diff --git a/docs/architecture-analysis.md b/docs/architecture-analysis.md
new file mode 100644
index 0000000..72f863e
--- /dev/null
+++ b/docs/architecture-analysis.md
@@ -0,0 +1,267 @@
+# Architecture Analysis & Improvement Recommendations
+
+*Generated: January 2025*
+
+## Executive Summary
+
+The VSCode StepZen extension demonstrates **excellent architectural implementation** that largely exceeds the documented architecture. The codebase follows solid patterns with comprehensive service registry, proper error handling, and extensive testing. The main gaps are documentation updates rather than implementation issues.
+
+**Overall Assessment: 🟢 EXCELLENT** - Implementation surpasses documentation in most areas.
+
+## Architecture Compliance Analysis
+
+### ✅ Fully Implemented Components
+
+#### 1. Service Registry Pattern
+- **Status**: Fully implemented with 6 services (vs 4 documented)
+- **Compliance**: Exceeds documentation
+- **Services**:
+  - ✅ `StepzenCliService` (documented)
+  - ✅ `Logger` (documented)  
+  - ✅ `ProjectResolver` (documented)
+  - ✅ `SchemaIndexService` (documented)
+  - ❌ `RequestService` (implemented but not documented)
+  - ❌ `ImportService` (implemented but not documented)
+
+#### 2. Error Handling System
+- **Status**: Perfectly implemented
+- **Compliance**: Exactly matches documentation
+- **Hierarchy**: `StepZenError` → `CliError`, `NetworkError`, `ValidationError`
+- **Handler**: Central error normalization with user notifications
+
+#### 3. Command Implementation
+- **Status**: 16 commands implemented (vs basic set documented)
+- **Compliance**: Exceeds documentation
+- **Pattern**: All commands follow documented patterns with workspace trust checks, validation, and error handling
+
+#### 4. Testing Strategy
+- **Status**: Comprehensive implementation
+- **Compliance**: Exceeds documentation
+- **Coverage**: Unit tests, integration tests, service mocking, test utilities
+
+### 🔍 Architecture Gaps & Inconsistencies
+
+#### Minor Documentation Gaps
+
+1. **Service Registry Documentation Mismatch**
+   - **Issue**: Documentation shows 4 services, implementation has 6
+   - **Impact**: Low - implementation is more complete
+   - **Recommendation**: Update documentation to include `RequestService` and `ImportService`
+
+2. **Missing Test Utility**
+   - **Issue**: Documentation mentions `createMockServiceRegistry()` but it's not implemented
+   - **Impact**: Low - existing mock utilities are sufficient
+   - **Recommendation**: Either implement the utility or remove from documentation
+
+3. **Schema Processing Layer Organization**
+   - **Issue**: Services are in `services/schema/` rather than top-level as documented
+   - **Impact**: None - current organization is better
+   - **Recommendation**: Update documentation to reflect actual organization
+
+## Architectural Strengths
+
+### 1. Service Registry Excellence
+```typescript
+// Actual implementation is more robust than documented
+export interface ServiceRegistry {
+  cli: StepzenCliService;
+  logger: Logger;
+  projectResolver: ProjectResolver;  
+  schemaIndex: SchemaIndexService;
+  request: RequestService;        // 🆕 Not in docs
+  import: ImportService;          // 🆕 Not in docs
+}
+```
+
+**Testing Support:**
+- ✅ `overrideServices()` - Individual service mocking
+- ✅ `resetServices()` - Service restoration
+- ✅ `setMockServices()` - Full registry replacement
+- ✅ Comprehensive test coverage
+
+### 2. Command Pattern Consistency
+All 16 commands follow the documented pattern:
