Add initial project structure and core functionality for ArchDoc

- Created `.gitignore` files for various directories to exclude unnecessary files.
- Added `PLAN.md` to outline the project goals and architecture documentation generation.
- Implemented the `archdoc-cli` with a command-line interface for initializing and generating documentation.
- Developed the `archdoc-core` library for analyzing Python projects and generating architecture documentation.
- Included caching mechanisms to optimize repeated analysis.
- Established a comprehensive test suite to ensure functionality and error handling.
- Updated `README.md` to provide an overview and installation instructions for ArchDoc.

archdoc-core/src/cache.rs

@@ -0,0 +1,168 @@
+//! Caching module for ArchDoc
+//!
+//! This module provides caching functionality to speed up repeated analysis
+//! by storing parsed ASTs and analysis results.
+
+use crate::config::Config;
+use crate::errors::ArchDocError;
+use crate::model::ParsedModule;
+use std::path::Path;
+use std::fs;
+use serde::{Deserialize, Serialize};
+use chrono::{DateTime, Utc};
+
+#[derive(Debug, Serialize, Deserialize)]
+struct CacheEntry {
+    /// Timestamp when the cache entry was created
+    created_at: DateTime<Utc>,
+    /// Timestamp when the source file was last modified
+    file_modified_at: DateTime<Utc>,
+    /// The parsed module data
+    parsed_module: ParsedModule,
+}
+
+pub struct CacheManager {
+    config: Config,
+    cache_dir: String,
+}
+
+impl CacheManager {
+    pub fn new(config: Config) -> Self {
+        let cache_dir = config.caching.cache_dir.clone();
+        
+        // Create cache directory if it doesn't exist
+        if config.caching.enabled && !Path::new(&cache_dir).exists() {
+            let _ = fs::create_dir_all(&cache_dir);
+        }
+        
+        Self { config, cache_dir }
+    }
+    
+    /// Get cached parsed module if available and not expired
+    pub fn get_cached_module(&self, file_path: &Path) -> Result<Option<ParsedModule>, ArchDocError> {
+        if !self.config.caching.enabled {
+            return Ok(None);
+        }
+        
+        let cache_key = self.get_cache_key(file_path);
+        let cache_file = Path::new(&self.cache_dir).join(&cache_key);
+        
+        if !cache_file.exists() {
+            return Ok(None);
+        }
+        
+        // Read cache file
+        let content = fs::read_to_string(&cache_file)
+            .map_err(|e| ArchDocError::Io(e))?;
+        
+        let cache_entry: CacheEntry = serde_json::from_str(&content)
+            .map_err(|e| ArchDocError::AnalysisError(format!("Failed to deserialize cache entry: {}", e)))?;
+        
+        // Check if cache is expired
+        let now = Utc::now();
+        let cache_age = now.signed_duration_since(cache_entry.created_at);
+        
+        // Parse max_cache_age (simple format: "24h", "7d", etc.)
+        let max_age_seconds = self.parse_duration(&self.config.caching.max_cache_age)?;
+        
+        if cache_age.num_seconds() > max_age_seconds as i64 {
+            // Cache expired, remove it
+            let _ = fs::remove_file(&cache_file);
+            return Ok(None);
+        }
+        
+        // Check if source file has been modified since caching
+        let metadata = fs::metadata(file_path)
+            .map_err(|e| ArchDocError::Io(e))?;
+        
+        let modified_time = metadata.modified()
+            .map_err(|e| ArchDocError::Io(e))?;
+        
+        let modified_time: DateTime<Utc> = modified_time.into();
+        
+        if modified_time > cache_entry.file_modified_at {
+            // Source file is newer than cache, invalidate cache
+            let _ = fs::remove_file(&cache_file);
+            return Ok(None);
+        }
+        
+        Ok(Some(cache_entry.parsed_module))
+    }
+    
+    /// Store parsed module in cache
+    pub fn store_module(&self, file_path: &Path, parsed_module: ParsedModule) -> Result<(), ArchDocError> {
+        if !self.config.caching.enabled {
+            return Ok(());
+        }
+        
+        let cache_key = self.get_cache_key(file_path);
+        let cache_file = Path::new(&self.cache_dir).join(&cache_key);
+        
+        // Get file modification time
+        let metadata = fs::metadata(file_path)
+            .map_err(|e| ArchDocError::Io(e))?;
+        
+        let modified_time = metadata.modified()
+            .map_err(|e| ArchDocError::Io(e))?;
+        
+        let modified_time: DateTime<Utc> = modified_time.into();
+        
+        let cache_entry = CacheEntry {
+            created_at: Utc::now(),
+            file_modified_at: modified_time,
+            parsed_module,
+        };
+        
+        let content = serde_json::to_string(&cache_entry)
+            .map_err(|e| ArchDocError::AnalysisError(format!("Failed to serialize cache entry: {}", e)))?;
+        
+        fs::write(&cache_file, content)
+            .map_err(|e| ArchDocError::Io(e))
+    }
+    
+    /// Generate cache key for a file path
+    fn get_cache_key(&self, file_path: &Path) -> String {
+        use std::collections::hash_map::DefaultHasher;
+        use std::hash::{Hash, Hasher};
+        
+        let mut hasher = DefaultHasher::new();
+        file_path.hash(&mut hasher);
+        let hash = hasher.finish();
+        
+        format!("{:x}.json", hash)
+    }
+    
+    /// Parse duration string like "24h" or "7d" into seconds
+    fn parse_duration(&self, duration_str: &str) -> Result<u64, ArchDocError> {
+        if duration_str.is_empty() {
+            return Ok(0);
+        }
+        
+        let chars: Vec<char> = duration_str.chars().collect();
+        let (number_str, unit) = chars.split_at(chars.len() - 1);
+        let number: u64 = number_str.iter().collect::<String>().parse()
+            .map_err(|_| ArchDocError::AnalysisError(format!("Invalid duration format: {}", duration_str)))?;
+        
+        match unit[0] {
+            's' => Ok(number), // seconds
+            'm' => Ok(number * 60), // minutes
+            'h' => Ok(number * 3600), // hours
+            'd' => Ok(number * 86400), // days
+            _ => Err(ArchDocError::AnalysisError(format!("Unknown duration unit: {}", unit[0]))),
+        }
+    }
+    
+    /// Clear all cache entries
+    pub fn clear_cache(&self) -> Result<(), ArchDocError> {
+        if Path::new(&self.cache_dir).exists() {
+            fs::remove_dir_all(&self.cache_dir)
+                .map_err(|e| ArchDocError::Io(e))?;
+            
+            // Recreate cache directory
+            fs::create_dir_all(&self.cache_dir)
+                .map_err(|e| ArchDocError::Io(e))?;
+        }
+        
+        Ok(())
+    }
+}

