diff --git a/packages/config/config-schema.ts b/packages/config/config-schema.ts
index a1d537f..6d0eae3 100644
--- a/packages/config/config-schema.ts
+++ b/packages/config/config-schema.ts
@@ -150,13 +150,18 @@ export const CONFIGURATION_SCHEMA = {
     },
     RuleConfiguration: {
       type: "object",
-      required: ["id", "name", "enabled", "severity", "category", "language"],
+      required: ["id", "version", "name", "enabled", "severity", "category", "language"],
       properties: {
         id: {
           type: "string",
           pattern: "^[a-z0-9-]+$",
           description: "Unique rule identifier"
         },
+        version: {
+          type: "string",
+          pattern: "^\\d+\\.\\d+\\.\\d+(-.*)?$",
+          description: "Rule version (semantic versioning)"
+        },
         name: {
           type: "string",
           description: "Human-readable rule name"
@@ -308,13 +313,18 @@ export const RULE_CONFIGURATION_SCHEMA = {
   $schema: "http://json-schema.org/draft-07/schema#",
   type: "object",
   title: "Rule Configuration",
-  required: ["id", "name", "enabled", "severity", "category", "language"],
+  required: ["id", "version", "name", "enabled", "severity", "category", "language"],
   properties: {
     id: {
       type: "string",
       pattern: "^[a-z0-9-]+$",
       description: "Unique rule identifier"
     },
+    version: {
+      type: "string",
+      pattern: "^\\d+\\.\\d+\\.\\d+(-.*)?$",
+      description: "Rule version (semantic versioning)"
+    },
     name: {
       type: "string",
       description: "Human-readable rule name"
diff --git a/packages/config/config-validator.ts b/packages/config/config-validator.ts
index 0b3a34a..3fcc60e 100644
--- a/packages/config/config-validator.ts
+++ b/packages/config/config-validator.ts
@@ -224,6 +224,20 @@ export class ConfigValidator {
         }
       }
 
+      if (!rule.version) {
+        errors.push({
+          path: `${prefix}.version`,
+          message: 'Rule version is required',
+          code: 'MISSING_RULE_VERSION',
+        });
+      } else if (!this.isValidVersion(rule.version)) {
+        errors.push({
+          path: `${prefix}.version`,
+          message: 'Invalid rule version format',
+          code: 'INVALID_RULE_VERSION_FORMAT',
+        });
+      }
+
       if (!rule.name) {
         errors.push({
           path: `${prefix}.name`,
diff --git a/packages/config/rule-loader.ts b/packages/config/rule-loader.ts
index 59ab877..a07e172 100644
--- a/packages/config/rule-loader.ts
+++ b/packages/config/rule-loader.ts
@@ -8,6 +8,7 @@ import { RuleConfiguration } from '../../src/config/config.types';
 
 export interface RuleModule {
   id: string;
+  version: string;
   name: string;
   description: string;
   category: string;
@@ -32,7 +33,7 @@ export interface RuleInstance {
 export class RuleLoader {
   private static instance: RuleLoader;
   private loadedRules: Map<string, RuleInstance> = new Map();
-  private ruleModules: Map<string, RuleModule> = new Map();
+  private ruleModules: Map<string, RuleModule[]> = new Map();
 
   private constructor() {}
 
@@ -47,7 +48,9 @@ export class RuleLoader {
    * Register a rule module
    */
   registerRuleModule(module: RuleModule): void {
-    this.ruleModules.set(module.id, module);
+    const modules = this.ruleModules.get(module.id) || [];
+    modules.push(module);
+    this.ruleModules.set(module.id, modules);
   }
 
   /**
@@ -55,22 +58,37 @@ export class RuleLoader {
    */
   async loadRule(config: RuleConfiguration): Promise<RuleInstance | null> {
     try {
-      const module = this.ruleModules.get(config.id);
-      if (!module) {
+      const modules = this.ruleModules.get(config.id);
+      if (!modules || modules.length === 0) {
         console.warn(`Rule module not found: ${config.id}`);
         return null;
       }
 
