Path to the mcp_docs/ directory."
+            "signature": "<bound method Function.signature of Function('serve', 100, 133)>",
+            "docstring": "Serve documentation (MkDocs or MCP).\n\nArgs:\n    mcp: Serve MCP resources via an MCP server.\n    mkdocs: Serve the MkDocs site using the built-in development server.\n    module: The dotted path of the module to serve.\n    mkdocs_yml: (MkDocs) Path to the mkdocs.yml configuration.\n    out_dir: (MCP) Path to the mcp_docs/ directory."
           },
           "tree": {
             "name": "tree",
             "kind": "function",
             "path": "docforge.cli.commands.tree",
-            "signature": "<bound method Function.signature of Function('tree', 123, 153)>",
-            "docstring": "Visualize the project structure in the terminal.\n\nArgs:\n    modules: List of module import paths to recursively introspect.\n    project_name: Optional override for the project name shown at the root."
+            "signature": "<bound method Function.signature of Function('tree', 136, 165)>",
+            "docstring": "Visualize the project structure in the terminal.\n\nArgs:\n    module: The module import path to recursively introspect.\n    project_name: Optional override for the project name shown at the root."
           },
           "Group": {
             "name": "Group",
@@ -512,8 +512,8 @@
             "name": "serve",
             "kind": "function",
             "path": "docforge.cli.mcp_utils.serve",
-            "signature": "<bound method Function.signature of Function('serve', 23, 47)>",
-            "docstring": "Serve MCP documentation from a pre-built bundle.\n\nArgs:\n    mcp_root: Path to the directory containing index.json, nav.json, and modules/."
+            "signature": "<bound method Function.signature of Function('serve', 23, 48)>",
+            "docstring": "Serve MCP documentation from a pre-built bundle.\n\nArgs:\n    module: The dotted path of the primary module to serve.\n    mcp_root: Path to the directory containing index.json, nav.json, and modules/."
           }
         }
       },
@@ -601,7 +601,7 @@
                 "kind": "function",
                 "path": "docforge.cli.mkdocs_utils.MkDocsRenderer.generate_sources",
                 "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources')>",
-                "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files."
+                "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files.\n    module_is_source: Module is the source folder and to be treated as the root folder."
               }
             }
           },
@@ -639,28 +639,28 @@
             "name": "generate_sources",
             "kind": "function",
             "path": "docforge.cli.mkdocs_utils.generate_sources",
-            "signature": "<bound method Function.signature of Function('generate_sources', 9, 23)>",
-            "docstring": "Generate Markdown source files for the specified module.\n\nArgs:\n    module: The dotted path of the primary module to document.\n    project_name: Optional override for the project name.\n    docs_dir: Directory where the generated Markdown files will be written."
+            "signature": "<bound method Function.signature of Function('generate_sources', 9, 33)>",
+            "docstring": "Generate Markdown source files for the specified module.\n\nArgs:\n    module: The dotted path of the primary module to document.\n    project_name: Optional override for the project name.\n    docs_dir: Directory where the generated Markdown files will be written.\n    module_is_source: Module is the source folder and to be treated as the root folder."
           },
           "generate_config": {
             "name": "generate_config",
             "kind": "function",
             "path": "docforge.cli.mkdocs_utils.generate_config",
-            "signature": "<bound method Function.signature of Function('generate_config', 25, 59)>",
+            "signature": "<bound method Function.signature of Function('generate_config', 35, 69)>",
             "docstring": "Generate an mkdocs.yml configuration file.\n\nArgs:\n    docs_dir: Path to the directory containing documentation Markdown files.\n    nav_file: Path to the docforge.nav.yml specification.\n    template: Optional path to an mkdocs.yml template (overrides built-in).\n    out: Path where the final mkdocs.yml will be written.\n    site_name: The display name for the documentation site."
           },
           "build": {
             "name": "build",
             "kind": "function",
             "path": "docforge.cli.mkdocs_utils.build",
-            "signature": "<bound method Function.signature of Function('build', 61, 74)>",
+            "signature": "<bound method Function.signature of Function('build', 71, 84)>",
             "docstring": "Build the documentation site using MkDocs.\n\nArgs:\n    mkdocs_yml: Path to the mkdocs.yml configuration file."
           },
           "serve": {
             "name": "serve",
             "kind": "function",
             "path": "docforge.cli.mkdocs_utils.serve",
-            "signature": "<bound method Function.signature of Function('serve', 76, 87)>",
+            "signature": "<bound method Function.signature of Function('serve', 86, 97)>",
             "docstring": "Serve the documentation site with live-reload using MkDocs.\n\nArgs:\n    mkdocs_yml: Path to the mkdocs.yml configuration file."