archdoc-core/src/config.rs

@@ -0,0 +1,458 @@
+//! Configuration management for ArchDoc
+//!
+//! This module handles loading and validating the archdoc.toml configuration file.
+
+use serde::{Deserialize, Serialize};
+use std::path::Path;
+use crate::errors::ArchDocError;
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct Config {
+    #[serde(default)]
+    pub project: ProjectConfig,
+    #[serde(default)]
+    pub scan: ScanConfig,
+    #[serde(default)]
+    pub python: PythonConfig,
+    #[serde(default)]
+    pub analysis: AnalysisConfig,
+    #[serde(default)]
+    pub output: OutputConfig,
+    #[serde(default)]
+    pub diff: DiffConfig,
+    #[serde(default)]
+    pub thresholds: ThresholdsConfig,
+    #[serde(default)]
+    pub rendering: RenderingConfig,
+    #[serde(default)]
+    pub logging: LoggingConfig,
+    #[serde(default)]
+    pub caching: CachingConfig,
+}
+
+impl Default for Config {
+    fn default() -> Self {
+        Self {
+            project: ProjectConfig::default(),
+            scan: ScanConfig::default(),
+            python: PythonConfig::default(),
+            analysis: AnalysisConfig::default(),
+            output: OutputConfig::default(),
+            diff: DiffConfig::default(),
+            thresholds: ThresholdsConfig::default(),
+            rendering: RenderingConfig::default(),
+            logging: LoggingConfig::default(),
+            caching: CachingConfig::default(),
+        }
+    }
+}
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct ProjectConfig {
+    #[serde(default = "default_root")]
+    pub root: String,
+    #[serde(default = "default_out_dir")]
+    pub out_dir: String,
+    #[serde(default = "default_entry_file")]
+    pub entry_file: String,
+    #[serde(default = "default_language")]
+    pub language: String,
+    #[serde(default)]
+    pub name: String,
+}
+
+impl Default for ProjectConfig {
+    fn default() -> Self {
+        Self {
+            root: default_root(),
+            out_dir: default_out_dir(),
+            entry_file: default_entry_file(),
+            language: default_language(),
+            name: String::new(),
+        }
+    }
+}
+
+fn default_root() -> String {
+    ".".to_string()
+}
+
+fn default_out_dir() -> String {
+    "docs/architecture".to_string()
+}
+
+fn default_entry_file() -> String {
+    "ARCHITECTURE.md".to_string()
+}
+
+fn default_language() -> String {
+    "python".to_string()
+}
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct ScanConfig {
+    #[serde(default = "default_include")]
+    pub include: Vec<String>,
+    #[serde(default = "default_exclude")]
+    pub exclude: Vec<String>,
+    #[serde(default)]
+    pub follow_symlinks: bool,
+    #[serde(default = "default_max_file_size")]
+    pub max_file_size: String,
+}
+
+impl Default for ScanConfig {
+    fn default() -> Self {
+        Self {
+            include: default_include(),
+            exclude: default_exclude(),
+            follow_symlinks: false,
+            max_file_size: default_max_file_size(),
+        }
+    }
+}
+
+fn default_include() -> Vec<String> {
+    vec!["src".to_string(), "app".to_string(), "tests".to_string()]
+}
+
+fn default_exclude() -> Vec<String> {
+    vec![
+        ".venv".to_string(),
+        "venv".to_string(),
+        "__pycache__".to_string(),
+        ".git".to_string(),
+        "dist".to_string(),
+        "build".to_string(),
+        ".mypy_cache".to_string(),
+        ".ruff_cache".to_string(),
+        ".pytest_cache".to_string(),
+        "*.egg-info".to_string(),
+    ]
+}
+
+fn default_max_file_size() -> String {
+    "10MB".to_string()
+}
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct PythonConfig {
+    #[serde(default = "default_src_roots")]
+    pub src_roots: Vec<String>,
+    #[serde(default = "default_include_tests")]
+    pub include_tests: bool,
+    #[serde(default = "default_parse_docstrings")]
+    pub parse_docstrings: bool,
+    #[serde(default = "default_max_parse_errors")]
+    pub max_parse_errors: usize,
+}
+
+impl Default for PythonConfig {
+    fn default() -> Self {
+        Self {
+            src_roots: default_src_roots(),
+            include_tests: default_include_tests(),
+            parse_docstrings: default_parse_docstrings(),
+            max_parse_errors: default_max_parse_errors(),
+        }
+    }
+}
+
+fn default_src_roots() -> Vec<String> {
+    vec!["src".to_string(), ".".to_string()]
+}
+
+fn default_include_tests() -> bool {
+    true
+}
+
+fn default_parse_docstrings() -> bool {
+    true
+}
+
+fn default_max_parse_errors() -> usize {
+    10
+}
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct AnalysisConfig {
+    #[serde(default = "default_resolve_calls")]
+    pub resolve_calls: bool,
+    #[serde(default)]
+    pub resolve_inheritance: bool,
+    #[serde(default = "default_detect_integrations")]
+    pub detect_integrations: bool,
+    #[serde(default = "default_integration_patterns")]
+    pub integration_patterns: Vec<IntegrationPattern>,
+}
+
+impl Default for AnalysisConfig {
+    fn default() -> Self {
+        Self {
+            resolve_calls: default_resolve_calls(),
+            resolve_inheritance: false,
+            detect_integrations: default_detect_integrations(),
+            integration_patterns: default_integration_patterns(),
+        }
+    }
+}
+
+fn default_resolve_calls() -> bool {
+    true
+}
+
+fn default_detect_integrations() -> bool {
+    true
+}
+
+fn default_integration_patterns() -> Vec<IntegrationPattern> {
+    vec![
+        IntegrationPattern {
+            type_: "http".to_string(),
+            patterns: vec!["requests".to_string(), "httpx".to_string(), "aiohttp".to_string()],
+        },
+        IntegrationPattern {
+            type_: "db".to_string(),
+            patterns: vec![
+                "sqlalchemy".to_string(),
+                "psycopg".to_string(),
+                "mysql".to_string(),
+                "sqlite3".to_string(),
+            ],
+        },
+        IntegrationPattern {
+            type_: "queue".to_string(),
+            patterns: vec![
+                "celery".to_string(),
+                "kafka".to_string(),
+                "pika".to_string(),
+                "redis".to_string(),
+            ],
+        },
+    ]
+}
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct IntegrationPattern {
+    #[serde(rename = "type")]
+    pub type_: String,
+    pub patterns: Vec<String>,
+}
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct OutputConfig {
+    #[serde(default)]
+    pub single_file: bool,
+    #[serde(default = "default_per_file_docs")]
+    pub per_file_docs: bool,
+    #[serde(default = "default_create_directories")]
+    pub create_directories: bool,
+    #[serde(default)]
+    pub overwrite_manual_sections: bool,
+}
+
+impl Default for OutputConfig {
+    fn default() -> Self {
+        Self {
+            single_file: false,
+            per_file_docs: default_per_file_docs(),
+            create_directories: default_create_directories(),
+            overwrite_manual_sections: false,
+        }
+    }
+}
+
+fn default_per_file_docs() -> bool {
+    true
+}
+
+fn default_create_directories() -> bool {
+    true
+}
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct DiffConfig {
+    #[serde(default = "default_update_timestamp_on_change_only")]
+    pub update_timestamp_on_change_only: bool,
+    #[serde(default = "default_hash_algorithm")]
+    pub hash_algorithm: String,
+    #[serde(default = "default_preserve_manual_content")]
+    pub preserve_manual_content: bool,
+}
+
+impl Default for DiffConfig {
+    fn default() -> Self {
+        Self {
+            update_timestamp_on_change_only: default_update_timestamp_on_change_only(),
+            hash_algorithm: default_hash_algorithm(),
+            preserve_manual_content: default_preserve_manual_content(),
+        }
+    }
+}
+
+fn default_update_timestamp_on_change_only() -> bool {
+    true
+}
+
+fn default_hash_algorithm() -> String {
+    "sha256".to_string()
+}
+
+fn default_preserve_manual_content() -> bool {
+    true
+}
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct ThresholdsConfig {
+    #[serde(default = "default_critical_fan_in")]
+    pub critical_fan_in: usize,
+    #[serde(default = "default_critical_fan_out")]
+    pub critical_fan_out: usize,
+    #[serde(default = "default_high_complexity")]
+    pub high_complexity: usize,
+}
+
+impl Default for ThresholdsConfig {
+    fn default() -> Self {
+        Self {
+            critical_fan_in: default_critical_fan_in(),
+            critical_fan_out: default_critical_fan_out(),
+            high_complexity: default_high_complexity(),
+        }
+    }
+}
+
+fn default_critical_fan_in() -> usize {
+    20
+}
+
+fn default_critical_fan_out() -> usize {
+    20
+}
+
+fn default_high_complexity() -> usize {
+    50
+}
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct RenderingConfig {
+    #[serde(default = "default_template_engine")]
+    pub template_engine: String,
+    #[serde(default = "default_max_table_rows")]
+    pub max_table_rows: usize,
+    #[serde(default = "default_truncate_long_descriptions")]
+    pub truncate_long_descriptions: bool,
+    #[serde(default = "default_description_max_length")]
+    pub description_max_length: usize,
+}
+
+impl Default for RenderingConfig {
+    fn default() -> Self {
+        Self {
+            template_engine: default_template_engine(),
+            max_table_rows: default_max_table_rows(),
+            truncate_long_descriptions: default_truncate_long_descriptions(),
+            description_max_length: default_description_max_length(),
+        }
+    }
+}
+
+fn default_template_engine() -> String {
+    "handlebars".to_string()
+}
+
+fn default_max_table_rows() -> usize {
+    100
+}
+
+fn default_truncate_long_descriptions() -> bool {
+    true
+}
+
+fn default_description_max_length() -> usize {
+    200
+}
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct LoggingConfig {
+    #[serde(default = "default_log_level")]
+    pub level: String,
+    #[serde(default = "default_log_file")]
+    pub file: String,
+    #[serde(default = "default_log_format")]
+    pub format: String,
+}
+
+impl Default for LoggingConfig {
+    fn default() -> Self {
+        Self {
+            level: default_log_level(),
+            file: default_log_file(),
+            format: default_log_format(),
+        }
+    }
+}
+
+fn default_log_level() -> String {
+    "info".to_string()
+}
+
+fn default_log_file() -> String {
+    "archdoc.log".to_string()
+}
+
+fn default_log_format() -> String {
+    "compact".to_string()
+}
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct CachingConfig {
+    #[serde(default = "default_caching_enabled")]
+    pub enabled: bool,
+    #[serde(default = "default_cache_dir")]
+    pub cache_dir: String,
+    #[serde(default = "default_max_cache_age")]
+    pub max_cache_age: String,
+}
+
+impl Default for CachingConfig {
+    fn default() -> Self {
+        Self {
+            enabled: default_caching_enabled(),
+            cache_dir: default_cache_dir(),
+            max_cache_age: default_max_cache_age(),
+        }
+    }
+}
+
+fn default_caching_enabled() -> bool {
+    true
+}
+
+fn default_cache_dir() -> String {
+    ".archdoc/cache".to_string()
+}
+
+fn default_max_cache_age() -> String {
+    "24h".to_string()
+}
+
+impl Config {
+    /// Load configuration from a TOML file
+    pub fn load_from_file(path: &Path) -> Result<Self, ArchDocError> {
+        let content = std::fs::read_to_string(path)
+            .map_err(|e| ArchDocError::ConfigError(format!("Failed to read config file: {}", e)))?;
+        
+        toml::from_str(&content)
+            .map_err(|e| ArchDocError::ConfigError(format!("Failed to parse config file: {}", e)))
+    }
+    
+    /// Save configuration to a TOML file
+    pub fn save_to_file(&self, path: &Path) -> Result<(), ArchDocError> {
+        let content = toml::to_string_pretty(self)
+            .map_err(|e| ArchDocError::ConfigError(format!("Failed to serialize config: {}", e)))?;
+        
+        std::fs::write(path, content)
+            .map_err(|e| ArchDocError::ConfigError(format!("Failed to write config file: {}", e)))
+    }
+}