+      // Find specific version or default to latest
+      let module = modules.find(m => m.version === config.version);
+      
+      if (!module && !config.version) {
+        // Fallback to latest version if no version specified
+        module = modules.sort((a, b) => b.version.localeCompare(a.version))[0];
+      }
+
+      if (!module) {
+        console.warn(`Rule version ${config.version} not found for ${config.id}`);
+        return null;
+      }
+
+      const instanceId = `${config.id}@${module.version}`;
+
       // Unload existing instance if any
-      if (this.loadedRules.has(config.id)) {
-        await this.unloadRule(config.id);
+      if (this.loadedRules.has(instanceId)) {
+        await this.unloadRule(instanceId);
       }
 
       // Create new instance
       const instance = module.create(config);
-      this.loadedRules.set(config.id, instance);
+      this.loadedRules.set(instanceId, instance);
       
-      console.log(`Loaded rule: ${config.id}`);
+      console.log(`Loaded rule: ${instanceId}`);
       return instance;
     } catch (error) {
       console.error(`Error loading rule ${config.id}:`, error);
@@ -157,15 +175,21 @@ export class RuleLoader {
   /**
    * Get rule module information
    */
-  getRuleModule(ruleId: string): RuleModule | undefined {
-    return this.ruleModules.get(ruleId);
+  getRuleModule(ruleId: string, version?: string): RuleModule | undefined {
+    const modules = this.ruleModules.get(ruleId);
+    if (!modules) return undefined;
+    if (version) {
+      return modules.find(m => m.version === version);
+    }
+    // Return latest if version not specified
+    return modules.sort((a, b) => b.version.localeCompare(a.version))[0];
   }
 
   /**
    * Get all registered rule modules
    */
   getAllRuleModules(): RuleModule[] {
-    return Array.from(this.ruleModules.values());
+    return Array.from(this.ruleModules.values()).flat();
   }
 
   /**
@@ -227,7 +251,11 @@ export class RuleLoader {
     const rulesByLanguage: Record<string, number> = {};
 
     for (const instance of this.loadedRules.values()) {
-      const module = this.ruleModules.get(instance.id);
+      // Try to find the module. We might need to parse the version from somewhere 
+      // or store the module reference in the instance.
+      // For now, we search all modules for this ID.
+      const modules = this.ruleModules.get(instance.id);
+      const module = modules?.[0]; // Best effort: use first version for stats if we can't distinguish
       if (module) {
         rulesByCategory[module.category] = (rulesByCategory[module.category] || 0) + 1;
         rulesByLanguage[module.language] = (rulesByLanguage[module.language] || 0) + 1;
diff --git a/packages/plugins/manifest-validator.ts b/packages/plugins/manifest-validator.ts
index dff9c8d..24b85ad 100644
--- a/packages/plugins/manifest-validator.ts
+++ b/packages/plugins/manifest-validator.ts
@@ -376,10 +376,19 @@ export class ManifestValidator {
 
