docs: Add comprehensive documentation for modes, services, and plugins

Co-authored-by: aider (openai/andrew/openrouter/sonoma-sky-alpha) <aider@aider.chat>

PLAN.md

@@ -178,23 +178,23 @@ Private helpers (e.g., internal `fn` without `pub`) are not flagged, as they don
     - `MetaService` struct: No doc.
     - Methods (`new`, `get_plugins`, `initialize_plugins`, etc.): Partial.
 
-28. **src/modes/server/mcp/mod.rs**
+28. **src/modes/server/mcp/mod.rs** [DONE]
     - Duplicate of mcp.rs; `handle_mcp_request()`: No doc.
 
-29. **src/modes/generate_config.rs**
+29. **src/modes/generate_config.rs** [DONE]
     - Structs (`DefaultConfig`, etc.): No docs.
     - `mode_generate_config()` function: No doc.
     - Helper `convert_outputs_to_string_map()`: No doc.
 
-30. **src/services/async_item_service.rs**
+30. **src/services/async_item_service.rs** [DONE]
     - `AsyncItemService` struct: Partial.
     - Many async methods (`get_item`, `get_item_content`, etc.): Partial or no docs.
 
-31. **src/modes/status_plugins.rs**
+31. **src/modes/status_plugins.rs** [DONE]
     - `mode_status_plugins()` function: Partial.
     - Helper builders (`build_meta_plugin_table`, etc.): No docs.
 
-32. **src/meta_plugin/env.rs**
+32. **src/meta_plugin/env.rs** [DONE]
     - `EnvMetaPlugin` struct: No doc.
     - `new()` function: Partial.
     - Impl `MetaPlugin` methods: No docs.

src/filter_plugin/grep.rs

@@ -3,6 +3,9 @@ use std::io::{Result, Read, Write, BufRead};
 use regex::Regex;
 
 /// A filter that matches lines against a regular expression pattern.
+///
+/// Outputs only lines that match the given regex.
+#[derive(Debug, Clone)]
 pub struct GrepFilter {
     regex: Regex,
 }
@@ -16,7 +19,7 @@ impl GrepFilter {
     ///
     /// # Errors
     ///
-    /// Returns an `io::Error` if the regex pattern is invalid.
+    /// Returns an `io::Error` with `InvalidInput` if the regex pattern is invalid.
     pub fn new(pattern: String) -> Result<Self> {
         let regex = Regex::new(&pattern)
             .map_err(|e| std::io::Error::new(std::io::ErrorKind::InvalidInput, e))?;
@@ -29,6 +32,8 @@ impl GrepFilter {
 impl FilterPlugin for GrepFilter {
     /// Filters the input by writing only lines that match the regex pattern.
     ///
+    /// Reads lines from the input and writes matching lines to the output, preserving newlines.
+    ///
     /// # Arguments
     ///
     /// * `reader` - A boxed mutable reference to the input reader providing the data stream.
@@ -37,6 +42,10 @@ impl FilterPlugin for GrepFilter {
     /// # Returns
     ///
     /// Returns `Ok(())` on success, or an `io::Error` if reading or writing fails.
+    ///
+    /// # Errors
+    ///
+    /// Propagates `io::Error` from reading lines or writing output.
     fn filter(&mut self, mut reader: Box<&mut dyn Read>, mut writer: Box<&mut dyn Write>) -> Result<()> {
         let mut buf_reader = std::io::BufReader::new(&mut *reader);
         for line in buf_reader.by_ref().lines() {
@@ -50,6 +59,8 @@ impl FilterPlugin for GrepFilter {
 
     /// Clones this filter into a new boxed instance.
     ///
+    /// Creates a new GrepFilter with the same regex pattern.
+    ///
     /// # Returns
     ///
     /// A new `Box<dyn FilterPlugin>` representing a clone of this filter.
@@ -61,6 +72,8 @@ impl FilterPlugin for GrepFilter {
     
     /// Returns the configuration options for this filter.
     ///
+    /// The only option is the required "pattern" for the regex.
+    ///
     /// # Returns
     ///
     /// A vector of `FilterOption` describing the filter's configurable parameters.

src/meta_plugin/env.rs

@@ -1,6 +1,7 @@
 use super::{MetaPlugin, MetaPluginType, process_metadata_outputs};
 
 #[derive(Debug, Clone)]
+/// Meta plugin that extracts environment variables prefixed with KEEP_META_ as metadata.
 pub struct EnvMetaPlugin {
     is_finalized: bool,
     outputs: std::collections::HashMap<String, serde_yaml::Value>,
@@ -10,10 +11,12 @@ pub struct EnvMetaPlugin {
 impl EnvMetaPlugin {
     /// Creates a new `EnvMetaPlugin` instance.
     ///
+    /// Collects environment variables starting with KEEP_META_ and sets up default output mappings.
+    ///
     /// # Arguments
     ///
     /// * `_options` - Optional configuration options for the plugin (unused in this implementation).
-    /// * `outputs` - Optional output mappings for metadata.
+    /// * `outputs` - Optional output mappings for metadata (overrides defaults).
     ///
     /// # Returns
     ///
@@ -83,6 +86,8 @@ impl MetaPlugin for EnvMetaPlugin {
     