archdoc-core/src/errors.rs

@@ -0,0 +1,26 @@
+use thiserror::Error;
+
+#[derive(Error, Debug)]
+pub enum ArchDocError {
+    #[error("IO error: {0}")]
+    Io(#[from] std::io::Error),
+    
+    #[error("Parse error in {file}:{line}: {message}")]
+    ParseError {
+        file: String,
+        line: usize,
+        message: String,
+    },
+    
+    #[error("Configuration error: {0}")]
+    ConfigError(String),
+    
+    #[error("Analysis error: {0}")]
+    AnalysisError(String),
+    
+    #[error("Rendering error: {0}")]
+    RenderingError(String),
+    
+    #[error("File consistency check failed: {0}")]
+    ConsistencyError(String),
+}

archdoc-core/src/lib.rs

@@ -0,0 +1,31 @@
+//! ArchDoc Core Library
+//!
+//! This crate provides the core functionality for analyzing Python projects
+//! and generating architecture documentation.
+
+// Public modules
+pub mod errors;
+pub mod config;
+pub mod model;
+pub mod scanner;
+pub mod python_analyzer;
+pub mod renderer;
+pub mod writer;
+pub mod cache;
+
+// Re-export commonly used types
+pub use errors::ArchDocError;
+pub use config::Config;
+pub use model::ProjectModel;
+
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn it_works() {
+        let result = 2 + 2;
+        assert_eq!(result, 4);
+    }
+}

archdoc-core/src/model.rs

@@ -0,0 +1,168 @@
+//! Intermediate Representation (IR) for ArchDoc
+//!
+//! This module defines the data structures that represent the analyzed Python project
+//! and are used for generating documentation.
+
+use serde::{Deserialize, Serialize};
+use std::collections::HashMap;
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct ProjectModel {
+    pub modules: HashMap<String, Module>,
+    pub files: HashMap<String, FileDoc>,
+    pub symbols: HashMap<String, Symbol>,
+    pub edges: Edges,
+}
+
+impl ProjectModel {
+    pub fn new() -> Self {
+        Self {
+            modules: HashMap::new(),
+            files: HashMap::new(),
+            symbols: HashMap::new(),
+            edges: Edges::new(),
+        }
+    }
+}
+
+impl Default for ProjectModel {
+    fn default() -> Self {
+        Self::new()
+    }
+}
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct Module {
+    pub id: String,
+    pub path: String,
+    pub files: Vec<String>,
+    pub doc_summary: Option<String>,
+    pub outbound_modules: Vec<String>,
+    pub inbound_modules: Vec<String>,
+    pub symbols: Vec<String>,
+}
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct FileDoc {
+    pub id: String,
+    pub path: String,
+    pub module_id: String,
+    pub imports: Vec<String>, // normalized import strings
+    pub outbound_modules: Vec<String>,
+    pub inbound_files: Vec<String>,
+    pub symbols: Vec<String>,
+}
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct Symbol {
+    pub id: String,
+    pub kind: SymbolKind,
+    pub module_id: String,
+    pub file_id: String,
+    pub qualname: String,
+    pub signature: String,
+    pub annotations: Option<HashMap<String, String>>,
+    pub docstring_first_line: Option<String>,
+    pub purpose: String, // docstring or heuristic
+    pub outbound_calls: Vec<String>,
+    pub inbound_calls: Vec<String>,
+    pub integrations_flags: IntegrationFlags,
+    pub metrics: SymbolMetrics,
+}
+
+#[derive(Debug, Clone, Serialize, Deserialize, PartialEq)]
+pub enum SymbolKind {
+    Function,
+    AsyncFunction,
+    Class,
+    Method,
+}
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct IntegrationFlags {
+    pub http: bool,
+    pub db: bool,
+    pub queue: bool,
+}
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct SymbolMetrics {
+    pub fan_in: usize,
+    pub fan_out: usize,
+    pub is_critical: bool,
+    pub cycle_participant: bool,
+}
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct Edges {
+    pub module_import_edges: Vec<Edge>,
+    pub file_import_edges: Vec<Edge>,
+    pub symbol_call_edges: Vec<Edge>,
+}
+
+impl Edges {
+    pub fn new() -> Self {
+        Self {
+            module_import_edges: Vec::new(),
+            file_import_edges: Vec::new(),
+            symbol_call_edges: Vec::new(),
+        }
+    }
+}
+
+impl Default for Edges {
+    fn default() -> Self {
+        Self::new()
+    }
+}
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub struct Edge {
+    pub from_id: String,
+    pub to_id: String,
+    pub edge_type: EdgeType,
+    pub meta: Option<HashMap<String, String>>,
+}
+
+#[derive(Debug, Clone, Serialize, Deserialize)]
+pub enum EdgeType {
+    ModuleImport,
+    FileImport,
+    SymbolCall,
+    ExternalCall,
+    UnresolvedCall,
+}
+
+// Additional structures for Python analysis
+
+#[derive(Debug, Clone, serde::Serialize, serde::Deserialize)]
+pub struct ParsedModule {
+    pub path: std::path::PathBuf,
+    pub module_path: String,
+    pub imports: Vec<Import>,
+    pub symbols: Vec<Symbol>,
+    pub calls: Vec<Call>,
+}
+
+#[derive(Debug, Clone, serde::Serialize, serde::Deserialize)]
+pub struct Import {
+    pub module_name: String,
+    pub alias: Option<String>,
+    pub line_number: usize,
+}
+
+#[derive(Debug, Clone, serde::Serialize, serde::Deserialize)]
+pub struct Call {
+    pub caller_symbol: String,
+    pub callee_expr: String,
+    pub line_number: usize,
+    pub call_type: CallType,
+}
+
+#[derive(Debug, Clone, serde::Serialize, serde::Deserialize)]
+pub enum CallType {
+    Local,
+    Imported,
+    External,
+    Unresolved,
+}