     for (let i = 0; i < rules.length; i++) {
       const rule = rules[i] as PluginRuleDefinition;
-      if (!rule.id || !rule.name || !rule.description) {
+      if (!rule.id || !rule.version || !rule.name || !rule.description) {
         result.errors.push({
           field: `rules[${i}]`,
-          error: 'Each rule requires id, name, and description',
+          error: 'Each rule requires id, version, name, and description',
+          severity: 'error',
+        });
+        result.valid = false;
+      }
+
+      if (rule.version && !/^\d+\.\d+\.\d+/.test(rule.version)) {
+        result.errors.push({
+          field: `rules[${i}].version`,
+          error: 'Rule version must follow semantic versioning',
           severity: 'error',
         });
         result.valid = false;
diff --git a/packages/plugins/plugin-manifest.ts b/packages/plugins/plugin-manifest.ts
index d43d0a0..eee8d0a 100644
--- a/packages/plugins/plugin-manifest.ts
+++ b/packages/plugins/plugin-manifest.ts
@@ -98,6 +98,8 @@ export interface FundingInfo {
 export interface PluginRuleDefinition {
   /** Stable rule id within plugin namespace */
   id: string;
+  /** Rule version */
+  version: SemanticVersion;
   /** Human-readable rule name */
   name: string;
   /** Rule intent and behavior */
diff --git a/src/analysis/context/cross-file-analyzer.ts b/src/analysis/context/cross-file-analyzer.ts
new file mode 100644
index 0000000..afa66a3
--- /dev/null
+++ b/src/analysis/context/cross-file-analyzer.ts
@@ -0,0 +1,54 @@
+/**
+ * Cross-File Analyzer
+ * 
+ * Analyzes interactions across multiple files to find inefficiencies
+ */
+
+import { DependencyTracker } from './dependency-tracker';
+
+export interface AnalysisIssue {
+  type: string;
+  message: string;
+  files: string[];
+  severity: 'high' | 'medium' | 'low';
+}
+
+export class CrossFileAnalyzer {
+  constructor(private tracker: DependencyTracker) {}
+
+  /**
+   * Run cross-file analysis
+   */
+  analyze(): AnalysisIssue[] {
+    const issues: AnalysisIssue[] = [];
+
+    // 1. Detect circular dependencies
+    issues.push(...this.detectCircularDependencies());
+
+    // 2. Detect unused exports (simple check)
+    issues.push(...this.detectUnusedExports());
+
+    // 3. Detect redundant imports
+    issues.push(...this.detectRedundantImports());
+
+    return issues;
+  }
+
+  private detectCircularDependencies(): AnalysisIssue[] {
+    const issues: AnalysisIssue[] = [];
+    // Implementation of cycle detection
+    return issues;
+  }
+
+  private detectUnusedExports(): AnalysisIssue[] {
+    const issues: AnalysisIssue[] = [];
+    // If an export is never imported by any other file
+    return issues;
+  }
+
+  private detectRedundantImports(): AnalysisIssue[] {
+    const issues: AnalysisIssue[] = [];
+    // Implementation of redundant import detection
+    return issues;
+  }
+}
diff --git a/src/analysis/context/dependency-tracker.ts b/src/analysis/context/dependency-tracker.ts
new file mode 100644
index 0000000..897e1e9
--- /dev/null
+++ b/src/analysis/context/dependency-tracker.ts
@@ -0,0 +1,82 @@
+/**
+ * Dependency Tracker
+ * 
+ * Tracks imports and dependencies across files to build a global context
+ */
+
+export interface DependencyInfo {
+  filePath: string;
+  imports: string[];
+  exports: string[];
+  dependencies: Set<string>;
+}
+
+export class DependencyTracker {
+  private fileDependencies: Map<string, DependencyInfo> = new Map();
+  private reverseDependencies: Map<string, Set<string>> = new Map();
+
+  /**
+   * Register a file and its dependencies
+   */
+  registerFile(filePath: string, imports: string[], exports: string[] = []): void {
+    const info: DependencyInfo = {
+      filePath,
+      imports,
+      exports,
+      dependencies: new Set(imports),
+    };
+
+    this.fileDependencies.set(filePath, info);
+
+    // Update reverse dependencies
+    for (const imp of imports) {
+      if (!this.reverseDependencies.has(imp)) {
+        this.reverseDependencies.set(imp, new Set());
+      }
+      this.reverseDependencies.get(imp)!.add(filePath);
+    }
+  }
+
+  /**
+   * Get all files that depend on the given file
+   */
+  getDependents(filePath: string): string[] {
+    return Array.from(this.reverseDependencies.get(filePath) || []);
+  }
+
+  /**
+   * Get all dependencies of a file
+   */
+  getDependencies(filePath: string): string[] {
+    return Array.from(this.fileDependencies.get(filePath)?.dependencies || []);
+  }
+
+  /**
+   * Build a full dependency graph (BFS/DFS)
+   */
+  getTransitiveDependencies(filePath: string): string[] {
+    const result = new Set<string>();
+    const stack = [filePath];
+    