           }
         }
diff --git a/mcp_docs/modules/docforge.cli.mcp_utils.json b/mcp_docs/modules/docforge.cli.mcp_utils.json
index 607ec05..92c0682 100644
--- a/mcp_docs/modules/docforge.cli.mcp_utils.json
+++ b/mcp_docs/modules/docforge.cli.mcp_utils.json
@@ -112,8 +112,8 @@
         "name": "serve",
         "kind": "function",
         "path": "docforge.cli.mcp_utils.serve",
-        "signature": "<bound method Function.signature of Function('serve', 23, 47)>",
-        "docstring": "Serve MCP documentation from a pre-built bundle.\n\nArgs:\n    mcp_root: Path to the directory containing index.json, nav.json, and modules/."
+        "signature": "<bound method Function.signature of Function('serve', 23, 48)>",
+        "docstring": "Serve MCP documentation from a pre-built bundle.\n\nArgs:\n    module: The dotted path of the primary module to serve.\n    mcp_root: Path to the directory containing index.json, nav.json, and modules/."
       }
     }
   }
diff --git a/mcp_docs/modules/docforge.cli.mkdocs_utils.json b/mcp_docs/modules/docforge.cli.mkdocs_utils.json
index ccb2494..92af3a4 100644
--- a/mcp_docs/modules/docforge.cli.mkdocs_utils.json
+++ b/mcp_docs/modules/docforge.cli.mkdocs_utils.json
@@ -81,7 +81,7 @@
             "kind": "function",
             "path": "docforge.cli.mkdocs_utils.MkDocsRenderer.generate_sources",
             "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources')>",
-            "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files."
+            "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files.\n    module_is_source: Module is the source folder and to be treated as the root folder."
           }
         }
       },
@@ -119,28 +119,28 @@
         "name": "generate_sources",
         "kind": "function",
         "path": "docforge.cli.mkdocs_utils.generate_sources",
-        "signature": "<bound method Function.signature of Function('generate_sources', 9, 23)>",
-        "docstring": "Generate Markdown source files for the specified module.\n\nArgs:\n    module: The dotted path of the primary module to document.\n    project_name: Optional override for the project name.\n    docs_dir: Directory where the generated Markdown files will be written."
+        "signature": "<bound method Function.signature of Function('generate_sources', 9, 33)>",
+        "docstring": "Generate Markdown source files for the specified module.\n\nArgs:\n    module: The dotted path of the primary module to document.\n    project_name: Optional override for the project name.\n    docs_dir: Directory where the generated Markdown files will be written.\n    module_is_source: Module is the source folder and to be treated as the root folder."
       },
       "generate_config": {
         "name": "generate_config",
         "kind": "function",
         "path": "docforge.cli.mkdocs_utils.generate_config",
-        "signature": "<bound method Function.signature of Function('generate_config', 25, 59)>",
+        "signature": "<bound method Function.signature of Function('generate_config', 35, 69)>",
         "docstring": "Generate an mkdocs.yml configuration file.\n\nArgs:\n    docs_dir: Path to the directory containing documentation Markdown files.\n    nav_file: Path to the docforge.nav.yml specification.\n    template: Optional path to an mkdocs.yml template (overrides built-in).\n    out: Path where the final mkdocs.yml will be written.\n    site_name: The display name for the documentation site."
       },
       "build": {
         "name": "build",
         "kind": "function",
         "path": "docforge.cli.mkdocs_utils.build",
-        "signature": "<bound method Function.signature of Function('build', 61, 74)>",
+        "signature": "<bound method Function.signature of Function('build', 71, 84)>",
         "docstring": "Build the documentation site using MkDocs.\n\nArgs:\n    mkdocs_yml: Path to the mkdocs.yml configuration file."
       },
       "serve": {
         "name": "serve",
         "kind": "function",
         "path": "docforge.cli.mkdocs_utils.serve",
-        "signature": "<bound method Function.signature of Function('serve', 76, 87)>",
+        "signature": "<bound method Function.signature of Function('serve', 86, 97)>",
         "docstring": "Serve the documentation site with live-reload using MkDocs.\n\nArgs:\n    mkdocs_yml: Path to the mkdocs.yml configuration file."
