diff --git a/apps/backend/agents/auto_claude_tools.py b/apps/backend/agents/auto_claude_tools.py
deleted file mode 100644
index ad6dc0a5..00000000
--- a/apps/backend/agents/auto_claude_tools.py
+++ /dev/null
@@ -1,62 +0,0 @@
-"""
-Custom MCP Tools for Auto-Claude Agents
-========================================
-
-DEPRECATED: This module is now a compatibility shim.
-Please import from the tools_pkg package instead:
-
-    from agents.tools_pkg import create_auto_claude_mcp_server, get_allowed_tools
-
-This file remains for backward compatibility with existing imports.
-All functionality has been moved to the tools_pkg package for better
-organization and maintainability.
-"""
-
-# Import everything from the package to maintain backward compatibility
-# Use try/except to handle both relative and absolute imports
-try:
-    from .tools_pkg import (
-        ELECTRON_TOOLS,
-        TOOL_GET_BUILD_PROGRESS,
-        TOOL_GET_SESSION_CONTEXT,
-        TOOL_RECORD_DISCOVERY,
-        TOOL_RECORD_GOTCHA,
-        TOOL_UPDATE_QA_STATUS,
-        TOOL_UPDATE_SUBTASK_STATUS,
-        create_auto_claude_mcp_server,
-        get_allowed_tools,
-        is_electron_mcp_enabled,
-        is_tools_available,
-    )
-except ImportError:
-    # Fallback for direct execution - import from tools_pkg directly
-    from tools_pkg import (
-        ELECTRON_TOOLS,
-        TOOL_GET_BUILD_PROGRESS,
-        TOOL_GET_SESSION_CONTEXT,
-        TOOL_RECORD_DISCOVERY,
-        TOOL_RECORD_GOTCHA,
-        TOOL_UPDATE_QA_STATUS,
-        TOOL_UPDATE_SUBTASK_STATUS,
-        create_auto_claude_mcp_server,
-        get_allowed_tools,
-        is_electron_mcp_enabled,
-        is_tools_available,
-    )
-
-__all__ = [
-    # Main API
-    "create_auto_claude_mcp_server",
-    "get_allowed_tools",
-    "is_tools_available",
-    # Tool name constants
-    "TOOL_UPDATE_SUBTASK_STATUS",
-    "TOOL_GET_BUILD_PROGRESS",
-    "TOOL_RECORD_DISCOVERY",
-    "TOOL_RECORD_GOTCHA",
-    "TOOL_GET_SESSION_CONTEXT",
-    "TOOL_UPDATE_QA_STATUS",
-    # Electron MCP
-    "ELECTRON_TOOLS",
-    "is_electron_mcp_enabled",
-]
diff --git a/apps/backend/cli/main.py b/apps/backend/cli/main.py
index 868bdacb..e0f8f29d 100644
--- a/apps/backend/cli/main.py
+++ b/apps/backend/cli/main.py
@@ -15,10 +15,6 @@ _PARENT_DIR = Path(__file__).parent.parent
 if str(_PARENT_DIR) not in sys.path:
     sys.path.insert(0, str(_PARENT_DIR))
 
-from ui import (
-    Icons,
-    icon,
-)
 
 from .batch_commands import (
     handle_batch_cleanup_command,
@@ -201,13 +197,6 @@ Environment Variables:
         help="Show human review/approval status for a spec",
     )
 
-    # Dev mode (deprecated)
-    parser.add_argument(
-        "--dev",
-        action="store_true",
-        help="[Deprecated] No longer has any effect - kept for compatibility",
-    )
-
     # Non-interactive mode (for UI/automation)
     parser.add_argument(
         "--auto-continue",
@@ -290,16 +279,10 @@ def main() -> None:
     # Get model (with env var fallback)
     model = args.model or os.environ.get("AUTO_BUILD_MODEL", DEFAULT_MODEL)
 
