refactor(agent): remove dead code and integrate McpToolsHandler

Remove dead code warnings and properly integrate McpToolsHandler:

- Remove #[allow(dead_code)] from McpToolsHandler (now actively used)
- Integrate McpToolsHandler into ReplHandler for MCP commands
- Refactor wizard to use into_result() pattern (cleaner error handling)
- Remove unused error variants: PathNotFound, Config, RoleExists, Network
- Remove unused functions: prompt_confirm, prompt_input
- Gate test-only function is_first_run with #[cfg(test)]

Changes:
- mcp_tools.rs: Remove dead_code attributes, simplify error handling
- handler.rs: Add mcp_handler field, use in MCP command handlers
- wizard.rs: Use into_result() instead of manual match blocks
- mod.rs: Remove unused OnboardingError variants
- validation.rs: Remove PathNotFound variant
- prompts.rs: Remove unused utility functions
- service.rs: Remove dead_code attributes from now-used methods

Verification:
- All 134 unit tests pass
- All 11 integration tests pass
- No breaking changes
- Code quality improved

Author: AlexMikhalev

crates/terraphim_agent/src/onboarding/mod.rs

@@ -43,10 +43,6 @@ pub enum OnboardingError {
     #[error("Validation failed: {0}")]
     Validation(String),
 
-    /// Configuration error from terraphim_config
-    #[error("Configuration error: {0}")]
-    Config(String),
-
     /// IO error during file operations
     #[error("IO error: {0}")]
     Io(#[from] std::io::Error),
@@ -55,22 +51,10 @@ pub enum OnboardingError {
     #[error("Not a TTY - interactive mode requires a terminal. Use --template for non-interactive mode.")]
     NotATty,
 
-    /// Role with this name already exists
-    #[error("Role already exists: {0}")]
-    RoleExists(String),
-
     /// JSON serialization/deserialization error
     #[error("JSON error: {0}")]
     Json(#[from] serde_json::Error),
 
-    /// Network error during URL validation
-    #[error("Network error: {0}")]
-    Network(String),
-
-    /// Path does not exist
-    #[error("Path does not exist: {0}")]
-    PathNotFound(String),
-
     /// User went back in wizard navigation
     #[error("User navigated back")]
     NavigateBack,

crates/terraphim_agent/src/onboarding/prompts.rs

@@ -572,27 +572,6 @@ pub fn prompt_knowledge_graph() -> Result<PromptResult<Option<KnowledgeGraph>>,
     }
 }
 
-/// Prompt for confirmation with custom message
-pub fn prompt_confirm(message: &str, default: bool) -> Result<bool, OnboardingError> {
-    let theme = ColorfulTheme::default();
-    Ok(Confirm::with_theme(&theme)
-        .with_prompt(message)
-        .default(default)
-        .interact()?)
-}
-
-/// Prompt for simple text input
-pub fn prompt_input(message: &str, default: Option<&str>) -> Result<String, OnboardingError> {
-    let theme = ColorfulTheme::default();
-    let mut input = Input::with_theme(&theme).with_prompt(message);
-
-    if let Some(d) = default {
-        input = input.default(d.to_string());
-    }
-
-    Ok(input.interact_text()?)
-}
-
 #[cfg(test)]
 mod tests {
     use super::*;

crates/terraphim_agent/src/onboarding/validation.rs

@@ -26,10 +26,6 @@ pub enum ValidationError {
     #[error("Service {0} requires: {1}")]
     ServiceRequirement(String, String),
 
-    /// Path does not exist on filesystem
-    #[error("Path does not exist: {0}")]
-    PathNotFound(String),
-
     /// URL is malformed
     #[error("Invalid URL: {0}")]
     InvalidUrl(String),

crates/terraphim_agent/src/onboarding/wizard.rs

@@ -3,15 +3,14 @@
 //! Provides the interactive setup wizard flow for first-time users
 //! and add-role capability for extending existing configurations.
 