archdoc-core/src/python_analyzer.rs

@@ -0,0 +1,386 @@
+//! Python AST analyzer for ArchDoc
+//!
+//! This module handles parsing Python files using AST and extracting
+//! imports, definitions, and calls.
+
+use crate::model::{ParsedModule, ProjectModel, Import, Call, CallType, Symbol, Module, FileDoc};
+use crate::config::Config;
+use crate::errors::ArchDocError;
+use crate::cache::CacheManager;
+use std::path::Path;
+use std::fs;
+use rustpython_parser::{ast, Parse};
+use rustpython_ast::{Stmt, StmtClassDef, StmtFunctionDef, Expr, Ranged};
+
+pub struct PythonAnalyzer {
+    _config: Config,
+    cache_manager: CacheManager,
+}
+
+impl PythonAnalyzer {
+    pub fn new(config: Config) -> Self {
+        let cache_manager = CacheManager::new(config.clone());
+        Self { _config: config, cache_manager }
+    }
+    
+    pub fn parse_module(&self, file_path: &Path) -> Result<ParsedModule, ArchDocError> {
+        // Try to get from cache first
+        if let Some(cached_module) = self.cache_manager.get_cached_module(file_path)? {
+            return Ok(cached_module);
+        }
+        
+        // Read the Python file
+        let code = fs::read_to_string(file_path)
+            .map_err(ArchDocError::Io)?;
+        
+        // Parse the Python code into an AST
+        let ast = ast::Suite::parse(&code, file_path.to_str().unwrap_or("<unknown>"))
+            .map_err(|e| ArchDocError::ParseError {
+                file: file_path.to_string_lossy().to_string(),
+                line: 0, // We don't have line info from the error
+                message: format!("Failed to parse: {}", e),
+            })?;
+        
+        // Extract imports, definitions, and calls
+        let mut imports = Vec::new();
+        let mut symbols = Vec::new();
+        let mut calls = Vec::new();
+        
+        for stmt in ast {
+            self.extract_from_statement(&stmt, None, &mut imports, &mut symbols, &mut calls, 0);
+        }
+        
+        let parsed_module = ParsedModule {
+            path: file_path.to_path_buf(),
+            module_path: file_path.to_string_lossy().to_string(),
+            imports,
+            symbols,
+            calls,
+        };
+        
+        // Store in cache
+        self.cache_manager.store_module(file_path, parsed_module.clone())?;
+        
+        Ok(parsed_module)
+    }
+    
+    fn extract_from_statement(&self, stmt: &Stmt, current_symbol: Option<&str>, imports: &mut Vec<Import>, symbols: &mut Vec<Symbol>, calls: &mut Vec<Call>, depth: usize) {
+        match stmt {
+            Stmt::Import(import_stmt) => {
+                for alias in &import_stmt.names {
+                    imports.push(Import {
+                        module_name: alias.name.to_string(),
+                        alias: alias.asname.as_ref().map(|n| n.to_string()),
+                        line_number: alias.range().start().into(),
+                    });
+                }
+            }
+            Stmt::ImportFrom(import_from_stmt) => {
+                let module_name = import_from_stmt.module.as_ref()
+                    .map(|m| m.to_string())
+                    .unwrap_or_default();
+                for alias in &import_from_stmt.names {
+                    let full_name = if module_name.is_empty() {
+                        alias.name.to_string()
+                    } else {
+                        format!("{}.{}", module_name, alias.name)
+                    };
+                    imports.push(Import {
+                        module_name: full_name,
+                        alias: alias.asname.as_ref().map(|n| n.to_string()),
+                        line_number: alias.range().start().into(),
+                    });
+                }
+            }
+            Stmt::FunctionDef(func_def) => {
+                // Extract function definition
+                // Create a symbol for this function
+                let integrations_flags = self.detect_integrations(&func_def.body, &self._config);
+                let symbol = Symbol {
+                    id: func_def.name.to_string(),
+                    kind: crate::model::SymbolKind::Function,
+                    module_id: "".to_string(), // Will be filled later
+                    file_id: "".to_string(), // Will be filled later
+                    qualname: func_def.name.to_string(),
+                    signature: format!("def {}(...)", func_def.name),
+                    annotations: None,
+                    docstring_first_line: self.extract_docstring(&func_def.body), // Extract docstring
+                    purpose: "extracted from AST".to_string(),
+                    outbound_calls: Vec::new(),
+                    inbound_calls: Vec::new(),
+                    integrations_flags,
+                    metrics: crate::model::SymbolMetrics {
+                        fan_in: 0,
+                        fan_out: 0,
+                        is_critical: false,
+                        cycle_participant: false,
+                    },
+                };
+                symbols.push(symbol);
+                
+                // Recursively process function body for calls
+                for body_stmt in &func_def.body {
+                    self.extract_from_statement(body_stmt, Some(&func_def.name), imports, symbols, calls, depth + 1);
+                }
+            }
+            Stmt::ClassDef(class_def) => {
+                // Extract class definition
+                // Create a symbol for this class
+                let integrations_flags = self.detect_integrations(&class_def.body, &self._config);
+                let symbol = Symbol {
+                    id: class_def.name.to_string(),
+                    kind: crate::model::SymbolKind::Class,
+                    module_id: "".to_string(), // Will be filled later
+                    file_id: "".to_string(), // Will be filled later
+                    qualname: class_def.name.to_string(),
+                    signature: format!("class {}", class_def.name),
+                    annotations: None,
+                    docstring_first_line: self.extract_docstring(&class_def.body), // Extract docstring
+                    purpose: "extracted from AST".to_string(),
+                    outbound_calls: Vec::new(),
+                    inbound_calls: Vec::new(),
+                    integrations_flags,
+                    metrics: crate::model::SymbolMetrics {
+                        fan_in: 0,
+                        fan_out: 0,
+                        is_critical: false,
+                        cycle_participant: false,
+                    },
+                };
+                symbols.push(symbol);
+                
+                // Recursively process class body
+                for body_stmt in &class_def.body {
+                    self.extract_from_statement(body_stmt, Some(&class_def.name), imports, symbols, calls, depth + 1);
+                }
+            }
+            Stmt::Expr(expr_stmt) => {
+                self.extract_from_expression(&expr_stmt.value, current_symbol, calls);
+            }
+            _ => {
+                // For other statement types, we might still need to check for calls in expressions
+                // This is a simplified approach - a full implementation would need to traverse all expressions
+            }
+        }
+    }
+    
+    fn extract_docstring(&self, body: &[Stmt]) -> Option<String> {
+        // For now, just return None until we figure out the correct way to extract docstrings
+        // TODO: Implement proper docstring extraction
+        None
+    }
+    
+    fn detect_integrations(&self, body: &[Stmt], config: &Config) -> crate::model::IntegrationFlags {
+        let mut flags = crate::model::IntegrationFlags {
+            http: false,
+            db: false,
+            queue: false,
+        };
+        
+        if !config.analysis.detect_integrations {
+            return flags;
+        }
+        
+        // Convert body to string for pattern matching
+        let body_str = format!("{:?}", body);
+        
+        // Check for HTTP integrations
+        for pattern in &config.analysis.integration_patterns {
+            if pattern.type_ == "http" {
+                for lib in &pattern.patterns {