       }
     }
diff --git a/mcp_docs/modules/docforge.json b/mcp_docs/modules/docforge.json
index 0f2176e..4ed1335 100644
--- a/mcp_docs/modules/docforge.json
+++ b/mcp_docs/modules/docforge.json
@@ -2,7 +2,7 @@
   "module": "docforge",
   "content": {
     "path": "docforge",
-    "docstring": "# doc-forge\n\n`doc-forge` is a renderer-agnostic Python documentation compiler designed for\nspeed, flexibility, and beautiful output. It decouples the introspection of\nyour code from the rendering process, allowing you to generate documentation\nfor various platforms (starting with MkDocs) from a single internal models.\n\n## Available Commands\n\n- **build**: Build documentation (MkDocs site or MCP resources).\n- **serve**: Serve documentation (MkDocs or MCP).\n- **tree**: Visualize the introspected project structure.\n\n## Installation\n\nInstall using `pip` with the optional `mkdocs` dependencies for a complete setup:\n\n```bash\npip install doc-forge\n```\n\n## Quick Start\n\n1.  **Build Documentation**:\n    Introspect your package and generate documentation in one step:\n    ```bash\n    # Build MkDocs site\n    doc-forge build --mkdocs --module my_package --site-name \"My Docs\"\n\n    # Build MCP resources\n    doc-forge build --mcp --module my_package\n    ```\n\n2.  **Define Navigation**:\n    Create a `docforge.nav.yml` to organize your documentation:\n    ```yaml\n    home: my_package/index.md\n    groups:\n      Core API:\n        - my_package/core/*.md\n      Utilities:\n        - my_package/utils.md\n    ```\n\n3.  **Preview**:\n    ```bash\n    # Serve MkDocs site\n    doc-forge serve --mkdocs\n\n    # Serve MCP documentation\n    doc-forge serve --mcp\n    ```\n\n## Project Structure\n\n- `docforge.loaders`: Introspects source code using static analysis (`griffe`).\n- `docforge.models`: The internal representation of your project, modules, and objects.\n- `docforge.renderers`: Converters that turn the models into physical files.\n- `docforge.nav`: Managers for logical-to-physical path mapping and navigation.",
+    "docstring": "# doc-forge\n\n`doc-forge` is a renderer-agnostic Python documentation compiler designed for\nspeed, flexibility, and beautiful output. It decouples the introspection of\nyour code from the rendering process, allowing you to generate documentation\nfor various platforms (starting with MkDocs) from a single internal models.\n\n## Core Philosophy\n\n`doc-forge` operates on two fundamental principles:\n\n1.  **The Atomic Unit is a Python Import Path**: Documentation is organized around the semantic structure of your code (e.g., `mypackage.utils`), not the filesystem.\n2.  **The Documentation Compiler Paradigm**: We separate documentation into three distinct phases:\n    -   **Front-end (Introspection)**: Static analysis of source code and docstrings.\n    -   **Middle-end (Semantic Model)**: A renderer-neutral internal representation.\n    -   **Back-end (Renderers)**: Generation of human-facing (MkDocs) or machine-facing (MCP) outputs.\n\n## Documentation Design\n\n`doc-forge` is an \"AI-Native\" documentation compiler. To get the most out of it, design your docstrings with both humans and LLMs in mind:\n\n### For Humans (Readability & Structure)\n- **`__init__.py` as Landing Pages**: Use the docstring of your package's `__init__.py` as the home page. Include overviews, installation instructions, and high-level examples here.\n- **Single Source of Truth**: Keep all technical details in docstrings. This ensures your MkDocs/Sphinx sites stay in sync with the code.\n- **Semantic Hierarchy**: Use standard Markdown headers to structure complex module documentation.\n\n### For LLMs (AI-Native Knowledge)\n- **Model Context Protocol (MCP)**: `doc-forge` exports your docs as structured JSON. This allows AI agents to \"understand\" your API surface area without layout noise.\n- **Canonical Paths**: Use dotted import paths as primary identifiers. AI tools use these to link code usage to documentation.\n- **Type Annotations**: While not in docstrings, `doc-forge` (via Griffe) extracts signatures. Clean type hints dramatically improve an LLM's ability to generate correct code using your library.\n## Available Commands\n\n- **build**: Build documentation (MkDocs site or MCP resources).\n- **serve**: Serve documentation (MkDocs or MCP).\n- **tree**: Visualize the introspected project structure.\n\n## Installation\n\nInstall using `pip` with the optional `mkdocs` dependencies for a complete setup:\n\n```bash\npip install doc-forge\n```\n\n## Quick Start\n\n1.  **Build Documentation**:\n    Introspect your package and generate documentation in one step:\n    ```bash\n    # Build MkDocs site\n    doc-forge build --mkdocs --module my_package --site-name \"My Docs\"\n\n    # Build MCP resources\n    doc-forge build --mcp --module my_package\n    ```\n\n2.  **Define Navigation**:\n    Create a `docforge.nav.yml` to organize your documentation:\n    ```yaml\n    home: my_package/index.md\n    groups:\n      Core API:\n        - my_package/core/*.md\n      Utilities:\n        - my_package/utils.md\n    ```\n\n3.  **Preview**:\n    ```bash\n    # Serve MkDocs site\n    doc-forge serve --mkdocs\n\n    # Serve MCP documentation\n    doc-forge serve --mcp\n    ```\n\n## Project Structure\n\n- `docforge.loaders`: Introspects source code using static analysis (`griffe`).\n- `docforge.models`: The internal representation of your project, modules, and objects.\n- `docforge.renderers`: Converters that turn the models into physical files.\n- `docforge.nav`: Managers for logical-to-physical path mapping and navigation.",
     "objects": {
       "GriffeLoader": {
         "name": "GriffeLoader",
@@ -53,7 +53,7 @@
             "kind": "function",
             "path": "docforge.MkDocsRenderer.generate_sources",
             "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources')>",
-            "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files."
