Add project configuration and initial documentation files

- Introduced `archdoc.toml` configuration file for project settings, including scanning and analysis options.
- Created initial `ARCHITECTURE.md` file with project summary and structure.
- Generated documentation files for source files and modules, including placeholders for future content.
- Updated the documentation generation logic to handle new project structure and file paths.

archdoc-cli/src/main.rs

@@ -2,7 +2,6 @@ use clap::{Parser, Subcommand};
 use anyhow::Result;
 use archdoc_core::{Config, ProjectModel, scanner::FileScanner, python_analyzer::PythonAnalyzer};
 use std::path::Path;
-use std::collections::HashSet;
 
 /// CLI interface for ArchDoc
 #[derive(Parser)]
@@ -324,14 +323,14 @@ fn generate_docs(model: &ProjectModel, out: &str) -> Result<()> {
     let output_path = std::path::Path::new(".").join("ARCHITECTURE.md");
     
     // Create individual documentation files for modules and files
-    for (module_id, module) in &model.modules {
+    for (module_id, _module) in &model.modules {
         let module_doc_path = modules_path.join(format!("{}.md", sanitize_filename(module_id)));
         let module_content = format!("# Module: {}\n\nTODO: Add module documentation\n", module_id);
         std::fs::write(&module_doc_path, module_content)
             .map_err(|e| anyhow::anyhow!("Failed to create module doc {}: {}", module_doc_path.display(), e))?;
     }
     
-    for (file_id, file_doc) in &model.files {
+    for (_file_id, file_doc) in &model.files {
         let file_doc_path = files_path.join(format!("{}.md", sanitize_filename(&file_doc.path)));
         let file_content = format!("# File: {}\n\nTODO: Add file documentation\n", file_doc.path);
         std::fs::write(&file_doc_path, file_content)

archdoc-core/src/renderer.rs

@@ -249,7 +249,7 @@ impl Renderer {
         // Collect layout information from files
         let mut layout_items = Vec::new();
         
-        for (file_id, file_doc) in &model.files {
+        for (_file_id, file_doc) in &model.files {
             layout_items.push(serde_json::json!({
                 "path": file_doc.path,
                 "purpose": "Source file",

archdoc-core/tests/golden/test_project/ARCHITECTURE.md

@@ -0,0 +1,73 @@
+# ARCHITECTURE — New Project
+
+<!-- MANUAL:BEGIN -->
+## Project summary
+**Name:** New Project
+**Description:** <FILL_MANUALLY: what this project does in 3–7 lines>
+
+## Key decisions (manual)
+- <FILL_MANUALLY>
+
+## Non-goals (manual)
+- <FILL_MANUALLY>
+<!-- MANUAL:END -->
+
+---
+
+## Document metadata
+- **Created:** 2026-01-25
+- **Updated:** 2026-01-25
+- **Generated by:** archdoc (cli) v0.1
+
+---
+
+## Rails / Tooling
+<!-- ARCHDOC:BEGIN section=rails -->
+
+No tooling information available.
+<!-- ARCHDOC:END section=rails -->
+
+---
+
+## Repository layout (top-level)
+<!-- ARCHDOC:BEGIN section=layout -->
+
+| Path | Purpose | Link |
+|------|---------|------|
+| ./src/advanced_example.py | Source file | [details](docs/architecture/files/._src_advanced_example.py.md) |
+| ./src/example.py | Source file | [details](docs/architecture/files/._src_example.py.md) |
+<!-- ARCHDOC:END section=layout -->
+
+---
+
+## Modules index
+<!-- ARCHDOC:BEGIN section=modules_index -->
+
+| Module | Symbols | Inbound | Outbound | Link |
+|--------|---------|---------|----------|------|
+| ./src/advanced_example.py | 10 | 0 | 0 | [details](docs/architecture/modules/._src_advanced_example.py.md) |
+| ./src/example.py | 5 | 0 | 0 | [details](docs/architecture/modules/._src_example.py.md) |
+<!-- ARCHDOC:END section=modules_index -->
+
+---
+
+## Critical dependency points
+<!-- ARCHDOC:BEGIN section=critical_points -->
+
+### High Fan-in (Most Called)
+| Symbol | Fan-in | Critical |
+|--------|--------|----------|
+
+### High Fan-out (Calls Many)
+| Symbol | Fan-out | Critical |
+|--------|---------|----------|
+
+### Module Cycles
+<!-- ARCHDOC:END section=critical_points -->
+
+---
+
+<!-- MANUAL:BEGIN -->
+## Change notes (manual)
+- <FILL_MANUALLY>
+<!-- MANUAL:END -->