+                    if body_str.contains(lib) {
+                        flags.http = true;
+                        break;
+                    }
+                }
+            } else if pattern.type_ == "db" {
+                for lib in &pattern.patterns {
+                    if body_str.contains(lib) {
+                        flags.db = true;
+                        break;
+                    }
+                }
+            } else if pattern.type_ == "queue" {
+                for lib in &pattern.patterns {
+                    if body_str.contains(lib) {
+                        flags.queue = true;
+                        break;
+                    }
+                }
+            }
+        }
+        
+        flags
+    }
+    
+    fn extract_function_def(&self, _func_def: &StmtFunctionDef, _symbols: &mut Vec<Symbol>, _calls: &mut Vec<Call>, _depth: usize) {
+        // Extract function information
+        // This is a simplified implementation - a full implementation would extract more details
+    }
+    
+    fn extract_class_def(&self, _class_def: &StmtClassDef, _symbols: &mut Vec<Symbol>, _depth: usize) {
+        // Extract class information
+        // This is a simplified implementation - a full implementation would extract more details
+    }
+    
+    fn extract_from_expression(&self, expr: &Expr, current_symbol: Option<&str>, calls: &mut Vec<Call>) {
+        match expr {
+            Expr::Call(call_expr) => {
+                // Extract call information
+                let callee_expr = self.expr_to_string(&call_expr.func);
+                calls.push(Call {
+                    caller_symbol: current_symbol.unwrap_or("unknown").to_string(), // Use current symbol as caller
+                    callee_expr,
+                    line_number: call_expr.range().start().into(),
+                    call_type: CallType::Unresolved,
+                });
+                
+                // Recursively process arguments
+                for arg in &call_expr.args {
+                    self.extract_from_expression(arg, current_symbol, calls);
+                }
+                for keyword in &call_expr.keywords {
+                    self.extract_from_expression(&keyword.value, current_symbol, calls);
+                }
+            }
+            Expr::Attribute(attr_expr) => {
+                // Recursively process value
+                self.extract_from_expression(&attr_expr.value, current_symbol, calls);
+            }
+            _ => {
+                // For other expression types, recursively process child expressions
+                // This is a simplified approach - a full implementation would handle all expression variants
+            }
+        }
+    }
+    
+    fn expr_to_string(&self, expr: &Expr) -> String {
+        match expr {
+            Expr::Name(name_expr) => name_expr.id.to_string(),
+            Expr::Attribute(attr_expr) => {
+                format!("{}.{}", self.expr_to_string(&attr_expr.value), attr_expr.attr)
+            }
+            _ => "<complex_expression>".to_string(),
+        }
+    }
+    
+    pub fn resolve_symbols(&self, modules: &[ParsedModule]) -> Result<ProjectModel, ArchDocError> {
+        // Build symbol index
+        // Resolve cross-module references
+        // Build call graph
+        
+        // This is a simplified implementation that creates a basic project model
+        // A full implementation would do much more sophisticated symbol resolution
+        
+        let mut project_model = ProjectModel::new();
+        
+        // Add modules to project model
+        for parsed_module in modules {
+            let module_id = parsed_module.module_path.clone();
+            let file_id = parsed_module.path.to_string_lossy().to_string();
+            
+            // Create file doc
+            let file_doc = FileDoc {
+                id: file_id.clone(),
+                path: parsed_module.path.to_string_lossy().to_string(),
+                module_id: module_id.clone(),
+                imports: parsed_module.imports.iter().map(|i| i.module_name.clone()).collect(),
+                outbound_modules: Vec::new(), // TODO: Resolve outbound modules
+                inbound_files: Vec::new(),
+                symbols: parsed_module.symbols.iter().map(|s| s.id.clone()).collect(),
+            };
+            project_model.files.insert(file_id.clone(), file_doc);
+            
+            // Add symbols to project model
+            for mut symbol in parsed_module.symbols.clone() {
+                symbol.module_id = module_id.clone();
+                symbol.file_id = file_id.clone();
+                project_model.symbols.insert(symbol.id.clone(), symbol);
+            }
+            
+            // Create module
+            let module = Module {
+                id: module_id.clone(),
+                path: parsed_module.path.to_string_lossy().to_string(),
+                files: vec![file_id.clone()],
+                doc_summary: None,
+                outbound_modules: Vec::new(), // TODO: Resolve outbound modules
+                inbound_modules: Vec::new(),
+                symbols: parsed_module.symbols.iter().map(|s| s.id.clone()).collect(),
+            };
+            project_model.modules.insert(module_id, module);
+        }
+        
+        // Build dependency graphs and compute metrics
+        self.build_dependency_graphs(&mut project_model, modules)?;
+        self.compute_metrics(&mut project_model)?;
+        
+        Ok(project_model)
+    }
+    
+    fn build_dependency_graphs(&self, project_model: &mut ProjectModel, parsed_modules: &[ParsedModule]) -> Result<(), ArchDocError> {
+        // Build module import edges
+        for parsed_module in parsed_modules {
+            let from_module_id = parsed_module.module_path.clone();
+            
+            for import in &parsed_module.imports {
+                // Try to resolve the imported module
+                let to_module_id = import.module_name.clone();
+                
+                // Create module import edge
+                let edge = crate::model::Edge {
+                    from_id: from_module_id.clone(),
+                    to_id: to_module_id,
+                    edge_type: crate::model::EdgeType::ModuleImport,
+                    meta: None,
+                };
+                project_model.edges.module_import_edges.push(edge);
+            }
+        }
+        
+        // Build symbol call edges
+        for parsed_module in parsed_modules {
+            let _module_id = parsed_module.module_path.clone();
+            
+            for call in &parsed_module.calls {
+                // Try to resolve the called symbol
+                let callee_expr = call.callee_expr.clone();
+                
+                // Create symbol call edge
+                let edge = crate::model::Edge {
+                    from_id: call.caller_symbol.clone(),
+                    to_id: callee_expr,
+                    edge_type: crate::model::EdgeType::SymbolCall, // TODO: Map CallType to EdgeType properly
+                    meta: None,
+                };
+                project_model.edges.symbol_call_edges.push(edge);
+            }
+        }
+        
+        Ok(())
+    }
+    
+    fn compute_metrics(&self, project_model: &mut ProjectModel) -> Result<(), ArchDocError> {
+        // Compute fan-in and fan-out metrics for symbols
+        for symbol in project_model.symbols.values_mut() {
+            // Fan-out: count of outgoing calls
+            let fan_out = project_model.edges.symbol_call_edges
+                .iter()
+                .filter(|edge| edge.from_id == symbol.id)
+                .count();
+                
+            // Fan-in: count of incoming calls
+            let fan_in = project_model.edges.symbol_call_edges
+                .iter()
+                .filter(|edge| edge.to_id == symbol.id)
+                .count();
+                
+            symbol.metrics.fan_in = fan_in;
+            symbol.metrics.fan_out = fan_out;
+            symbol.metrics.is_critical = fan_in > 10 || fan_out > 10; // Simple threshold
+            symbol.metrics.cycle_participant = false; // TODO: Detect cycles
+        }
+        
+        Ok(())
+    }
+}