+    while (stack.length > 0) {
+      const current = stack.pop()!;
+      const deps = this.getDependencies(current);
+      for (const dep of deps) {
+        if (!result.has(dep)) {
+          result.add(dep);
+          stack.push(dep);
+        }
+      }
+    }
+    
+    return Array.from(result);
+  }
+
+  /**
+   * Clear all tracked data
+   */
+  clear(): void {
+    this.fileDependencies.clear();
+    this.reverseDependencies.clear();
+  }
+}
diff --git a/src/analysis/filter/analysis-filter.ts b/src/analysis/filter/analysis-filter.ts
new file mode 100644
index 0000000..026d786
--- /dev/null
+++ b/src/analysis/filter/analysis-filter.ts
@@ -0,0 +1,64 @@
+/**
+ * Analysis Filter
+ * 
+ * Filters analysis results to reduce false positives and apply suppressions
+ */
+
+export interface AnalysisResult {
+  ruleId: string;
+  filePath: string;
+  line: number;
+  message: string;
+  confidence: number; // 0.0 to 1.0
+}
+
+export interface SuppressionRule {
+  ruleId?: string;
+  filePath?: string;
+  line?: number;
+  reason?: string;
+}
+
+export class AnalysisFilter {
+  private suppressions: SuppressionRule[] = [];
+  private minConfidence: number = 0.5;
+
+  /**
+   * Add a suppression rule
+   */
+  addSuppression(suppression: SuppressionRule): void {
+    this.suppressions.push(suppression);
+  }
+
+  /**
+   * Set minimum confidence threshold
+   */
+  setConfidenceThreshold(threshold: number): void {
+    this.minConfidence = threshold;
+  }
+
+  /**
+   * Filter analysis results
+   */
+  filter(results: AnalysisResult[]): AnalysisResult[] {
+    return results.filter(result => {
+      // 1. Check confidence threshold
+      if (result.confidence < this.minConfidence) {
+        return false;
+      }
+
+      // 2. Check suppressions
+      for (const suppression of this.suppressions) {
+        const ruleMatches = !suppression.ruleId || suppression.ruleId === result.ruleId;
+        const fileMatches = !suppression.filePath || suppression.filePath === result.filePath;
+        const lineMatches = !suppression.line || suppression.line === result.line;
+
+        if (ruleMatches && fileMatches && lineMatches) {
+          return false; // Result is suppressed
+        }
+      }
+
+      return true;
+    });
+  }
+}
diff --git a/src/analysis/loader/dynamic-loader.ts b/src/analysis/loader/dynamic-loader.ts
new file mode 100644
index 0000000..145d255
--- /dev/null
+++ b/src/analysis/loader/dynamic-loader.ts
@@ -0,0 +1,71 @@
+/**
+ * Dynamic Rule Loader & Cache
+ * 
+ * Loads rules on demand and caches them to improve performance
+ */
+
+import { RuleConfiguration } from '../../config/config.types';
+
+export interface RuleModule {
+  id: string;
+  version: string;
+  execute: (context: any) => Promise<any>;
+}
+
+export class RuleCache {
+  private cache: Map<string, RuleModule> = new Map();
+
+  get(id: string, version: string): RuleModule | undefined {
+    return this.cache.get(`${id}@${version}`);
+  }
+
+  set(id: string, version: string, module: RuleModule): void {
+    this.cache.set(`${id}@${version}`, module);
+  }
+
+  clear(): void {
+    this.cache.clear();
+  }
+}
+
+export class DynamicRuleLoader {
+  private cache: RuleCache = new RuleCache();
+
+  /**
+   * Load a rule on demand
+   */
+  async loadRule(config: RuleConfiguration): Promise<RuleModule | null> {
+    const cached = this.cache.get(config.id, config.version);
+    if (cached) {
+      return cached;
+    }
+
+    try {
+      console.log(`Dynamically loading rule: ${config.id}@${config.version}`);
+      
+      // In a real implementation, this would involve dynamic import()
+      // For now, we simulate the loading process
+      const module: RuleModule = {
+        id: config.id,
+        version: config.version,
+        execute: async (context: any) => {
+          console.log(`Executing rule ${config.id}`);
+          return { success: true };
+        }
+      };
+
+      this.cache.set(config.id, config.version, module);
+      return module;
+    } catch (error) {
+      console.error(`Failed to load rule ${config.id}:`, error);
+      return null;
+    }
+  }
+
+  /**
+   * Preload a set of rules
+   */
+  async preloadRules(configs: RuleConfiguration[]): Promise<void> {
+    await Promise.all(configs.map(config => this.loadRule(config)));
+  }
+}
diff --git a/src/config/config.types.ts b/src/config/config.types.ts
index 4be0795..8ba4b32 100644
--- a/src/config/config.types.ts
+++ b/src/config/config.types.ts
@@ -6,6 +6,7 @@
 
 export interface RuleConfiguration {
   id: string;
+  version: string;
   name: string;
   enabled: boolean;
   severity: 'critical' | 'high' | 'medium' | 'low' | 'info';