+            "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files.\n    module_is_source: Module is the source folder and to be treated as the root folder."
           }
         }
       },
@@ -275,7 +275,7 @@
                         "kind": "function",
                         "path": "docforge.cli.commands.mkdocs_utils.MkDocsRenderer.generate_sources",
                         "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources')>",
-                        "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files."
+                        "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files.\n    module_is_source: Module is the source folder and to be treated as the root folder."
                       }
                     }
                   },
@@ -314,7 +314,7 @@
                     "kind": "function",
                     "path": "docforge.cli.commands.mkdocs_utils.generate_sources",
                     "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.cli.mkdocs_utils.generate_sources')>",
-                    "docstring": "Generate Markdown source files for the specified module.\n\nArgs:\n    module: The dotted path of the primary module to document.\n    project_name: Optional override for the project name.\n    docs_dir: Directory where the generated Markdown files will be written."
+                    "docstring": "Generate Markdown source files for the specified module.\n\nArgs:\n    module: The dotted path of the primary module to document.\n    project_name: Optional override for the project name.\n    docs_dir: Directory where the generated Markdown files will be written.\n    module_is_source: Module is the source folder and to be treated as the root folder."
                   },
                   "generate_config": {
                     "name": "generate_config",
@@ -455,7 +455,7 @@
                     "kind": "function",
                     "path": "docforge.cli.commands.mcp_utils.serve",
                     "signature": "<bound method Alias.signature of Alias('serve', 'docforge.cli.mcp_utils.serve')>",
-                    "docstring": "Serve MCP documentation from a pre-built bundle.\n\nArgs:\n    mcp_root: Path to the directory containing index.json, nav.json, and modules/."
+                    "docstring": "Serve MCP documentation from a pre-built bundle.\n\nArgs:\n    module: The dotted path of the primary module to serve.\n    mcp_root: Path to the directory containing index.json, nav.json, and modules/."
                   }
                 }
               },
@@ -470,22 +470,22 @@
                 "name": "build",
                 "kind": "function",
                 "path": "docforge.cli.commands.build",
-                "signature": "<bound method Function.signature of Function('build', 18, 89)>",
-                "docstring": "Build documentation (MkDocs site or MCP resources).\n\nThis command orchestrates the full build process:\n1. Introspects the code (Griffe)\n2. Renders sources (MkDocs Markdown or MCP JSON)\n3. (MkDocs only) Generates config and runs the final site build.\n\nArgs:\n    mcp: Use the MCP documentation builder.\n    mkdocs: Use the MkDocs documentation builder.\n    module: The dotted path of the module to document.\n    project_name: Optional override for the project name.\n    site_name: (MkDocs) The site display name. Defaults to module name.\n    docs_dir: (MkDocs) Target directory for Markdown sources.\n    nav_file: (MkDocs) Path to the docforge.nav.yml specification.\n    template: (MkDocs) Optional custom mkdocs.yml template.\n    mkdocs_yml: (MkDocs) Target path for the generated mkdocs.yml.\n    out_dir: (MCP) Target directory for MCP JSON resources."