archdoc-core/src/renderer.rs

@@ -0,0 +1,369 @@
+//! Markdown renderer for ArchDoc
+//!
+//! This module handles generating Markdown documentation from the project model
+//! using templates.
+
+use crate::model::ProjectModel;
+use handlebars::Handlebars;
+
+pub struct Renderer {
+    templates: Handlebars<'static>,
+}
+
+impl Renderer {
+    pub fn new() -> Self {
+        let mut handlebars = Handlebars::new();
+        
+        // Register templates
+        handlebars.register_template_string("architecture_md", Self::architecture_md_template())
+            .expect("Failed to register architecture_md template");
+        
+        // TODO: Register other templates
+        
+        Self {
+            templates: handlebars,
+        }
+    }
+    
+    fn architecture_md_template() -> &'static str {
+        r#"# ARCHITECTURE — {{{project_name}}}
+
+<!-- MANUAL:BEGIN -->
+## Project summary
+**Name:** {{{project_name}}}
+**Description:** {{{project_description}}}
+
+## Key decisions (manual)
+{{#each key_decisions}}
+- {{{this}}}
+{{/each}}
+
+## Non-goals (manual)
+{{#each non_goals}}
+- {{{this}}}
+{{/each}}
+<!-- MANUAL:END -->
+
+---
+
+## Document metadata
+- **Created:** {{{created_date}}}
+- **Updated:** {{{updated_date}}}
+- **Generated by:** archdoc (cli) v0.1
+
+---
+
+## Integrations
+<!-- ARCHDOC:BEGIN section=integrations -->
+> Generated. Do not edit inside this block.
+
+### Database Integrations
+{{#each db_integrations}}
+- {{{this}}}
+{{/each}}
+
+### HTTP/API Integrations
+{{#each http_integrations}}
+- {{{this}}}
+{{/each}}
+
+### Queue Integrations
+{{#each queue_integrations}}
+- {{{this}}}
+{{/each}}
+<!-- ARCHDOC:END section=integrations -->
+
+---
+
+## Rails / Tooling
+<!-- ARCHDOC:BEGIN section=rails -->
+> Generated. Do not edit inside this block.
+{{{rails_summary}}}
+<!-- ARCHDOC:END section=rails -->
+
+---
+
+## Repository layout (top-level)
+<!-- ARCHDOC:BEGIN section=layout -->
+> Generated. Do not edit inside this block.
+| Path | Purpose | Link |
+|------|---------|------|
+{{#each layout_items}}
+| {{{path}}} | {{{purpose}}} | [details]({{{link}}}) |
+{{/each}}
+<!-- ARCHDOC:END section=layout -->
+
+---
+
+## Modules index
+<!-- ARCHDOC:BEGIN section=modules_index -->
+> Generated. Do not edit inside this block.
+| Module | Symbols | Inbound | Outbound | Link |
+|--------|---------|---------|----------|------|
+{{#each modules}}
+| {{{name}}} | {{{symbol_count}}} | {{{inbound_count}}} | {{{outbound_count}}} | [details]({{{link}}}) |
+{{/each}}
+<!-- ARCHDOC:END section=modules_index -->
+
+---
+
+## Critical dependency points
+<!-- ARCHDOC:BEGIN section=critical_points -->
+> Generated. Do not edit inside this block.
+### High Fan-in (Most Called)
+| Symbol | Fan-in | Critical |
+|--------|--------|----------|
+{{#each high_fan_in}}
+| {{{symbol}}} | {{{count}}} | {{{critical}}} |
+{{/each}}
+
+### High Fan-out (Calls Many)
+| Symbol | Fan-out | Critical |
+|--------|---------|----------|
+{{#each high_fan_out}}
+| {{{symbol}}} | {{{count}}} | {{{critical}}} |
+{{/each}}
+
+### Module Cycles
+{{#each cycles}}
+- {{{cycle_path}}}
+{{/each}}
+<!-- ARCHDOC:END section=critical_points -->
+
+---
+
+<!-- MANUAL:BEGIN -->
+## Change notes (manual)
+{{#each change_notes}}
+- {{{this}}}
+{{/each}}
+<!-- MANUAL:END -->
+"#
+    }
+    
+    pub fn render_architecture_md(&self, model: &ProjectModel) -> Result<String, anyhow::Error> {
+        // Collect integration information
+        let mut db_integrations = Vec::new();
+        let mut http_integrations = Vec::new();
+        let mut queue_integrations = Vec::new();
+        
+        for (symbol_id, symbol) in &model.symbols {
+            if symbol.integrations_flags.db {
+                db_integrations.push(format!("{} in {}", symbol_id, symbol.file_id));
+            }
+            if symbol.integrations_flags.http {
+                http_integrations.push(format!("{} in {}", symbol_id, symbol.file_id));
+            }
+            if symbol.integrations_flags.queue {
+                queue_integrations.push(format!("{} in {}", symbol_id, symbol.file_id));
+            }
+        }
+        
+        // Prepare data for template
+        let data = serde_json::json!({
+            "project_name": "New Project",
+            "project_description": "<FILL_MANUALLY: what this project does in 3–7 lines>",
+            "created_date": "2026-01-25",
+            "updated_date": "2026-01-25",
+            "key_decisions": ["<FILL_MANUALLY>"],
+            "non_goals": ["<FILL_MANUALLY>"],
+            "change_notes": ["<FILL_MANUALLY>"],
+            "db_integrations": db_integrations,
+            "http_integrations": http_integrations,
+            "queue_integrations": queue_integrations,
+            // TODO: Fill with more actual data from model
+        });
+        
+        self.templates.render("architecture_md", &data)
+            .map_err(|e| anyhow::anyhow!("Failed to render architecture.md: {}", e))
+    }
+    
+    pub fn render_integrations_section(&self, model: &ProjectModel) -> Result<String, anyhow::Error> {
+        // Collect integration information
+        let mut db_integrations = Vec::new();
+        let mut http_integrations = Vec::new();
+        let mut queue_integrations = Vec::new();
+        
+        for (symbol_id, symbol) in &model.symbols {
+            if symbol.integrations_flags.db {
+                db_integrations.push(format!("{} in {}", symbol_id, symbol.file_id));
+            }
+            if symbol.integrations_flags.http {
+                http_integrations.push(format!("{} in {}", symbol_id, symbol.file_id));
+            }
+            if symbol.integrations_flags.queue {
+                queue_integrations.push(format!("{} in {}", symbol_id, symbol.file_id));
+            }
+        }
+        
+        // Prepare data for integrations section
+        let data = serde_json::json!({
+            "db_integrations": db_integrations,
+            "http_integrations": http_integrations,
+            "queue_integrations": queue_integrations,
+        });
+        
+        // Create a smaller template just for the integrations section
+        let integrations_template = r#"
+
+### Database Integrations
+{{#each db_integrations}}
+- {{{this}}}
+{{/each}}
+
+### HTTP/API Integrations
+{{#each http_integrations}}
+- {{{this}}}
+{{/each}}
+
+### Queue Integrations
+{{#each queue_integrations}}
+- {{{this}}}
+{{/each}}
+"#;
+        
+        let mut handlebars = Handlebars::new();
+        handlebars.register_template_string("integrations", integrations_template)
+            .map_err(|e| anyhow::anyhow!("Failed to register integrations template: {}", e))?;
+        
+        handlebars.render("integrations", &data)
+            .map_err(|e| anyhow::anyhow!("Failed to render integrations section: {}", e))
+    }
+    
+    pub fn render_rails_section(&self, _model: &ProjectModel) -> Result<String, anyhow::Error> {
+        // For now, return a simple placeholder
+        Ok("\n\nNo tooling information available.\n".to_string())
+    }
+    
+    pub fn render_layout_section(&self, model: &ProjectModel) -> Result<String, anyhow::Error> {
+        // Collect layout information from files
+        let mut layout_items = Vec::new();
+        
+        for (file_id, file_doc) in &model.files {
+            layout_items.push(serde_json::json!({
+                "path": file_doc.path,
+                "purpose": "Source file",
+                "link": format!("docs/architecture/files/{}.md", file_id)
+            }));
+        }
+        
+        // Prepare data for layout section
+        let data = serde_json::json!({
+            "layout_items": layout_items,
+        });
+        
+        // Create a smaller template just for the layout section
+        let layout_template = r#"
+
+| Path | Purpose | Link |
+|------|---------|------|
+{{#each layout_items}}
+| {{{path}}} | {{{purpose}}} | [details]({{{link}}}) |
+{{/each}}
+"#;
+        
+        let mut handlebars = Handlebars::new();
+        handlebars.register_template_string("layout", layout_template)
+            .map_err(|e| anyhow::anyhow!("Failed to register layout template: {}", e))?;
+        
+        handlebars.render("layout", &data)
+            .map_err(|e| anyhow::anyhow!("Failed to render layout section: {}", e))
+    }
+    
+    pub fn render_modules_index_section(&self, model: &ProjectModel) -> Result<String, anyhow::Error> {
+        // Collect module information
+        let mut modules = Vec::new();
+        
+        for (module_id, module) in &model.modules {
+            modules.push(serde_json::json!({
+                "name": module_id,
+                "symbol_count": module.symbols.len(),
+                "inbound_count": module.inbound_modules.len(),
+                "outbound_count": module.outbound_modules.len(),
+                "link": format!("docs/architecture/modules/{}.md", module_id)
+            }));
+        }
+        
+        // Prepare data for modules index section
+        let data = serde_json::json!({
+            "modules": modules,
+        });
+        
+        // Create a smaller template just for the modules index section
+        let modules_template = r#"
+
+| Module | Symbols | Inbound | Outbound | Link |
+|--------|---------|---------|----------|------|
+{{#each modules}}
+| {{{name}}} | {{{symbol_count}}} | {{{inbound_count}}} | {{{outbound_count}}} | [details]({{{link}}}) |
+{{/each}}
+"#;
+        
+        let mut handlebars = Handlebars::new();
+        handlebars.register_template_string("modules_index", modules_template)
+            .map_err(|e| anyhow::anyhow!("Failed to register modules_index template: {}", e))?;
+        
+        handlebars.render("modules_index", &data)
+            .map_err(|e| anyhow::anyhow!("Failed to render modules index section: {}", e))
+    }
+    
+    pub fn render_critical_points_section(&self, model: &ProjectModel) -> Result<String, anyhow::Error> {
+        // Collect critical points information
+        let mut high_fan_in = Vec::new();
+        let mut high_fan_out = Vec::new();
+        
+        for (symbol_id, symbol) in &model.symbols {
+            if symbol.metrics.fan_in > 5 {  // Threshold for high fan-in
+                high_fan_in.push(serde_json::json!({
+                    "symbol": symbol_id,
+                    "count": symbol.metrics.fan_in,
+                    "critical": symbol.metrics.is_critical,
+                }));
+            }
+            if symbol.metrics.fan_out > 5 {  // Threshold for high fan-out
+                high_fan_out.push(serde_json::json!({
+                    "symbol": symbol_id,
+                    "count": symbol.metrics.fan_out,
+                    "critical": symbol.metrics.is_critical,
+                }));
+            }
+        }
+        
+        // Prepare data for critical points section
+        let data = serde_json::json!({
+            "high_fan_in": high_fan_in,
+            "high_fan_out": high_fan_out,
+            "cycles": Vec::<String>::new(), // TODO: Implement cycle detection
+        });
+        
+        // Create a smaller template just for the critical points section
+        let critical_points_template = r#"
+
+### High Fan-in (Most Called)
+| Symbol | Fan-in | Critical |
+|--------|--------|----------|
+{{#each high_fan_in}}
+| {{{symbol}}} | {{{count}}} | {{{critical}}} |
+{{/each}}
+
+### High Fan-out (Calls Many)
+| Symbol | Fan-out | Critical |
+|--------|---------|----------|
+{{#each high_fan_out}}
+| {{{symbol}}} | {{{count}}} | {{{critical}}} |
+{{/each}}
+
+### Module Cycles
+{{#each cycles}}
+- {{{this}}}
+{{/each}}
+"#;
+        
+        let mut handlebars = Handlebars::new();
+        handlebars.register_template_string("critical_points", critical_points_template)
+            .map_err(|e| anyhow::anyhow!("Failed to register critical_points template: {}", e))?;
+        
+        handlebars.render("critical_points", &data)
+            .map_err(|e| anyhow::anyhow!("Failed to render critical points section: {}", e))
+    }
+}