+```typescript
+export async function commandName() {
+  // 1. Workspace trust check
+  if (!vscode.workspace.isTrusted) { return; }
+  
+  // 2. Precondition validation  
+  if (!precondition) { showError(); return; }
+  
+  // 3. Service usage with error handling
+  try {
+    services.logger.info("Command started");
+    // Implementation
+  } catch (err) {
+    handleError(err);
+  }
+}
+```
+
+### 3. Error Handling Robustness
+- **Hierarchical**: Clear error type hierarchy
+- **Centralized**: Single error handler with normalization
+- **User-Friendly**: Consistent notifications with "Show Logs" action
+- **Developer-Friendly**: Full context logging
+
+### 4. Schema Processing Architecture
+```
+src/services/schema/
+├── indexer.ts    # Symbol indexing & location tracking
+├── linker.ts     # SDL traversal & file linking  
+└── parser.ts     # GraphQL AST utilities
+```
+- **Better Organization**: More logical than documented flat structure
+- **Clear Separation**: Each component has distinct responsibility
+
+## Improvement Recommendations
+
+### 🔴 High Priority (Documentation Updates)
+
+#### 1. Update Service Registry Documentation
+**File**: `docs/architecture.md:97-114`
+```typescript
+// Current documentation
+export interface ServiceRegistry {
+  cli: StepzenCliService;
+  logger: Logger;
+  projectResolver: ProjectResolver;
+  schemaIndex: SchemaIndexService;
+}
+
+// Should be updated to
+export interface ServiceRegistry {
+  cli: StepzenCliService;
+  logger: Logger;
+  projectResolver: ProjectResolver;
+  schemaIndex: SchemaIndexService;
+  request: RequestService;        // 🆕 Add
+  import: ImportService;          // 🆕 Add
+}
+```
+
+#### 2. Document Schema Processing Organization
+**File**: `docs/architecture.md:42-46`
+Update to reflect actual file organization:
+```
+Schema Processing Layer (src/services/schema/)
+├── indexer.ts    # Build searchable indexes
+├── linker.ts     # SDL traversal & linking
+└── parser.ts     # AST processing utilities
+```
+
+#### 3. Add Command Categorization
+**File**: `docs/architecture.md:66`
+Document all 16 commands with categorization:
+```
+Commands (16 total):
+├── Core Operations: deploy, executeStepZenRequest, runRequest
+├── Navigation: goToDefinition, openExplorer, openSchemaVisualizer  
+├── Project Management: initializeProject, generateOperations
+├── Import Commands: importCurl, importDatabase, importGraphql, importOpenapi
+└── Schema Enhancement: addDirective, addMaterializer, addTool, addValue
+```
+
+### 🟡 Medium Priority (Implementation)
+
+#### 4. Add Missing Test Utility
+Either implement the documented utility or remove from documentation:
+```typescript
+// Option 1: Implement utility
+export function createMockServiceRegistry(): ServiceRegistry {
+  return {
+    cli: createMock<StepzenCliService>(),
+    logger: createMock<Logger>(),
+    projectResolver: createMock<ProjectResolver>(),
+    schemaIndex: createMock<SchemaIndexService>(),
+    request: createMock<RequestService>(),
+    import: createMock<ImportService>(),
+  };
+}
+
+// Option 2: Remove from documentation
+```
+
+#### 5. Service Documentation Enhancement
+Add service descriptions to architecture documentation:
+- `RequestService`: GraphQL request execution and result handling
+- `ImportService`: Import command coordination and validation
+
+### 🟢 Low Priority (Future Considerations)
+
+#### 6. Service Composition Patterns
+Consider grouping related services for complex operations:
+```typescript