-    # Note: --dev flag is deprecated but kept for API compatibility
-    if args.dev:
-        print(
-            f"\n{icon(Icons.GEAR)} Note: --dev flag is deprecated. All specs now use .auto-claude/specs/\n"
-        )
-
     # Handle --list command
     if args.list:
         print_banner()
-        print_specs_list(project_dir, args.dev)
+        print_specs_list(project_dir)
         return
 
     # Handle --list-worktrees command
@@ -337,14 +320,14 @@ def main() -> None:
         sys.exit(1)
 
     # Find the spec
-    debug("run.py", "Finding spec", spec_identifier=args.spec, dev_mode=args.dev)
-    spec_dir = find_spec(project_dir, args.spec, args.dev)
+    debug("run.py", "Finding spec", spec_identifier=args.spec)
+    spec_dir = find_spec(project_dir, args.spec)
     if not spec_dir:
         debug_error("run.py", "Spec not found", spec=args.spec)
         print_banner()
         print(f"\nError: Spec '{args.spec}' not found")
         print("\nAvailable specs:")
-        print_specs_list(project_dir, args.dev)
+        print_specs_list(project_dir)
         sys.exit(1)
 
     debug_success("run.py", "Spec found", spec_dir=str(spec_dir))
diff --git a/apps/backend/cli/spec_commands.py b/apps/backend/cli/spec_commands.py
index 2fa1d02c..ed2b5a38 100644
--- a/apps/backend/cli/spec_commands.py
+++ b/apps/backend/cli/spec_commands.py
@@ -19,18 +19,17 @@ from workspace import get_existing_build_worktree
 from .utils import get_specs_dir
 
 
-def list_specs(project_dir: Path, dev_mode: bool = False) -> list[dict]:
+def list_specs(project_dir: Path) -> list[dict]:
     """
     List all specs in the project.
 
     Args:
         project_dir: Project root directory
-        dev_mode: If True, use dev/auto-claude/specs/
 
     Returns:
         List of spec info dicts with keys: number, name, path, status, progress
     """
-    specs_dir = get_specs_dir(project_dir, dev_mode)
+    specs_dir = get_specs_dir(project_dir)
     specs = []
 
     if not specs_dir.exists():
@@ -93,19 +92,16 @@ def list_specs(project_dir: Path, dev_mode: bool = False) -> list[dict]:
     return specs
 
 
-def print_specs_list(
-    project_dir: Path, dev_mode: bool = False, auto_create: bool = True
-) -> None:
+def print_specs_list(project_dir: Path, auto_create: bool = True) -> None:
     """Print a formatted list of all specs.
 
     Args:
         project_dir: Project root directory
-        dev_mode: If True, use dev/auto-claude/specs/
         auto_create: If True and no specs exist, automatically launch spec creation
     """
     import subprocess
 
-    specs = list_specs(project_dir, dev_mode)
+    specs = list_specs(project_dir)
 
     if not specs:
         print("\nNo specs found.")
diff --git a/apps/backend/cli/utils.py b/apps/backend/cli/utils.py
index c5dd6766..f1895465 100644
--- a/apps/backend/cli/utils.py
+++ b/apps/backend/cli/utils.py
@@ -54,21 +54,18 @@ def setup_environment() -> Path:
     return script_dir
 
 
-def find_spec(
-    project_dir: Path, spec_identifier: str, dev_mode: bool = False
-) -> Path | None:
+def find_spec(project_dir: Path, spec_identifier: str) -> Path | None:
     """
     Find a spec by number or full name.
 