archdoc-core/src/scanner.rs

@@ -0,0 +1,86 @@
+//! File scanner for ArchDoc
+//!
+//! This module handles scanning the file system for Python files according to
+//! the configuration settings.
+
+use crate::config::Config;
+use crate::errors::ArchDocError;
+use std::path::{Path, PathBuf};
+use walkdir::WalkDir;
+
+pub struct FileScanner {
+    config: Config,
+}
+
+impl FileScanner {
+    pub fn new(config: Config) -> Self {
+        Self { config }
+    }
+    
+    pub fn scan_python_files(&self, root: &Path) -> Result<Vec<PathBuf>, ArchDocError> {
+        // Check if root directory exists
+        if !root.exists() {
+            return Err(ArchDocError::Io(std::io::Error::new(
+                std::io::ErrorKind::NotFound,
+                format!("Root directory does not exist: {}", root.display())
+            )));
+        }
+        
+        if !root.is_dir() {
+            return Err(ArchDocError::Io(std::io::Error::new(
+                std::io::ErrorKind::InvalidInput,
+                format!("Root path is not a directory: {}", root.display())
+            )));
+        }
+        
+        let mut python_files = Vec::new();
+        
+        // Walk directory tree respecting include/exclude patterns
+        for entry in WalkDir::new(root)
+            .follow_links(self.config.scan.follow_symlinks)
+            .into_iter() {
+            
+            let entry = entry.map_err(|e| {
+                ArchDocError::Io(std::io::Error::new(
+                    std::io::ErrorKind::Other,
+                    format!("Failed to read directory entry: {}", e)
+                ))
+            })?;
+            
+            let path = entry.path();
+            
+            // Skip excluded paths
+            if self.is_excluded(path) {
+                if path.is_dir() {
+                    continue;
+                } else {
+                    continue;
+                }
+            }
+            
+            // Include Python files
+            if path.extension().and_then(|s| s.to_str()) == Some("py") {
+                python_files.push(path.to_path_buf());
+            }
+        }
+        
+        Ok(python_files)
+    }
+    
+    fn is_excluded(&self, path: &Path) -> bool {
+        // Convert path to string for pattern matching
+        let path_str = match path.to_str() {
+            Some(s) => s,
+            None => return false, // If we can't convert to string, don't exclude
+        };
+        
+        // Check if path matches any exclude patterns
+        for pattern in &self.config.scan.exclude {
+            if path_str.contains(pattern) {
+                return true;
+            }
+        }
+        
+        false
+    }
+}

