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-core/src/codebase/context.rs

@@ -387,7 +387,7 @@ impl ContextCapture {
         // Get last modified time
         let last_modified = fs::metadata(path)
             .ok()
-            .and_then(|m| m.modified().ok().map(|t| DateTime::<Utc>::from(t)));
+            .and_then(|m| m.modified().ok().map(DateTime::<Utc>::from));
 
         // Detect module
         let module = self.detect_module(path);
@@ -640,7 +640,7 @@ impl ContextCapture {
                     let name = line
                         .trim_start_matches("module ")
                         .split('/')
-                        .last()
+                        .next_back()
                         .unwrap_or("")
                         .to_string();
                     if !name.is_empty() {

crates/vestige-core/src/codebase/git.rs

@@ -133,7 +133,7 @@ impl GitAnalyzer {
         let mut has_untracked = false;
 
         for entry in statuses.iter() {
-            let path = entry.path().map(|p| PathBuf::from(p)).unwrap_or_default();
+            let path = entry.path().map(PathBuf::from).unwrap_or_default();
 
             let status = entry.status();
 

crates/vestige-core/src/codebase/types.rs

@@ -208,10 +208,12 @@ pub struct ArchitecturalDecision {
 /// Status of an architectural decision
 #[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)]
 #[serde(rename_all = "snake_case")]
+#[derive(Default)]
 pub enum DecisionStatus {
     /// Decision is proposed but not yet implemented
     Proposed,
     /// Decision is accepted and being implemented
+    #[default]
     Accepted,
     /// Decision has been superseded by another
     Superseded,
@@ -219,11 +221,6 @@ pub enum DecisionStatus {
     Deprecated,
 }
 
-impl Default for DecisionStatus {
-    fn default() -> Self {
-        Self::Accepted
-    }
-}
 
 // ============================================================================
 // BUG FIX
@@ -266,19 +263,16 @@ pub struct BugFix {
 /// Severity level of a bug
 #[derive(Debug, Clone, Copy, PartialEq, Eq, Serialize, Deserialize)]
 #[serde(rename_all = "snake_case")]
+#[derive(Default)]
 pub enum BugSeverity {
     Critical,
     High,
+    #[default]
     Medium,
     Low,
     Trivial,
 }
 
-impl Default for BugSeverity {
-    fn default() -> Self {
-        Self::Medium
-    }
-}
 
 // ============================================================================
 // CODE PATTERN