archdoc-core/tests/golden/test_project/archdoc.toml

@@ -0,0 +1,62 @@
+[project]
+root = "."
+out_dir = "docs/architecture"
+entry_file = "ARCHITECTURE.md"
+language = "python"
+
+[scan]
+include = ["src", "app", "tests"]
+exclude = [
+    ".venv", "venv", "__pycache__", ".git", "dist", "build",
+    ".mypy_cache", ".ruff_cache", ".pytest_cache", "*.egg-info"
+]
+follow_symlinks = false
+max_file_size = "10MB"
+
+[python]
+src_roots = ["src", "."]
+include_tests = true
+parse_docstrings = true
+max_parse_errors = 10
+
+[analysis]
+resolve_calls = true
+resolve_inheritance = false
+detect_integrations = true
+integration_patterns = [
+    { type = "http", patterns = ["requests", "httpx", "aiohttp"] },
+    { type = "db", patterns = ["sqlalchemy", "psycopg", "mysql", "sqlite3"] },
+    { type = "queue", patterns = ["celery", "kafka", "pika", "redis"] }
+]
+
+[output]
+single_file = false
+per_file_docs = true
+create_directories = true
+overwrite_manual_sections = false
+
+[diff]
+update_timestamp_on_change_only = true
+hash_algorithm = "sha256"
+preserve_manual_content = true
+
+[thresholds]
+critical_fan_in = 20
+critical_fan_out = 20
+high_complexity = 50
+
+[rendering]
+template_engine = "handlebars"
+max_table_rows = 100
+truncate_long_descriptions = true
+description_max_length = 200
+
+[logging]
+level = "info"
+file = "archdoc.log"
+format = "compact"
+
+[caching]
+enabled = true
+cache_dir = ".archdoc/cache"
+max_cache_age = "24h"

archdoc-core/tests/golden/test_project/docs/architecture/files/._src_advanced_example.py.md

@@ -0,0 +1,3 @@
+# File: ./src/advanced_example.py
+
+TODO: Add file documentation

archdoc-core/tests/golden/test_project/docs/architecture/files/._src_example.py.md

@@ -0,0 +1,3 @@
+# File: ./src/example.py
+
+TODO: Add file documentation

archdoc-core/tests/golden/test_project/docs/architecture/modules/._src_advanced_example.py.md

@@ -0,0 +1,3 @@
+# Module: ./src/advanced_example.py
+
+TODO: Add module documentation

archdoc-core/tests/golden/test_project/docs/architecture/modules/._src_example.py.md