+// Future consideration - not needed currently
+interface ImportServiceGroup {
+  import: ImportService;
+  curl: CurlImportService;
+  database: DatabaseImportService;
+  graphql: GraphqlImportService;
+  openapi: OpenapiImportService;
+}
+```
+
+#### 7. Performance Monitoring
+Add hooks for future telemetry integration:
+```typescript
+// Future service addition
+interface ServiceRegistry {
+  // ... existing services
+  telemetry?: TelemetryService;
+  performance?: PerformanceService;
+}
+```
+
+## Code Quality Assessment
+
+### ✅ Excellent Areas
+
+1. **TypeScript Usage**: Strict typing, proper interfaces, clear types
+2. **Error Propagation**: Consistent error handling patterns
+3. **Logging**: Structured logging with appropriate levels
+4. **Testing**: Comprehensive coverage with proper mocking
+5. **Code Organization**: Clear separation of concerns
+6. **Security**: Proper workspace trust checks, safe command registration
+
+### 🔧 Minor Improvements
+
+1. **JSDoc Coverage**: Some public APIs could benefit from documentation
+2. **Configuration Management**: Consider centralized configuration service
+3. **Async Patterns**: Consistent promise handling (already quite good)
+
+## Future Architecture Considerations
+
+### 1. Planned Enhancements Support
+The current architecture provides excellent foundation for:
+- **Telemetry Integration**: Service registry easily extensible
+- **Language Server Protocol**: Schema processing layer ready
+- **Enhanced WebViews**: Panel architecture supports extensions
+- **Performance Monitoring**: Logging infrastructure ready
+
+### 2. Migration Readiness
+- **Backward Compatibility**: Well-established patterns
+- **Incremental Changes**: Service-based architecture supports gradual updates
+- **Testing Infrastructure**: Comprehensive test coverage protects against regressions
+
+## Conclusion
+
+The VSCode StepZen extension demonstrates **exceptional architectural implementation** that follows best practices and provides a solid foundation for future enhancements. The implementation quality exceeds the documented architecture in several areas.
+
+### Key Achievements
+- ✅ **Robust Service Registry**: Full dependency injection with testing support
+- ✅ **Comprehensive Commands**: 16 well-structured command implementations
+- ✅ **Excellent Error Handling**: Hierarchical, user-friendly, developer-friendly
+- ✅ **Strong Testing**: Unit, integration, and service mocking patterns
+- ✅ **Clear Code Organization**: Logical separation of concerns
+
+### Immediate Actions Required
+1. **Update architecture documentation** to reflect actual implementation
+2. **Add missing test utility** or remove from documentation
+3. **Document all implemented commands** with categorization
+
+### Long-term Strengths
+The architecture is well-positioned for future enhancements including telemetry, LSP integration, and advanced schema processing features. The service registry pattern and comprehensive error handling provide excellent foundation for extension growth.
+
+**Recommendation**: Focus on documentation updates rather than implementation changes. The code architecture is exemplary and should serve as a model for similar VSCode extensions.
\ No newline at end of file
diff --git a/src/commands/generateOperations.ts b/src/commands/generateOperations.ts
index 815c536..b33c11e 100644
--- a/src/commands/generateOperations.ts
+++ b/src/commands/generateOperations.ts
@@ -134,7 +134,7 @@ export async function generateOperations() {
 
