chore: cleanup dead code warnings and apply clippy fixes for v1.1.1

- Add #![allow(dead_code)] to deprecated tool modules (kept for
  backwards compatibility but not exposed in MCP tool list)
- Mark unused functions with #[allow(dead_code)] annotations
- Fix unused variable warnings (prefix with _)
- Apply clippy auto-fixes for redundant closures and derives
- Fix test to account for protocol version negotiation
- Reorganize tools/mod.rs to clarify active vs deprecated tools

Security review: LOW RISK - no critical vulnerabilities found
Dead code review: deprecated tools properly annotated

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

crates/vestige-mcp/src/protocol/types.rs

@@ -127,6 +127,7 @@ impl JsonRpcError {
         Self::new(ErrorCode::ServerNotInitialized, "Server not initialized")
     }
 
+    #[allow(dead_code)] // Reserved for future resource handling
     pub fn resource_not_found(uri: &str) -> Self {
         Self::new(ErrorCode::ResourceNotFound, &format!("Resource not found: {}", uri))
     }

crates/vestige-mcp/src/server.rs

@@ -619,7 +619,13 @@ mod tests {
     #[tokio::test]
     async fn test_initialize_returns_server_info() {
         let (mut server, _dir) = test_server().await;
-        let request = make_request("initialize", None);
+        // Send with current protocol version to get it back
+        let params = serde_json::json!({
+            "protocolVersion": MCP_VERSION,
+            "capabilities": {},
+            "clientInfo": { "name": "test", "version": "1.0" }
+        });
+        let request = make_request("initialize", Some(params));
 
         let response = server.handle_request(request).await.unwrap();
         let result = response.result.unwrap();

crates/vestige-mcp/src/tools/codebase.rs

@@ -1,4 +1,5 @@
-//! Codebase Tools
+#![allow(dead_code)]
+//! Codebase Tools (Deprecated - use codebase_unified instead)
 //!
 //! Remember patterns, decisions, and context about codebases.
 //! This is a differentiating feature for AI-assisted development.

crates/vestige-mcp/src/tools/consolidate.rs

@@ -1,4 +1,5 @@
-//! Consolidation Tool
+#![allow(dead_code)]
+//! Consolidation Tool (Deprecated)
 //!
 //! Run memory consolidation cycle with FSRS decay and embedding generation.
 

crates/vestige-mcp/src/tools/context.rs

@@ -1,4 +1,5 @@
-//! Context-Dependent Memory Tool
+#![allow(dead_code)]
+//! Context-Dependent Memory Tool (Deprecated)
 //!
 //! Retrieval based on encoding context match.
 //! Based on Tulving & Thomson's Encoding Specificity Principle (1973).

crates/vestige-mcp/src/tools/feedback.rs

@@ -1,4 +1,5 @@
-//! Feedback Tools
+#![allow(dead_code)]
+//! Feedback Tools (Deprecated - use promote_memory/demote_memory instead)
 //!
 //! Promote and demote memories based on outcome quality.
 //! Implements preference learning for Vestige.

crates/vestige-mcp/src/tools/intentions.rs

@@ -1,4 +1,5 @@
-//! Intentions Tools
+#![allow(dead_code)]
+//! Intentions Tools (Deprecated - use intention_unified instead)
 //!
 //! Prospective memory tools for setting and checking future intentions.
 

crates/vestige-mcp/src/tools/knowledge.rs

@@ -1,4 +1,5 @@
-//! Knowledge Tools
+#![allow(dead_code)]
+//! Knowledge Tools (Deprecated - use memory_unified instead)
 //!
 //! Get and delete specific knowledge nodes.
 

crates/vestige-mcp/src/tools/memory_states.rs

@@ -1,4 +1,5 @@
-//! Memory States Tool
+#![allow(dead_code)]
+//! Memory States Tool (Deprecated - use memory_unified instead)
 //!
 //! Query and manage memory states (Active, Dormant, Silent, Unavailable).
 //! Based on accessibility continuum theory.

crates/vestige-mcp/src/tools/mod.rs

@@ -1,28 +1,42 @@
 //! MCP Tools
 //!
 //! Tool implementations for the Vestige MCP server.
+//!
+//! The unified tools (codebase_unified, intention_unified, memory_unified, search_unified)
+//! are the primary API. The granular tools below are kept for backwards compatibility
+//! but are not exposed in the MCP tool list.
 
-pub mod codebase;
-pub mod consolidate;
-pub mod ingest;
-pub mod intentions;
-pub mod knowledge;
-pub mod recall;
-pub mod review;
-pub mod search;
-pub mod smart_ingest;
-pub mod stats;
-
-// Neuroscience-inspired tools
-pub mod context;
-pub mod memory_states;
-pub mod tagging;
-
-// Feedback / preference learning
-pub mod feedback;
-
-// Unified tools (consolidate multiple operations into single tools)
+// Active unified tools
 pub mod codebase_unified;
+pub mod ingest;
 pub mod intention_unified;
 pub mod memory_unified;
 pub mod search_unified;
+pub mod smart_ingest;
+
+// Deprecated tools - kept for internal backwards compatibility
+// These modules are intentionally unused in the public API
+#[allow(dead_code)]
+pub mod codebase;
+#[allow(dead_code)]
+pub mod consolidate;
+#[allow(dead_code)]
+pub mod context;
+#[allow(dead_code)]
+pub mod feedback;
+#[allow(dead_code)]
+pub mod intentions;
+#[allow(dead_code)]
+pub mod knowledge;
+#[allow(dead_code)]
+pub mod memory_states;
+#[allow(dead_code)]
+pub mod recall;
+#[allow(dead_code)]
+pub mod review;
+#[allow(dead_code)]
+pub mod search;
+#[allow(dead_code)]
+pub mod stats;
+#[allow(dead_code)]
+pub mod tagging;

crates/vestige-mcp/src/tools/recall.rs

@@ -1,4 +1,5 @@
-//! Recall Tool
+#![allow(dead_code)]
+//! Recall Tool (Deprecated - use search_unified instead)
 //!
 //! Search and retrieve knowledge from memory.
 

crates/vestige-mcp/src/tools/review.rs

@@ -1,4 +1,5 @@
-//! Review Tool
+#![allow(dead_code)]
+//! Review Tool (Deprecated)
 //!
 //! Mark memories as reviewed using FSRS-6 algorithm.
 

crates/vestige-mcp/src/tools/search.rs

@@ -1,4 +1,5 @@
-//! Search Tools
+#![allow(dead_code)]
+//! Search Tools (Deprecated - use search_unified instead)
 //!
 //! Semantic and hybrid search implementations.
 

crates/vestige-mcp/src/tools/stats.rs

@@ -1,4 +1,5 @@
-//! Stats Tools
+#![allow(dead_code)]
+//! Stats Tools (Deprecated - use memory_unified instead)
 //!
 //! Memory statistics and health check.
 

crates/vestige-mcp/src/tools/tagging.rs

@@ -1,4 +1,5 @@
-//! Synaptic Tagging Tool
+#![allow(dead_code)]
+//! Synaptic Tagging Tool (Deprecated)
 //!
 //! Retroactive importance assignment based on Synaptic Tagging & Capture theory.
 //! Frey & Morris (1997), Redondo & Morris (2011).