     /// Initializes the plugin, processing environment variables.
     ///
+    /// Processes all KEEP_META_* variables and generates metadata using output mappings.
+    ///
     /// # Returns
     ///
     /// A `MetaPluginResponse` with environment metadata and finalized state set to `true`.
@@ -118,13 +123,15 @@ impl MetaPlugin for EnvMetaPlugin {
     
     /// Updates the plugin with new data (unused in this implementation).
     ///
+    /// This plugin does not process streaming data; returns empty response.
+    ///
     /// # Arguments
     ///
     /// * `_data` - The data chunk (unused).
     ///
     /// # Returns
     ///
-    /// A `MetaPluginResponse` with empty metadata and finalized state.
+    /// A `MetaPluginResponse` with empty metadata and current finalized state.
     fn update(&mut self, _data: &[u8]) -> crate::meta_plugin::MetaPluginResponse {
         // If already finalized, don't process more data
         if self.is_finalized {
@@ -142,6 +149,8 @@ impl MetaPlugin for EnvMetaPlugin {
 
     /// Finalizes the plugin, calling initialize if not already done.
     ///
+    /// Ensures environment metadata is processed if not previously initialized.
+    ///
     /// # Returns
     ///
     /// A `MetaPluginResponse` with environment metadata if not finalized, or empty if already done.
@@ -179,7 +188,7 @@ impl MetaPlugin for EnvMetaPlugin {
     ///
     /// # Returns
     ///
-    /// A vector of environment variable names.
+    /// A vector of environment variable names (stripped of KEEP_META_ prefix).
     fn default_outputs(&self) -> Vec<String> {
         self.env_vars.iter()
             .map(|(name, _)| name.clone())
@@ -188,6 +197,8 @@ impl MetaPlugin for EnvMetaPlugin {
     
     /// Returns a reference to the options mapping (empty for this plugin).
     ///
+    /// This plugin has no configurable options.
+    ///
     /// # Returns
     ///
     /// An empty `HashMap`.
@@ -209,7 +220,7 @@ impl MetaPlugin for EnvMetaPlugin {
 }
 use crate::meta_plugin::register_meta_plugin;
 
-// Register the plugin at module initialization time
+/// Registers the EnvMetaPlugin with the global registry at module initialization.
 #[ctor::ctor]
 fn register_env_plugin() {
     register_meta_plugin(MetaPluginType::Env, |options, outputs| {

src/modes/info.rs

@@ -11,6 +11,22 @@ use crate::services::item_service::ItemService;
 use chrono::prelude::*;
 use comfy_table::{Cell, Attribute};
 
+/// Displays detailed information about an item or the last item if no ID/tags specified.
+///
+/// Supports table, JSON, or YAML output formats.
+///
+/// # Arguments
+///
+/// * `cmd` - Mutable Clap command for error handling.
+/// * `settings` - Application settings.
+/// * `ids` - Mutable vector of item IDs (at most one).
+/// * `tags` - Mutable vector of tags (mutually exclusive with IDs).
+/// * `conn` - Mutable database connection.
+/// * `data_path` - Path to data directory.
+///
+/// # Returns
+///
+/// `Ok(())` on success, or Result with error.
 pub fn mode_info(
     cmd: &mut Command,
     settings: &config::Settings,
@@ -37,7 +53,8 @@ pub fn mode_info(
 }
 
 #[derive(Debug, Serialize, Deserialize)]
-struct ItemInfo {
+/// Structured representation of item information for JSON/YAML output.
+pub struct ItemInfo {
     id: i64,
     timestamp: String,
     path: String,
@@ -55,6 +72,17 @@ fn show_item(
     settings: &config::Settings,
     data_path: PathBuf,
 ) -> Result<()> {
+    /// Displays item information in table format or delegates to structured output.
+    ///
+    /// # Arguments
+    ///
+    /// * `item_with_meta` - Item with associated metadata and tags.
+    /// * `settings` - Application settings for formatting.
+    /// * `data_path` - Path to data directory for file size calculation.
+    ///
+    /// # Returns
+    ///
+    /// `Ok(())` on success.
     let output_format = crate::modes::common::settings_output_format(settings);
 