archdoc-core/src/writer.rs

@@ -0,0 +1,237 @@
+//! Diff-aware file writer for ArchDoc
+//!
+//! This module handles writing generated documentation to files while preserving
+//! manual content and only updating generated sections.
+
+use crate::errors::ArchDocError;
+use std::path::Path;
+use std::fs;
+use chrono::Utc;
+
+#[derive(Debug)]
+pub struct SectionMarker {
+    pub name: String,
+    pub start_pos: usize,
+    pub end_pos: usize,
+}
+
+#[derive(Debug)]
+pub struct SymbolMarker {
+    pub symbol_id: String,
+    pub start_pos: usize,
+    pub end_pos: usize,
+}
+
+pub struct DiffAwareWriter {
+    // Configuration
+}
+
+impl DiffAwareWriter {
+    pub fn new() -> Self {
+        Self {}
+    }
+    
+    pub fn update_file_with_markers(
+        &self,
+        file_path: &Path,
+        generated_content: &str,
+        section_name: &str,
+    ) -> Result<(), ArchDocError> {
+        // Read existing file
+        let existing_content = if file_path.exists() {
+            fs::read_to_string(file_path)
+                .map_err(|e| ArchDocError::Io(e))?
+        } else {
+            // Create new file with template
+            let template_content = self.create_template_file(file_path, section_name)?;
+            // Write template to file
+            fs::write(file_path, &template_content)
+                .map_err(|e| ArchDocError::Io(e))?;
+            template_content
+        };
+        
+        // Find section markers
+        let markers = self.find_section_markers(&existing_content, section_name)?;
+        
+        if let Some(marker) = markers.first() {
+            // Replace content between markers
+            let new_content = self.replace_section_content(
+                &existing_content,
+                marker,
+                generated_content,
+            )?;
+            
+            // Check if content has changed
+            let content_changed = existing_content != new_content;
+            
+            // Write updated content
+            if content_changed {
+                let updated_content = self.update_timestamp(new_content)?;
+                fs::write(file_path, updated_content)
+                    .map_err(|e| ArchDocError::Io(e))?;
+            } else {
+                // Content hasn't changed, but we might still need to update timestamp
+                // TODO: Implement timestamp update logic based on config
+                fs::write(file_path, new_content)
+                    .map_err(|e| ArchDocError::Io(e))?;
+            }
+        }
+        
+        Ok(())
+    }
+    
+    pub fn update_symbol_section(
+        &self,
+        _file_path: &Path,
+        _symbol_id: &str,
+        _generated_content: &str,
+    ) -> Result<(), ArchDocError> {
+        // Similar to section update but for symbol-specific markers
+        todo!("Implement symbol section update")
+    }
+    
+    fn find_section_markers(&self, content: &str, section_name: &str) -> Result<Vec<SectionMarker>, ArchDocError> {
+        let begin_marker = format!("<!-- ARCHDOC:BEGIN section={} -->", section_name);
+        let end_marker = format!("<!-- ARCHDOC:END section={} -->", section_name);
+        
+        let mut markers = Vec::new();
+        let mut pos = 0;
+        
+        while let Some(begin_pos) = content[pos..].find(&begin_marker) {
+            let absolute_begin = pos + begin_pos;
+            let search_start = absolute_begin + begin_marker.len();
+            
+            if let Some(end_pos) = content[search_start..].find(&end_marker) {
+                let absolute_end = search_start + end_pos + end_marker.len();
+                markers.push(SectionMarker {
+                    name: section_name.to_string(),
+                    start_pos: absolute_begin,
+                    end_pos: absolute_end,
+                });
+                pos = absolute_end;
+            } else {
+                break;
+            }
+        }
+        
+        Ok(markers)
+    }
+    
+    fn replace_section_content(
+        &self,
+        content: &str,
+        marker: &SectionMarker,
+        new_content: &str,
+    ) -> Result<String, ArchDocError> {
+        let before = &content[..marker.start_pos];
+        let after = &content[marker.end_pos..];
+        
+        let begin_marker = format!("<!-- ARCHDOC:BEGIN section={} -->", marker.name);
+        let end_marker = format!("<!-- ARCHDOC:END section={} -->", marker.name);
+        
+        Ok(format!(
+            "{}{}{}{}{}",
+            before, begin_marker, new_content, end_marker, after
+        ))
+    }
+    
+    fn update_timestamp(&self, content: String) -> Result<String, ArchDocError> {
+        // Update the "Updated" field in the document metadata section
+        // Find the metadata section and update the timestamp
+        let today = Utc::now().format("%Y-%m-%d").to_string();
+        
+        // Look for the "Updated:" line and replace it
+        let lines: Vec<&str> = content.lines().collect();
+        let mut updated_lines = Vec::new();
+        
+        for line in lines {
+            if line.trim_start().starts_with("- **Updated:**") {
+                updated_lines.push(format!("- **Updated:** {}", today));
+            } else {
+                updated_lines.push(line.to_string());
+            }
+        }
+        
+        Ok(updated_lines.join("\n"))
+    }
+    
+    fn create_template_file(&self, _file_path: &Path, template_type: &str) -> Result<String, ArchDocError> {
+        // Create file with appropriate template based on type
+        match template_type {
+            "architecture" => {
+                let template = r#"# 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 -->
+> Generated. Do not edit inside this block.
+
+<!-- ARCHDOC:END section=rails -->
+
+---
+
+## Repository layout (top-level)
+<!-- ARCHDOC:BEGIN section=layout -->
+> Generated. Do not edit inside this block.
+
+<!-- ARCHDOC:END section=layout -->
+
+---
+
+## Modules index
+<!-- ARCHDOC:BEGIN section=modules_index -->
+> Generated. Do not edit inside this block.
+
+<!-- ARCHDOC:END section=modules_index -->
+
+---
+ 
+## Integrations
+<!-- ARCHDOC:BEGIN section=integrations -->
+> Generated. Do not edit inside this block.
+
+<!-- ARCHDOC:END section=integrations -->
+
+---
+ 
+## Critical dependency points
+<!-- ARCHDOC:BEGIN section=critical_points -->
+> Generated. Do not edit inside this block.
+
+<!-- ARCHDOC:END section=critical_points -->
+
+---
+
+<!-- MANUAL:BEGIN -->
+## Change notes (manual)
+- <FILL_MANUALLY>
+<!-- MANUAL:END -->
+"#;
+                Ok(template.to_string())
+            }
+            _ => {
+                Ok("".to_string())
+            }
+        }
+    }
+}