     Args:
         project_dir: Project root directory
         spec_identifier: Either "001" or "001-feature-name"
-        dev_mode: If True, use dev/auto-claude/specs/
 
     Returns:
         Path to spec folder, or None if not found
     """
-    specs_dir = get_specs_dir(project_dir, dev_mode)
+    specs_dir = get_specs_dir(project_dir)
 
     if specs_dir.exists():
         # Try exact match first
diff --git a/apps/backend/implementation_plan/main.py b/apps/backend/implementation_plan/main.py
deleted file mode 100644
index 733e78a4..00000000
--- a/apps/backend/implementation_plan/main.py
+++ /dev/null
@@ -1,168 +0,0 @@
-#!/usr/bin/env python3
-"""
-Implementation Plan Manager
-============================
-
-DEPRECATED: This module is now a compatibility shim. The implementation has been
-refactored into the implementation_plan/ package for better modularity.
-
-Please import from the package directly:
-    from implementation_plan import ImplementationPlan, Subtask, Phase, etc.
-
-This file re-exports all public APIs for backwards compatibility.
-
-Core data structures and utilities for subtask-based implementation plans.
-Replaces the test-centric feature_list.json with implementation_plan.json.
-
-The key insight: Tests verify outcomes, but SUBTASKS define implementation steps.
-For complex multi-service features, implementation order matters.
-
-Workflow Types:
-- feature: Standard multi-service feature (phases = services)
-- refactor: Migration/refactor work (phases = stages: add, migrate, remove)
-- investigation: Bug hunting (phases = investigate, hypothesize, fix)
-- migration: Data migration (phases = prepare, test, execute, cleanup)
-- simple: Single-service enhancement (minimal overhead)
-"""
-
-# Re-export everything from the implementation_plan package
-from implementation_plan import (
-    Chunk,
-    ChunkStatus,
-    ImplementationPlan,
-    Phase,
-    PhaseType,
-    Subtask,
-    SubtaskStatus,
-    Verification,
-    VerificationType,
-    WorkflowType,
-    create_feature_plan,
-    create_investigation_plan,
-    create_refactor_plan,
-)
-
-__all__ = [
-    # Enums
-    "WorkflowType",
-    "PhaseType",
-    "SubtaskStatus",
-    "VerificationType",
-    # Models
-    "Verification",
-    "Subtask",
-    "Phase",
-    "ImplementationPlan",
-    # Factories
-    "create_feature_plan",
-    "create_investigation_plan",
-    "create_refactor_plan",
-    # Backwards compatibility
-    "Chunk",
-    "ChunkStatus",
-]
-
-
-# CLI for testing
-if __name__ == "__main__":
-    import json
-    import sys
-    from pathlib import Path
-
-    if len(sys.argv) < 2:
-        print("Usage: python implementation_plan.py <plan.json>")
-        print("       python implementation_plan.py --demo")
-        sys.exit(1)
-
-    if sys.argv[1] == "--demo":
-        # Create a demo plan
-        plan = create_feature_plan(
-            feature="Avatar Upload with Processing",
-            services=["backend", "worker", "frontend"],
-            phases_config=[
-                {
-                    "name": "Backend Foundation",
-                    "parallel_safe": True,
-                    "subtasks": [
-                        {
-                            "id": "avatar-model",
-                            "service": "backend",
-                            "description": "Add avatar fields to User model",
-                            "files_to_modify": ["app/models/user.py"],
-                            "files_to_create": ["migrations/add_avatar.py"],
-                            "verification": {
-                                "type": "command",
-                                "run": "flask db upgrade",
-                            },
-                        },
-                        {
-                            "id": "avatar-endpoint",
-                            "service": "backend",
-                            "description": "POST /api/users/avatar endpoint",
-                            "files_to_modify": ["app/routes/users.py"],
-                            "patterns_from": ["app/routes/profile.py"],
-                            "verification": {
-                                "type": "api",
-                                "method": "POST",
-                                "url": "/api/users/avatar",
-                            },
-                        },
-                    ],
-                },
-                {
-                    "name": "Worker Pipeline",
-                    "depends_on": [1],
-                    "subtasks": [
-                        {
-                            "id": "image-task",
-                            "service": "worker",
-                            "description": "Celery task for image processing",
-                            "files_to_create": ["app/tasks/images.py"],
-                            "patterns_from": ["app/tasks/reports.py"],
-                        },
-                    ],
-                },
-                {
-                    "name": "Frontend",
-                    "depends_on": [1],
-                    "subtasks": [
-                        {
-                            "id": "avatar-component",
-                            "service": "frontend",
-                            "description": "AvatarUpload React component",
-                            "files_to_create": ["src/components/AvatarUpload.tsx"],
-                            "patterns_from": ["src/components/FileUpload.tsx"],
-                        },
-                    ],
-                },
-                {
-                    "name": "Integration",
-                    "depends_on": [2, 3],
-                    "type": "integration",
-                    "subtasks": [
-                        {
-                            "id": "e2e-wiring",
-                            "all_services": True,
-                            "description": "Connect frontend → backend → worker",
-                            "verification": {
-                                "type": "browser",
-                                "scenario": "Upload → Process → Display",
-                            },
-                        },
-                    ],
-                },
-            ],
-        )
-        plan.final_acceptance = [
-            "User can upload avatar from profile page",
-            "Avatar is automatically resized",
-            "Large/invalid files show error",
-        ]
-
-        print(json.dumps(plan.to_dict(), indent=2))
-        print("\n---\n")
-        print(plan.get_status_summary())
-    else:
-        # Load and display existing plan
-        plan = ImplementationPlan.load(Path(sys.argv[1]))
-        print(plan.get_status_summary())
diff --git a/apps/backend/runners/github/batch_issues.py b/apps/backend/runners/github/batch_issues.py
index 765c689e..743a172e 100644
--- a/apps/backend/runners/github/batch_issues.py
+++ b/apps/backend/runners/github/batch_issues.py
@@ -240,30 +240,6 @@ Respond with JSON only:
         return response_text
 