     // Update SDL directive in index.graphql
     if (generatedFiles.length > 0) {
-      updateSdlDirective(indexPath, generatedFiles); // TODO: cleanup when safe, projectRoot);
+      updateSdlDirective(indexPath, generatedFiles);
       vscode.window.showInformationMessage(
         `Generated ${generatedFiles.length} operation files in the operations directory.`,
       );
@@ -286,8 +286,6 @@ function updateSdlDirective(
     // Also check for SDL directive without executables
     const sdlRegex = /@sdl\(([^)]*)\)/gs;
     let sdlWithoutExecutablesMatch = null;
-    // TODO: remove
-    // let originalLineEnding = content.includes("\r\n") ? "\r\n" : "\n";
 
     // Find the schema directive that doesn't include executables
     let isSchemaDirective = false;
diff --git a/src/commands/importCurl.ts b/src/commands/importCurl.ts
index cb5a9a0..c04b6d4 100644
--- a/src/commands/importCurl.ts
+++ b/src/commands/importCurl.ts
@@ -39,8 +39,6 @@ export async function importCurl(): Promise<void> {
         `Schema imported successfully to ${result.targetDir}/${result.schemaName}`
       );
       
-      // TODO: Offer Phase 2 functional enhancements
-      // await offerFunctionalEnhancements(result);
     } else {
       vscode.window.showErrorMessage(`Import failed: ${result.error}`);
     }
diff --git a/src/commands/importDatabase.ts b/src/commands/importDatabase.ts
index 057e6aa..748cb4d 100644
--- a/src/commands/importDatabase.ts
+++ b/src/commands/importDatabase.ts
@@ -39,8 +39,6 @@ export async function importDatabase(): Promise<void> {
         `Database schema imported successfully to ${result.targetDir}/${result.schemaName}`
       );
       
-      // TODO: Offer Phase 2 functional enhancements
-      // await offerFunctionalEnhancements(result);
     } else {
       vscode.window.showErrorMessage(`Import failed: ${result.error}`);
     }
diff --git a/src/commands/importGraphql.ts b/src/commands/importGraphql.ts
index ce2a130..e0df2a0 100644
--- a/src/commands/importGraphql.ts
+++ b/src/commands/importGraphql.ts
@@ -39,8 +39,6 @@ export async function importGraphql(): Promise<void> {
         `GraphQL schema imported successfully to ${result.targetDir}/${result.schemaName}`
       );
       
-      // TODO: Offer Phase 2 functional enhancements
-      // await offerFunctionalEnhancements(result);
     } else {
       vscode.window.showErrorMessage(`Import failed: ${result.error}`);
     }
diff --git a/src/commands/importOpenapi.ts b/src/commands/importOpenapi.ts
index ed18567..710a89e 100644
--- a/src/commands/importOpenapi.ts
+++ b/src/commands/importOpenapi.ts
@@ -39,8 +39,6 @@ export async function importOpenapi(): Promise<void> {
         `OpenAPI schema imported successfully to ${result.targetDir}/${result.schemaName}`
       );
       
-      // TODO: Offer Phase 2 functional enhancements
-      // await offerFunctionalEnhancements(result);
     } else {
       vscode.window.showErrorMessage(`Import failed: ${result.error}`);
     }
diff --git a/src/services/cli.ts b/src/services/cli.ts
index d1d7300..528c404 100644
--- a/src/services/cli.ts
+++ b/src/services/cli.ts
@@ -245,64 +245,6 @@ export class StepzenCliService {
     }
   }
   
-  // TODO: CLEANUP
-  //  /**
-  //  * Spawn a StepZen CLI process with inherited stdio
-  //  * 
-  //  * @param command The StepZen command to execute
-  //  * @param args Command arguments
-  //  * @param options Spawn options
-  //  * @returns Promise that resolves when the process completes
-  //  * @throws CliError if the process fails
-  //  */
-  // private async spawnProcess(
-  //   command: string,
-  //   args: string[] = [],
-  //   options: cp.SpawnOptions = {}
-  // ): Promise<void> {
-  //   return new Promise<void>((resolve, reject) => {
-  //     const fullArgs = [command, ...args];
-  //     const proc = cp.spawn('stepzen', fullArgs, {
-  //       shell: true,
-  //       ...options
-  //     });
-      
-  //     let stderr = '';
-      
-  //     if (proc.stderr) {
-  //       proc.stderr.on('data', (data) => {
-  //         const chunk = data.toString();
-  //         stderr += chunk;
-  //         logger.debug(`StepZen CLI stderr: ${chunk.trim()}`);
-  //       });
-  //     }
-      
-  //     proc.on('error', (err) => {
-  //       reject(new CliError(
-  //         `Failed to spawn StepZen CLI: ${err.message}`,
-  //         'SPAWN_FAILED',
-  //         err
-  //       ));
-  //     });
-      
-  //     proc.on('close', (code) => {
-  //       if (code !== 0) {
-  //         // Create a more descriptive error with exit code and stderr
-  //         const errorMsg = stderr.trim() 
-  //           ? `StepZen ${command} exited with code ${code}: ${stderr.trim()}`
-  //           : `StepZen ${command} exited with code ${code}`;
-            
-  //         reject(new CliError(
-  //           errorMsg,
-  //           'COMMAND_FAILED',
-  //           stderr ? new Error(stderr) : undefined
-  //         ));
-  //       } else {
-  //         resolve();
-  //       }
-  //     });
-  //   });
-  // }
   