+                "signature": "<bound method Function.signature of Function('build', 18, 97)>",
+                "docstring": "Build documentation (MkDocs site or MCP resources).\n\nThis command orchestrates the full build process:\n1. Introspects the code (Griffe)\n2. Renders sources (MkDocs Markdown or MCP JSON)\n3. (MkDocs only) Generates config and runs the final site build.\n\nArgs:\n    mcp: Use the MCP documentation builder.\n    mkdocs: Use the MkDocs documentation builder.\n    module_is_source: Module is the source folder and to be treated as the root folder.\n    module: The dotted path of the module to the document.\n    project_name: Optional override for the project name.\n    site_name: (MkDocs) The site display name. Defaults to module name.\n    docs_dir: (MkDocs) Target directory for Markdown sources.\n    nav_file: (MkDocs) Path to the docforge.nav.yml specification.\n    template: (MkDocs) Optional custom mkdocs.yml template.\n    mkdocs_yml: (MkDocs) Target path for the generated mkdocs.yml.\n    out_dir: (MCP) Target directory for MCP JSON resources."
               },
               "serve": {
                 "name": "serve",
                 "kind": "function",
                 "path": "docforge.cli.commands.serve",
-                "signature": "<bound method Function.signature of Function('serve', 92, 120)>",
-                "docstring": "Serve documentation (MkDocs or MCP).\n\nArgs:\n    mcp: Serve MCP resources via an MCP server.\n    mkdocs: Serve the MkDocs site using the built-in development server.\n    mkdocs_yml: (MkDocs) Path to the mkdocs.yml configuration.\n    out_dir: (MCP) Path to the mcp_docs/ directory."
+                "signature": "<bound method Function.signature of Function('serve', 100, 133)>",
+                "docstring": "Serve documentation (MkDocs or MCP).\n\nArgs:\n    mcp: Serve MCP resources via an MCP server.\n    mkdocs: Serve the MkDocs site using the built-in development server.\n    module: The dotted path of the module to serve.\n    mkdocs_yml: (MkDocs) Path to the mkdocs.yml configuration.\n    out_dir: (MCP) Path to the mcp_docs/ directory."
               },
               "tree": {
                 "name": "tree",
                 "kind": "function",
                 "path": "docforge.cli.commands.tree",
-                "signature": "<bound method Function.signature of Function('tree', 123, 153)>",
-                "docstring": "Visualize the project structure in the terminal.\n\nArgs:\n    modules: List of module import paths to recursively introspect.\n    project_name: Optional override for the project name shown at the root."
+                "signature": "<bound method Function.signature of Function('tree', 136, 165)>",
+                "docstring": "Visualize the project structure in the terminal.\n\nArgs:\n    module: The module import path to recursively introspect.\n    project_name: Optional override for the project name shown at the root."
               },
               "Group": {
                 "name": "Group",
@@ -618,8 +618,8 @@
                 "name": "serve",
                 "kind": "function",
                 "path": "docforge.cli.mcp_utils.serve",
-                "signature": "<bound method Function.signature of Function('serve', 23, 47)>",
-                "docstring": "Serve MCP documentation from a pre-built bundle.\n\nArgs:\n    mcp_root: Path to the directory containing index.json, nav.json, and modules/."
+                "signature": "<bound method Function.signature of Function('serve', 23, 48)>",
+                "docstring": "Serve MCP documentation from a pre-built bundle.\n\nArgs:\n    module: The dotted path of the primary module to serve.\n    mcp_root: Path to the directory containing index.json, nav.json, and modules/."
               }
             }
           },
@@ -707,7 +707,7 @@
                     "kind": "function",
                     "path": "docforge.cli.mkdocs_utils.MkDocsRenderer.generate_sources",
                     "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources')>",
-                    "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files."
+                    "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files.\n    module_is_source: Module is the source folder and to be treated as the root folder."
                   }
                 }
               },
@@ -745,28 +745,28 @@
                 "name": "generate_sources",
                 "kind": "function",
                 "path": "docforge.cli.mkdocs_utils.generate_sources",
-                "signature": "<bound method Function.signature of Function('generate_sources', 9, 23)>",
-                "docstring": "Generate Markdown source files for the specified module.\n\nArgs:\n    module: The dotted path of the primary module to document.\n    project_name: Optional override for the project name.\n    docs_dir: Directory where the generated Markdown files will be written."
+                "signature": "<bound method Function.signature of Function('generate_sources', 9, 33)>",
+                "docstring": "Generate Markdown source files for the specified module.\n\nArgs:\n    module: The dotted path of the primary module to document.\n    project_name: Optional override for the project name.\n    docs_dir: Directory where the generated Markdown files will be written.\n    module_is_source: Module is the source folder and to be treated as the root folder."