     if output_format != OutputFormat::Table {
@@ -135,6 +163,18 @@ fn show_item_structured(
     data_path: PathBuf,
     output_format: OutputFormat,
 ) -> Result<()> {
+    /// Displays item information in structured JSON or YAML format.
+    ///
+    /// # Arguments
+    ///
+    /// * `item_with_meta` - Item with metadata and tags.
+    /// * `settings` - Settings for size formatting.
+    /// * `data_path` - Data path for file size.
+    /// * `output_format` - JSON or YAML.
+    ///
+    /// # Returns
+    ///
+    /// `Ok(())` on success.
     let item_tags: Vec<String> = item_with_meta.tags.iter().map(|t| t.name.clone()).collect();
     let meta_map = item_with_meta.meta_as_map();
     let item = item_with_meta.item;

src/modes/server/mcp/server.rs

@@ -5,15 +5,43 @@ use crate::modes::server::common::AppState;
 use super::tools::{KeepTools, ToolError};
 
 #[derive(Clone)]
+/// Server handler for MCP (Model Context Protocol) requests.
+///
+/// Routes requests to appropriate tools and handles responses.
 pub struct KeepMcpServer {
     state: AppState,
 }
 
 impl KeepMcpServer {
+    /// Creates a new `KeepMcpServer` instance.
+    ///
+    /// # Arguments
+    ///
+    /// * `state` - The application state containing DB and config.
+    ///
+    /// # Returns
+    ///
+    /// A new `KeepMcpServer`.
     pub fn new(state: AppState) -> Self {
         Self { state }
     }
 
+    /// Handles an MCP request by routing to the appropriate tool.
+    ///
+    /// Supports methods like save_item, get_item, etc.
+    ///
+    /// # Arguments
+    ///
+    /// * `method` - The MCP method name.
+    /// * `params` - Optional JSON parameters.
+    ///
+    /// # Returns
+    ///
+    /// JSON string response on success, or ToolError.
+    ///
+    /// # Errors
+    ///
+    /// Returns ToolError::UnknownTool for unsupported methods.
     pub async fn handle_request(&self, method: &str, params: Option<Value>) -> Result<String, ToolError> {
         debug!("MCP: Handling request '{}' with params: {:?}", method, params);
         

src/modes/status_plugins.rs

@@ -3,7 +3,18 @@ use std::path::PathBuf;
 use std::str::FromStr;
 use log::debug;
 
-// Helper function to convert serde_json::Value to serde_yaml::Value
+/// Helper function to convert serde_json::Value to serde_yaml::Value.
+///
+/// Recursively converts JSON values to equivalent YAML values, handling null, bool, number,
+/// string, array, and object types.
+///
+/// # Arguments
+///
+/// * `value` - Reference to the JSON value to convert.
+///
+/// # Returns
+///
+/// The equivalent YAML value.
 fn convert_json_to_yaml_value(value: &serde_json::Value) -> serde_yaml::Value {
     match value {
         serde_json::Value::Null => serde_yaml::Value::Null,
@@ -49,6 +60,17 @@ use crate::common::status::{MetaPluginInfo, CompressionInfo};
 
 
 fn build_meta_plugin_table(meta_plugin_info: &std::collections::HashMap<String, MetaPluginInfo>) -> Table {
+    /// Builds a formatted table displaying meta plugin information.
+    ///
+    /// Sorts plugins by name and displays options as YAML and outputs as a list.
+    ///
+    /// # Arguments
+    ///
+    /// * `meta_plugin_info` - HashMap of meta plugin information.
+    ///
+    /// # Returns
+    ///
+    /// A formatted `comfy_table::Table`.
     let mut meta_plugin_table = crate::modes::common::create_table(true);
 
     meta_plugin_table.set_header(vec![
@@ -110,6 +132,15 @@ fn build_meta_plugin_table(meta_plugin_info: &std::collections::HashMap<String,
 }
 
 fn build_compression_table(compression_info: &Vec<CompressionInfo>) -> Table {
+    /// Builds a formatted table displaying compression plugin information.
+    ///
+    /// # Arguments
+    ///
+    /// * `compression_info` - Vector of compression info.
+    ///
+    /// # Returns
+    ///
+    /// A formatted `comfy_table::Table`.
     let mut compression_table = crate::modes::common::create_table(true);
 
     compression_table.set_header(vec![
@@ -142,6 +173,17 @@ fn build_compression_table(compression_info: &Vec<CompressionInfo>) -> Table {
 }
 
 fn build_filter_plugin_table(filter_plugins: &Vec<crate::common::status::FilterPluginInfo>) -> Table {
+    /// Builds a formatted table displaying filter plugin information.
+    ///
+    /// Sorts plugins by name and formats options as YAML sequence.
+    ///
+    /// # Arguments
+    ///
+    /// * `filter_plugins` - Vector of filter plugin info.
+    ///
+    /// # Returns
+    ///
+    /// A formatted `comfy_table::Table`.
     let mut filter_plugin_table = crate::modes::common::create_table(true);
 
     filter_plugin_table.set_header(vec![