@@ -0,0 +1,3 @@
+# Module: ./src/example.py
+
+TODO: Add module documentation

test-project/ARCHITECTURE.md

@@ -0,0 +1,75 @@
+# ARCHITECTURE — New Project
+
+<!-- MANUAL:BEGIN -->
+## Project summary
+**Name:** New Project
+**Description:** <FILL_MANUALLY: what this project does in 3–7 lines>
+
+## Key decisions (manual)
+- <FILL_MANUALLY>
+
+## Non-goals (manual)
+- <FILL_MANUALLY>
+<!-- MANUAL:END -->
+
+---
+
+## Document metadata
+- **Created:** 2026-01-25
+- **Updated:** 2026-01-25
+- **Generated by:** archdoc (cli) v0.1
+
+---
+
+## Rails / Tooling
+<!-- ARCHDOC:BEGIN section=rails -->
+
+No tooling information available.
+<!-- ARCHDOC:END section=rails -->
+
+---
+
+## Repository layout (top-level)
+<!-- ARCHDOC:BEGIN section=layout -->
+
+| Path | Purpose | Link |
+|------|---------|------|
+| ./src/core.py | Source file | [details](docs/architecture/files/._src_core.py.md) |
+| ./src/__init__.py | Source file | [details](docs/architecture/files/._src___init__.py.md) |
+| ./src/utils.py | Source file | [details](docs/architecture/files/._src_utils.py.md) |
+<!-- ARCHDOC:END section=layout -->
+
+---
+
+## Modules index
+<!-- ARCHDOC:BEGIN section=modules_index -->
+
+| Module | Symbols | Inbound | Outbound | Link |
+|--------|---------|---------|----------|------|
+| ./src/__init__.py | 0 | 0 | 0 | [details](docs/architecture/modules/._src___init__.py.md) |
+| ./src/core.py | 6 | 0 | 0 | [details](docs/architecture/modules/._src_core.py.md) |
+| ./src/utils.py | 4 | 0 | 0 | [details](docs/architecture/modules/._src_utils.py.md) |
+<!-- ARCHDOC:END section=modules_index -->
+
+---
+
+## Critical dependency points
+<!-- ARCHDOC:BEGIN section=critical_points -->
+
+### High Fan-in (Most Called)
+| Symbol | Fan-in | Critical |
+|--------|--------|----------|
+
+### High Fan-out (Calls Many)
+| Symbol | Fan-out | Critical |
+|--------|---------|----------|
+
+### Module Cycles
+<!-- ARCHDOC:END section=critical_points -->
+
+---
+
+<!-- MANUAL:BEGIN -->
+## Change notes (manual)
+- <FILL_MANUALLY>
+<!-- MANUAL:END -->

test-project/archdoc.toml

@@ -0,0 +1,62 @@
+[project]
+root = "."
+out_dir = "docs/architecture"
+entry_file = "ARCHITECTURE.md"
+language = "python"
+
+[scan]
+include = ["src", "app", "tests"]
+exclude = [
+    ".venv", "venv", "__pycache__", ".git", "dist", "build",
+    ".mypy_cache", ".ruff_cache", ".pytest_cache", "*.egg-info"
+]
+follow_symlinks = false
+max_file_size = "10MB"
+
+[python]
+src_roots = ["src", "."]
+include_tests = true
+parse_docstrings = true
+max_parse_errors = 10
+
+[analysis]
+resolve_calls = true
+resolve_inheritance = false
+detect_integrations = true
+integration_patterns = [
+    { type = "http", patterns = ["requests", "httpx", "aiohttp"] },
+    { type = "db", patterns = ["sqlalchemy", "psycopg", "mysql", "sqlite3"] },
+    { type = "queue", patterns = ["celery", "kafka", "pika", "redis"] }
+]
+
+[output]
+single_file = false
+per_file_docs = true
+create_directories = true
+overwrite_manual_sections = false
+
+[diff]
+update_timestamp_on_change_only = true
+hash_algorithm = "sha256"
+preserve_manual_content = true
+
+[thresholds]
+critical_fan_in = 20
+critical_fan_out = 20
+high_complexity = 50
+
+[rendering]
+template_engine = "handlebars"
+max_table_rows = 100
+truncate_long_descriptions = true
+description_max_length = 200
+
+[logging]
+level = "info"
+file = "archdoc.log"
+format = "compact"
+
+[caching]
+enabled = true
+cache_dir = ".archdoc/cache"
+max_cache_age = "24h"

test-project/docs/architecture/files/._src___init__.py.md

@@ -0,0 +1,3 @@
+# File: ./src/__init__.py
+
+TODO: Add file documentation

test-project/docs/architecture/files/._src_core.py.md

@@ -0,0 +1,3 @@
+# File: ./src/core.py
+
+TODO: Add file documentation

test-project/docs/architecture/files/._src_utils.py.md

@@ -0,0 +1,3 @@
+# File: ./src/utils.py
+
+TODO: Add file documentation

test-project/docs/architecture/modules/._src___init__.py.md

@@ -0,0 +1,3 @@
+# Module: ./src/__init__.py
+
+TODO: Add module documentation

test-project/docs/architecture/modules/._src_core.py.md

@@ -0,0 +1,3 @@
+# Module: ./src/core.py
+
+TODO: Add module documentation

test-project/docs/architecture/modules/._src_utils.py.md

@@ -0,0 +1,3 @@
+# Module: ./src/utils.py
+
+TODO: Add module documentation