refactor: Remove redundant doc comments throughout codebase

Removes module-level doc comments (//! lines) and excessive inline doc
comments that were duplicating information already evident from:
- Function/struct names (self-documenting code)
- Type signatures (the what is clear from types)
- Implementation context (the how is clear from code)

Affected modules:
- cli/* - Removed command descriptions duplicating clap help text
- core/* - Removed module headers and obvious function docs
- documents/* - Removed extractor/regenerator/truncation docs
- embedding/* - Removed pipeline and chunking docs
- gitlab/* - Removed client and transformer docs (kept type definitions)
- ingestion/* - Removed orchestrator and ingestion docs
- search/* - Removed FTS and vector search docs

Philosophy: Code should be self-documenting. Comments should explain
"why" (business decisions, non-obvious constraints) not "what" (which
the code itself shows). This change reduces noise and maintenance burden
while keeping the codebase just as understandable.

Retains comments for:
- Non-obvious business logic
- Important safety invariants
- Complex algorithm explanations
- Public API boundaries where generated docs matter

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

src/cli/commands/init.rs

@@ -1,5 +1,3 @@
-//! Init command - initialize configuration and database.
-
 use std::fs;
 
 use crate::core::config::{MinimalConfig, MinimalGitLabConfig, ProjectConfig};
@@ -8,21 +6,18 @@ use crate::core::error::{LoreError, Result};
 use crate::core::paths::{get_config_path, get_data_dir};
 use crate::gitlab::{GitLabClient, GitLabProject};
 
-/// Input data for init command.
 pub struct InitInputs {
     pub gitlab_url: String,
     pub token_env_var: String,
     pub project_paths: Vec<String>,
 }
 
-/// Options for init command.
 pub struct InitOptions {
     pub config_path: Option<String>,
     pub force: bool,
     pub non_interactive: bool,
 }
 
-/// Result of successful init.
 pub struct InitResult {
     pub config_path: String,
     pub data_dir: String,
@@ -40,12 +35,10 @@ pub struct ProjectInfo {
     pub name: String,
 }
 
-/// Run the init command programmatically.
 pub async fn run_init(inputs: InitInputs, options: InitOptions) -> Result<InitResult> {
     let config_path = get_config_path(options.config_path.as_deref());
     let data_dir = get_data_dir();
 
-    // 1. Check if config exists (force takes precedence over non_interactive)
     if config_path.exists() && !options.force {
         if options.non_interactive {
             return Err(LoreError::Other(format!(
@@ -59,7 +52,6 @@ pub async fn run_init(inputs: InitInputs, options: InitOptions) -> Result<InitRe
         ));
     }
 
-    // 2. Validate GitLab URL format
     if url::Url::parse(&inputs.gitlab_url).is_err() {
         return Err(LoreError::Other(format!(
             "Invalid GitLab URL: {}",
@@ -67,12 +59,10 @@ pub async fn run_init(inputs: InitInputs, options: InitOptions) -> Result<InitRe
         )));
     }
 
-    // 3. Check token is set in environment
     let token = std::env::var(&inputs.token_env_var).map_err(|_| LoreError::TokenNotSet {
         env_var: inputs.token_env_var.clone(),
     })?;
 
-    // 4. Create GitLab client and test authentication
     let client = GitLabClient::new(&inputs.gitlab_url, &token, None);
 
     let gitlab_user = client.get_current_user().await.map_err(|e| {
@@ -88,7 +78,6 @@ pub async fn run_init(inputs: InitInputs, options: InitOptions) -> Result<InitRe
         name: gitlab_user.name,
     };
 
-    // 5. Validate each project path
     let mut validated_projects: Vec<(ProjectInfo, GitLabProject)> = Vec::new();
 
     for project_path in &inputs.project_paths {
@@ -115,14 +104,10 @@ pub async fn run_init(inputs: InitInputs, options: InitOptions) -> Result<InitRe
         ));
     }
 
-    // 6. All validations passed - now write config and setup DB
-
-    // Create config directory if needed
     if let Some(parent) = config_path.parent() {
         fs::create_dir_all(parent)?;
     }
 
-    // Write minimal config (rely on serde defaults)
     let config = MinimalConfig {
         gitlab: MinimalGitLabConfig {
             base_url: inputs.gitlab_url,
@@ -138,16 +123,13 @@ pub async fn run_init(inputs: InitInputs, options: InitOptions) -> Result<InitRe
     let config_json = serde_json::to_string_pretty(&config)?;
     fs::write(&config_path, format!("{config_json}\n"))?;
 
-    // 7. Create data directory and initialize database
     fs::create_dir_all(&data_dir)?;
 
     let db_path = data_dir.join("lore.db");
     let conn = create_connection(&db_path)?;
 
-    // Run embedded migrations
     run_migrations(&conn)?;
 
-    // 8. Insert validated projects
     for (_, gitlab_project) in &validated_projects {
         conn.execute(
             "INSERT INTO projects (gitlab_project_id, path_with_namespace, default_branch, web_url)