 
-# Keep old class for backwards compatibility but mark as deprecated
-class ClaudeSimilarityDetector(ClaudeBatchAnalyzer):
-    """DEPRECATED: Use ClaudeBatchAnalyzer instead."""
-
-    async def compare_issues(
-        self,
-        repo: str,
-        issue_a: dict[str, Any],
-        issue_b: dict[str, Any],
-    ) -> dict[str, Any]:
-        """DEPRECATED: Pairwise comparison. Use analyze_and_batch_issues instead."""
-        logger.warning("ClaudeSimilarityDetector.compare_issues is deprecated")
-        # Simple fallback for any code still using this
-        return {
-            "is_similar": False,
-            "overall_score": 0.0,
-            "reasoning": "DEPRECATED: Use ClaudeBatchAnalyzer.analyze_and_batch_issues",
-        }
-
-    async def precompute_embeddings(self, repo: str, issues: list[dict]) -> int:
-        """No-op for compatibility."""
-        return 0
-
-
 class BatchStatus(str, Enum):
     """Status of an issue batch."""
 
@@ -446,12 +422,9 @@ class IssueBatcher:
         self.max_batch_size = max_batch_size
         self.validate_batches_enabled = validate_batches
 
-        # Initialize Claude batch analyzer (replaces pairwise similarity detector)
+        # Initialize Claude batch analyzer
         self.analyzer = ClaudeBatchAnalyzer(project_dir=self.project_dir)
 
-        # Keep detector for backwards compatibility (deprecated)
-        self.detector = self.analyzer
-
         # Initialize batch validator (uses Claude SDK with OAuth token)
         self.validator = (
             BatchValidator(
diff --git a/apps/backend/runners/spec_runner.py b/apps/backend/runners/spec_runner.py
index 660ab6d2..fe48bf8a 100644
--- a/apps/backend/runners/spec_runner.py
+++ b/apps/backend/runners/spec_runner.py
@@ -95,7 +95,7 @@ from debug import debug, debug_error, debug_section, debug_success
 from phase_config import resolve_model_id
 from review import ReviewState
 from spec import SpecOrchestrator
-from ui import Icons, highlight, icon, muted, print_section, print_status
+from ui import Icons, highlight, muted, print_section, print_status
 
 
 def main():
@@ -177,11 +177,6 @@ Examples:
         action="store_true",
         help="Use heuristic complexity assessment instead of AI (faster but less accurate)",
     )
-    parser.add_argument(
-        "--dev",
-        action="store_true",
-        help="[Deprecated] No longer has any effect - kept for compatibility",
-    )
     parser.add_argument(
         "--no-build",
         action="store_true",
@@ -236,12 +231,6 @@ Examples:
                 project_dir = parent
                 break
 