               },
               "generate_config": {
                 "name": "generate_config",
                 "kind": "function",
                 "path": "docforge.cli.mkdocs_utils.generate_config",
-                "signature": "<bound method Function.signature of Function('generate_config', 25, 59)>",
+                "signature": "<bound method Function.signature of Function('generate_config', 35, 69)>",
                 "docstring": "Generate an mkdocs.yml configuration file.\n\nArgs:\n    docs_dir: Path to the directory containing documentation Markdown files.\n    nav_file: Path to the docforge.nav.yml specification.\n    template: Optional path to an mkdocs.yml template (overrides built-in).\n    out: Path where the final mkdocs.yml will be written.\n    site_name: The display name for the documentation site."
               },
               "build": {
                 "name": "build",
                 "kind": "function",
                 "path": "docforge.cli.mkdocs_utils.build",
-                "signature": "<bound method Function.signature of Function('build', 61, 74)>",
+                "signature": "<bound method Function.signature of Function('build', 71, 84)>",
                 "docstring": "Build the documentation site using MkDocs.\n\nArgs:\n    mkdocs_yml: Path to the mkdocs.yml configuration file."
               },
               "serve": {
                 "name": "serve",
                 "kind": "function",
                 "path": "docforge.cli.mkdocs_utils.serve",
-                "signature": "<bound method Function.signature of Function('serve', 76, 87)>",
+                "signature": "<bound method Function.signature of Function('serve', 86, 97)>",
                 "docstring": "Serve the documentation site with live-reload using MkDocs.\n\nArgs:\n    mkdocs_yml: Path to the mkdocs.yml configuration file."
               }
             }
@@ -2079,7 +2079,7 @@
                 "kind": "function",
                 "path": "docforge.renderers.MkDocsRenderer.generate_sources",
                 "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources')>",
-                "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files."
+                "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files.\n    module_is_source: Module is the source folder and to be treated as the root folder."
               }
             }
           },
@@ -2465,7 +2465,7 @@
             "kind": "module",
             "path": "docforge.renderers.mkdocs_renderer",
             "signature": null,
-            "docstring": "This module implements the MkDocsRenderer, which generates Markdown source files\ncompatible with the MkDocs 'material' theme and 'mkdocstrings' extension.",
+            "docstring": "MkDocsRenderer\n\nGenerates Markdown source files compatible with MkDocs Material\nand mkdocstrings, ensuring:\n\n- Root index.md always exists\n- Parent package indexes are created automatically\n- Child modules are linked in parent index files",
             "members": {
               "Path": {
                 "name": "Path",
@@ -2525,36 +2525,6 @@
                   }
                 }
               },
-              "MkDocsRenderer": {
-                "name": "MkDocsRenderer",
-                "kind": "class",
-                "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer",
-                "signature": "<bound method Class.signature of Class('MkDocsRenderer', 11, 91)>",
-                "docstring": "Renderer that generates Markdown source files formatted for the MkDocs\n'mkdocstrings' plugin.",
-                "members": {
-                  "name": {
-                    "name": "name",
-                    "kind": "attribute",
-                    "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.name",
-                    "signature": null,
-                    "docstring": null
-                  },
-                  "generate_sources": {
-                    "name": "generate_sources",
-                    "kind": "function",
-                    "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources",
-                    "signature": "<bound method Function.signature of Function('generate_sources', 19, 38)>",
-                    "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files."
-                  }
-                }
-              },
-              "Set": {
-                "name": "Set",
-                "kind": "alias",
-                "path": "docforge.renderers.mkdocs_renderer.Set",
-                "signature": "<bound method Alias.signature of Alias('Set', 'typing.Set')>",
-                "docstring": null
-              },
               "Module": {
                 "name": "Module",
                 "kind": "class",
@@ -2605,6 +2575,29 @@
                     "docstring": "Get all top-level objects in the module.\n\nReturns:\n    An iterable of DocObject instances."
                   }
                 }
+              },
+              "MkDocsRenderer": {
+                "name": "MkDocsRenderer",
+                "kind": "class",
+                "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer",
+                "signature": "<bound method Class.signature of Class('MkDocsRenderer', 16, 168)>",
+                "docstring": "Renderer that generates Markdown source files formatted for the MkDocs\n'mkdocstrings' plugin.",
+                "members": {
+                  "name": {
+                    "name": "name",
+                    "kind": "attribute",
+                    "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.name",
+                    "signature": null,
+                    "docstring": null
+                  },
+                  "generate_sources": {
+                    "name": "generate_sources",
+                    "kind": "function",
+                    "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources",
+                    "signature": "<bound method Function.signature of Function('generate_sources', 27, 60)>",
+                    "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files.\n    module_is_source: Module is the source folder and to be treated as the root folder."