-use std::path::PathBuf;
-
 use dialoguer::{theme::ColorfulTheme, Confirm, Select};
+use std::path::PathBuf;
 use terraphim_config::Role;
 use terraphim_types::RelevanceFunction;
 
 use super::prompts::{
     prompt_haystacks, prompt_knowledge_graph, prompt_llm_config, prompt_relevance_function,
-    prompt_role_basics, prompt_theme, PromptResult,
+    prompt_role_basics, prompt_theme,
 };
 use super::templates::{ConfigTemplate, TemplateRegistry};
 use super::validation::validate_role;
@@ -110,6 +109,7 @@ impl QuickStartChoice {
 }
 
 /// Check if this is a first run (no existing configuration)
+#[cfg(test)]
 pub fn is_first_run(config_path: &PathBuf) -> bool {
     !config_path.exists()
 }
@@ -312,7 +312,7 @@ fn prompt_path_for_template(
             .map_err(|_| OnboardingError::Cancelled)?;
 
         if !proceed {
-            return Err(OnboardingError::PathNotFound(expanded));
+            return Err(OnboardingError::Cancelled);
         }
     }
 
@@ -328,84 +328,53 @@ fn custom_wizard(theme: &ColorfulTheme) -> Result<Role, OnboardingError> {
     println!();
 
     // Step 1: Role basics (name and shortname)
-    let (name, shortname) = match prompt_role_basics()? {
-        PromptResult::Value(v) => v,
-        PromptResult::Back => return Err(OnboardingError::NavigateBack),
-    };
+    let (name, shortname) = prompt_role_basics()?.into_result()?;
 
     let mut role = Role::new(name);
     role.shortname = shortname;
 
     // Step 2: Theme selection
-    role.theme = match prompt_theme()? {
-        PromptResult::Value(t) => t,
-        PromptResult::Back => {
-            // Go back to role basics - restart wizard
-            return Err(OnboardingError::NavigateBack);
-        }
-    };
+    role.theme = prompt_theme()?.into_result()?;
 
     // Step 3: Relevance function
-    let relevance = match prompt_relevance_function()? {
-        PromptResult::Value(r) => r,
-        PromptResult::Back => {
-            // Go back - restart wizard
-            return Err(OnboardingError::NavigateBack);
-        }
-    };
+    let relevance = prompt_relevance_function()?.into_result()?;
     role.relevance_function = relevance;
     // Set terraphim_it based on relevance function (TerraphimGraph requires it)
     role.terraphim_it = matches!(relevance, RelevanceFunction::TerraphimGraph);
 
     // Step 4: Haystacks
-    role.haystacks = match prompt_haystacks()? {
-        PromptResult::Value(haystacks) => haystacks,
-        PromptResult::Back => {
-            return Err(OnboardingError::NavigateBack);
-        }
-    };
+    role.haystacks = prompt_haystacks()?.into_result()?;
 
     // Step 5: LLM configuration (optional)
-    match prompt_llm_config()? {
-        PromptResult::Value(llm_config) => {
-            if let Some(provider) = llm_config.provider {
-                role.llm_enabled = true;
-                role.extra.insert(
-                    "llm_provider".to_string(),
-                    serde_json::Value::String(provider),
-                );
-                if let Some(model) = llm_config.model {
-                    role.extra
-                        .insert("ollama_model".to_string(), serde_json::Value::String(model));
-                }
-                if let Some(base_url) = llm_config.base_url {
-                    role.extra.insert(
-                        "ollama_base_url".to_string(),
-                        serde_json::Value::String(base_url),
-                    );
-                }
-                if let Some(api_key) = llm_config.api_key {
-                    role.extra.insert(
-                        "openrouter_api_key".to_string(),
-                        serde_json::Value::String(api_key),
-                    );
-                }
-            } else {
-                role.llm_enabled = false;
-            }
+    let llm_config = prompt_llm_config()?.into_result()?;
+    if let Some(provider) = llm_config.provider {
+        role.llm_enabled = true;
+        role.extra.insert(
+            "llm_provider".to_string(),
+            serde_json::Value::String(provider),
+        );
+        if let Some(model) = llm_config.model {
+            role.extra
+                .insert("ollama_model".to_string(), serde_json::Value::String(model));
+        }
+        if let Some(base_url) = llm_config.base_url {
+            role.extra.insert(
+                "ollama_base_url".to_string(),
+                serde_json::Value::String(base_url),
+            );
         }
-        PromptResult::Back => {
-            return Err(OnboardingError::NavigateBack);
+        if let Some(api_key) = llm_config.api_key {
+            role.extra.insert(
+                "openrouter_api_key".to_string(),
+                serde_json::Value::String(api_key),
+            );
         }
+    } else {
+        role.llm_enabled = false;
     }
 
     // Step 6: Knowledge graph (optional)
-    role.kg = match prompt_knowledge_graph()? {
-        PromptResult::Value(kg) => kg,
-        PromptResult::Back => {
-            return Err(OnboardingError::NavigateBack);
-        }
-    };
+    role.kg = prompt_knowledge_graph()?.into_result()?;
 
     // Validate the complete role
     validate_role(&role).map_err(|errors| {