   /**
    * Spawn a StepZen CLI process and capture output
diff --git a/src/services/importService.ts b/src/services/importService.ts
index 23bb73b..d261862 100644
--- a/src/services/importService.ts
+++ b/src/services/importService.ts
@@ -93,7 +93,7 @@ export class ImportService {
           success: true,
           targetDir: config.dir || './stepzen',
           schemaName: config.name,
-          files: [] // TODO: Parse CLI output to get generated files
+          files: [] // Note: CLI output parsing not implemented yet
         };
       } catch (cliError: any) {
         this.logger.error(`Import failed: ${cliError.message}`);
diff --git a/src/test/helpers/test-utils.ts b/src/test/helpers/test-utils.ts
index b07dafb..19636f3 100644
--- a/src/test/helpers/test-utils.ts
+++ b/src/test/helpers/test-utils.ts
@@ -12,48 +12,3 @@ export function createMock<T>(properties: Partial<T> = {}): T {
   return properties as T;
 }
 
-// TODO: CLEANUP ?
-// /**
-//  * Asserts that an async function throws an error matching the expected error
-//  * 
-//  * @param fn The async function to test
-//  * @param expectedError The expected error (string, regex, or error instance)
-//  */
-// async function assertThrowsAsync(
-//   fn: () => Promise<any>,
-//   expectedError?: string | RegExp | Error
-// ): Promise<void> {
-//   let error: Error | undefined;
-  
-//   try {
-//     await fn();
-//   } catch (err) {
-//     error = err instanceof Error ? err : new Error(String(err));
-//   }
-  
-//   if (!error) {
-//     assert.fail('Expected function to throw an error');
-//   }
-  
-//   if (expectedError) {
-//     if (typeof expectedError === 'string') {
-//       assert.strictEqual(error.message, expectedError);
-//     } else if (expectedError instanceof RegExp) {
-//       assert.ok(expectedError.test(error.message), `Error message "${error.message}" does not match ${expectedError}`);
-//     } else {
-//       assert.strictEqual(error.name, expectedError.name);
-//       assert.strictEqual(error.message, expectedError.message);
-//     }
-//   }
-// }
-
-// TODO: CLEANUP ?
-// /**
-//  * Timeout utility for tests
-//  * 
-//  * @param ms Milliseconds to wait
-//  * @returns A promise that resolves after the specified time
-//  */
-// function wait(ms: number): Promise<void> {
-//   return new Promise(resolve => setTimeout(resolve, ms));
-// }
diff --git a/src/test/unit/scanner.test.ts b/src/test/unit/scanner.test.ts
index 1fd0974..3e13285 100644
--- a/src/test/unit/scanner.test.ts
+++ b/src/test/unit/scanner.test.ts
@@ -294,7 +294,7 @@ suite("StepZen Project Scanner Test Suite", () => {
 
       // Current behavior: findDefinition only works for root operation fields, not regular type fields
       // This is the current scanner behavior that we're capturing with golden-path tests
-      // TODO: In the future, findDefinition could be enhanced to also find fields within regular types
+      // Note: Current limitation - see issue #55 for enhancement to find fields within regular types
       const recentOrdersDefs = services.schemaIndex.findDefinition("recentOrders");
       assert.strictEqual(recentOrdersDefs, undefined, "Current scanner behavior: findDefinition doesn't find non-root fields");