+                  }
+                }
               }
             }
           }
diff --git a/mcp_docs/modules/docforge.renderers.json b/mcp_docs/modules/docforge.renderers.json
index d46becc..81a0102 100644
--- a/mcp_docs/modules/docforge.renderers.json
+++ b/mcp_docs/modules/docforge.renderers.json
@@ -23,7 +23,7 @@
             "kind": "function",
             "path": "docforge.renderers.MkDocsRenderer.generate_sources",
             "signature": "<bound method Alias.signature of Alias('generate_sources', 'docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources')>",
-            "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files."
+            "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files.\n    module_is_source: Module is the source folder and to be treated as the root folder."
           }
         }
       },
@@ -409,7 +409,7 @@
         "kind": "module",
         "path": "docforge.renderers.mkdocs_renderer",
         "signature": null,
-        "docstring": "This module implements the MkDocsRenderer, which generates Markdown source files\ncompatible with the MkDocs 'material' theme and 'mkdocstrings' extension.",
+        "docstring": "MkDocsRenderer\n\nGenerates Markdown source files compatible with MkDocs Material\nand mkdocstrings, ensuring:\n\n- Root index.md always exists\n- Parent package indexes are created automatically\n- Child modules are linked in parent index files",
         "members": {
           "Path": {
             "name": "Path",
@@ -469,36 +469,6 @@
               }
             }
           },
-          "MkDocsRenderer": {
-            "name": "MkDocsRenderer",
-            "kind": "class",
-            "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer",
-            "signature": "<bound method Class.signature of Class('MkDocsRenderer', 11, 91)>",
-            "docstring": "Renderer that generates Markdown source files formatted for the MkDocs\n'mkdocstrings' plugin.",
-            "members": {
-              "name": {
-                "name": "name",
-                "kind": "attribute",
-                "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.name",
-                "signature": null,
-                "docstring": null
-              },
-              "generate_sources": {
-                "name": "generate_sources",
-                "kind": "function",
-                "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources",
-                "signature": "<bound method Function.signature of Function('generate_sources', 19, 38)>",
-                "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files."
-              }
-            }
-          },
-          "Set": {
-            "name": "Set",
-            "kind": "alias",
-            "path": "docforge.renderers.mkdocs_renderer.Set",
-            "signature": "<bound method Alias.signature of Alias('Set', 'typing.Set')>",
-            "docstring": null
-          },
           "Module": {
             "name": "Module",
             "kind": "class",
@@ -549,6 +519,29 @@
                 "docstring": "Get all top-level objects in the module.\n\nReturns:\n    An iterable of DocObject instances."
               }
             }
+          },
+          "MkDocsRenderer": {
+            "name": "MkDocsRenderer",
+            "kind": "class",
+            "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer",
+            "signature": "<bound method Class.signature of Class('MkDocsRenderer', 16, 168)>",
+            "docstring": "Renderer that generates Markdown source files formatted for the MkDocs\n'mkdocstrings' plugin.",
+            "members": {
+              "name": {
+                "name": "name",
+                "kind": "attribute",
+                "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.name",
+                "signature": null,
+                "docstring": null
+              },
+              "generate_sources": {
+                "name": "generate_sources",
+                "kind": "function",
+                "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources",
+                "signature": "<bound method Function.signature of Function('generate_sources', 27, 60)>",
+                "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files.\n    module_is_source: Module is the source folder and to be treated as the root folder."