-    # Note: --dev flag is deprecated but kept for API compatibility
-    if args.dev:
-        print(
-            f"\n{icon(Icons.GEAR)} Note: --dev flag is deprecated. All specs now go to .auto-claude/specs/\n"
-        )
-
     # Resolve model shorthand to full model ID
     resolved_model = resolve_model_id(args.model)
 
@@ -267,7 +256,6 @@ Examples:
         thinking_level=args.thinking_level,
         complexity_override=args.complexity,
         use_ai_assessment=not args.no_ai_assessment,
-        dev_mode=args.dev,
     )
 
     try:
@@ -330,10 +318,6 @@ Examples:
                 "--auto-continue",  # Non-interactive mode for chained execution
             ]
 
-            # Pass through dev mode
-            if args.dev:
-                run_cmd.append("--dev")
-
             # Note: Model configuration for subsequent phases (planning, coding, qa)
             # is read from task_metadata.json by run.py, so we don't pass it here.
             # This allows per-phase configuration when using Auto profile.
diff --git a/apps/backend/spec/complexity.py b/apps/backend/spec/complexity.py
index cf38c47d..5be32544 100644
--- a/apps/backend/spec/complexity.py
+++ b/apps/backend/spec/complexity.py
@@ -435,9 +435,7 @@ async def run_ai_complexity_assessment(
         return None
 
 
-def save_assessment(
-    spec_dir: Path, assessment: ComplexityAssessment, dev_mode: bool = False
-) -> Path:
+def save_assessment(spec_dir: Path, assessment: ComplexityAssessment) -> Path:
     """Save complexity assessment to file."""
     assessment_file = spec_dir / "complexity_assessment.json"
     phases = assessment.phases_to_run()
@@ -456,7 +454,6 @@ def save_assessment(
                 "phases_to_run": phases,
                 "needs_research": assessment.needs_research,
                 "needs_self_critique": assessment.needs_self_critique,
-                "dev_mode": dev_mode,
                 "created_at": datetime.now().isoformat(),
             },
             f,
diff --git a/apps/backend/spec/pipeline/models.py b/apps/backend/spec/pipeline/models.py
index f1a08303..6675c9c6 100644
--- a/apps/backend/spec/pipeline/models.py
+++ b/apps/backend/spec/pipeline/models.py
@@ -21,7 +21,7 @@ if TYPE_CHECKING:
     from core.workspace.models import SpecNumberLock
 
 
-def get_specs_dir(project_dir: Path, dev_mode: bool = False) -> Path:
+def get_specs_dir(project_dir: Path) -> Path:
     """Get the specs directory path.
 
     IMPORTANT: Only .auto-claude/ is considered an "installed" auto-claude.
@@ -32,7 +32,6 @@ def get_specs_dir(project_dir: Path, dev_mode: bool = False) -> Path:
 
     Args:
         project_dir: The project root directory
-        dev_mode: Deprecated, kept for API compatibility. Has no effect.
 
     Returns:
         Path to the specs directory within .auto-claude/
diff --git a/apps/backend/spec/pipeline/orchestrator.py b/apps/backend/spec/pipeline/orchestrator.py
index 1f57cd16..76c04d47 100644
--- a/apps/backend/spec/pipeline/orchestrator.py
+++ b/apps/backend/spec/pipeline/orchestrator.py
@@ -61,7 +61,6 @@ class SpecOrchestrator:
         thinking_level: str = "medium",  # Thinking level for extended thinking
         complexity_override: str | None = None,  # Force a specific complexity
         use_ai_assessment: bool = True,  # Use AI for complexity assessment (vs heuristics)
-        dev_mode: bool = False,  # Dev mode: specs in gitignored folder, code changes to auto-claude/
     ):
         """Initialize the spec orchestrator.
 