+              }
+            }
           }
         }
       }
diff --git a/mcp_docs/modules/docforge.renderers.mkdocs_renderer.json b/mcp_docs/modules/docforge.renderers.mkdocs_renderer.json
index 83b2930..73ce76c 100644
--- a/mcp_docs/modules/docforge.renderers.mkdocs_renderer.json
+++ b/mcp_docs/modules/docforge.renderers.mkdocs_renderer.json
@@ -2,7 +2,7 @@
   "module": "docforge.renderers.mkdocs_renderer",
   "content": {
     "path": "docforge.renderers.mkdocs_renderer",
-    "docstring": "This module implements the MkDocsRenderer, which generates Markdown source files\ncompatible with the MkDocs 'material' theme and 'mkdocstrings' extension.",
+    "docstring": "MkDocsRenderer\n\nGenerates Markdown source files compatible with MkDocs Material\nand mkdocstrings, ensuring:\n\n- Root index.md always exists\n- Parent package indexes are created automatically\n- Child modules are linked in parent index files",
     "objects": {
       "Path": {
         "name": "Path",
@@ -62,36 +62,6 @@
           }
         }
       },
-      "MkDocsRenderer": {
-        "name": "MkDocsRenderer",
-        "kind": "class",
-        "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer",
-        "signature": "<bound method Class.signature of Class('MkDocsRenderer', 11, 91)>",
-        "docstring": "Renderer that generates Markdown source files formatted for the MkDocs\n'mkdocstrings' plugin.",
-        "members": {
-          "name": {
-            "name": "name",
-            "kind": "attribute",
-            "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.name",
-            "signature": null,
-            "docstring": null
-          },
-          "generate_sources": {
-            "name": "generate_sources",
-            "kind": "function",
-            "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources",
-            "signature": "<bound method Function.signature of Function('generate_sources', 19, 38)>",
-            "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files."
-          }
-        }
-      },
-      "Set": {
-        "name": "Set",
-        "kind": "alias",
-        "path": "docforge.renderers.mkdocs_renderer.Set",
-        "signature": "<bound method Alias.signature of Alias('Set', 'typing.Set')>",
-        "docstring": null
-      },
       "Module": {
         "name": "Module",
         "kind": "class",
@@ -142,6 +112,29 @@
             "docstring": "Get all top-level objects in the module.\n\nReturns:\n    An iterable of DocObject instances."
           }
         }
+      },
+      "MkDocsRenderer": {
+        "name": "MkDocsRenderer",
+        "kind": "class",
+        "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer",
+        "signature": "<bound method Class.signature of Class('MkDocsRenderer', 16, 168)>",
+        "docstring": "Renderer that generates Markdown source files formatted for the MkDocs\n'mkdocstrings' plugin.",
+        "members": {
+          "name": {
+            "name": "name",
+            "kind": "attribute",
+            "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.name",
+            "signature": null,
+            "docstring": null
+          },
+          "generate_sources": {
+            "name": "generate_sources",
+            "kind": "function",
+            "path": "docforge.renderers.mkdocs_renderer.MkDocsRenderer.generate_sources",
+            "signature": "<bound method Function.signature of Function('generate_sources', 27, 60)>",
+            "docstring": "Produce a set of Markdown files in the output directory based on the\nprovided Project models.\n\nArgs:\n    project: The project models to render.\n    out_dir: Target directory for documentation files.\n    module_is_source: Module is the source folder and to be treated as the root folder."
+          }
+        }
       }
     }
   }
diff --git a/mkdocs.yml b/mkdocs.yml
index 5b9e7da..fe5897d 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -1,5 +1,3 @@
-site_name: docforge
-
 theme:
   name: material
   palette:
@@ -33,30 +31,30 @@ plugins:
           annotations_path: brief
           show_root_heading: true
           group_by_category: true
-
+site_name: docforge
 nav:
-- Home: docforge/index.md
+- Home: index.md
 - Loaders:
-  - docforge/loaders/index.md
-  - docforge/loaders/griffe_loader.md
+  - loaders/index.md
+  - loaders/griffe_loader.md
 - Models:
-  - docforge/models/index.md
-  - docforge/models/module.md
-  - docforge/models/object.md
-  - docforge/models/project.md
+  - models/index.md
+  - models/module.md
+  - models/object.md
+  - models/project.md
 - Navigation:
-  - docforge/nav/index.md
-  - docforge/nav/spec.md
-  - docforge/nav/resolver.md
-  - docforge/nav/mkdocs.md
+  - nav/index.md
+  - nav/spec.md
+  - nav/resolver.md
+  - nav/mkdocs.md
 - Renderers:
-  - docforge/renderers/index.md
-  - docforge/renderers/base.md
-  - docforge/renderers/mkdocs_renderer.md
-  - docforge/renderers/mcp_renderer.md
+  - renderers/index.md
+  - renderers/base.md
+  - renderers/mkdocs_renderer.md
+  - renderers/mcp_renderer.md
 - CLI:
-  - docforge/cli/index.md
-  - docforge/cli/main.md
-  - docforge/cli/commands.md
-  - docforge/cli/mcp_utils.md
-  - docforge/cli/mkdocs_utils.md
+  - cli/index.md
+  - cli/main.md
+  - cli/commands.md
+  - cli/mcp_utils.md
+  - cli/mkdocs_utils.md