@@ -74,7 +73,6 @@ class SpecOrchestrator:
             thinking_level: Thinking level (none, low, medium, high, ultrathink)
             complexity_override: Force a specific complexity level
             use_ai_assessment: Whether to use AI for complexity assessment
-            dev_mode: Deprecated, kept for API compatibility
         """
         self.project_dir = Path(project_dir)
         self.task_description = task_description
@@ -82,10 +80,9 @@ class SpecOrchestrator:
         self.thinking_level = thinking_level
         self.complexity_override = complexity_override
         self.use_ai_assessment = use_ai_assessment
-        self.dev_mode = dev_mode
 
         # Get the appropriate specs directory (within the project)
-        self.specs_dir = get_specs_dir(self.project_dir, dev_mode)
+        self.specs_dir = get_specs_dir(self.project_dir)
 
         # Clean up orphaned pending folders before creating new spec
         cleanup_orphaned_pending_folders(self.specs_dir)
@@ -462,7 +459,7 @@ class SpecOrchestrator:
 
         # Save assessment
         if not assessment_file.exists():
-            complexity.save_assessment(self.spec_dir, self.assessment, self.dev_mode)
+            complexity.save_assessment(self.spec_dir, self.assessment)
 
         return phases.PhaseResult(
             "complexity_assessment", True, [str(assessment_file)], [], 0
diff --git a/apps/frontend/src/main/ipc-handlers/project-handlers.ts b/apps/frontend/src/main/ipc-handlers/project-handlers.ts
index c0c65a20..ea139151 100644
--- a/apps/frontend/src/main/ipc-handlers/project-handlers.ts
+++ b/apps/frontend/src/main/ipc-handlers/project-handlers.ts
@@ -319,29 +319,6 @@ export function registerProjectHandlers(
     }
   );
 
-  // PROJECT_UPDATE_AUTOBUILD is deprecated - .auto-claude only contains data, no code to update
-  // Kept for API compatibility, returns success immediately
-  ipcMain.handle(
-    IPC_CHANNELS.PROJECT_UPDATE_AUTOBUILD,
-    async (_, projectId: string): Promise<IPCResult<InitializationResult>> => {
-      try {
-        const project = projectStore.getProject(projectId);
-        if (!project) {
-          return { success: false, error: 'Project not found' };
-        }
-
-        // Nothing to update - .auto-claude only contains data directories
-        // The framework runs from the source repo
-        return { success: true, data: { success: true } };
-      } catch (error) {
-        return {
-          success: false,
-          error: error instanceof Error ? error.message : 'Unknown error'
-        };
-      }
-    }
-  );
-
   // PROJECT_CHECK_VERSION now just checks if project is initialized
   // Version tracking for .auto-claude is removed since it only contains data
   ipcMain.handle(
diff --git a/apps/frontend/src/preload/api/project-api.ts b/apps/frontend/src/preload/api/project-api.ts
index 420f8270..3ad83a00 100644
--- a/apps/frontend/src/preload/api/project-api.ts
+++ b/apps/frontend/src/preload/api/project-api.ts
@@ -31,7 +31,6 @@ export interface ProjectAPI {
     settings: Partial<ProjectSettings>
   ) => Promise<IPCResult>;
   initializeProject: (projectId: string) => Promise<IPCResult<InitializationResult>>;
-  updateProjectAutoBuild: (projectId: string) => Promise<IPCResult<InitializationResult>>;
   checkProjectVersion: (projectId: string) => Promise<IPCResult<AutoBuildVersionInfo>>;
 
   // Tab State (persisted in main process for reliability)
@@ -155,9 +154,6 @@ export const createProjectAPI = (): ProjectAPI => ({
   initializeProject: (projectId: string): Promise<IPCResult<InitializationResult>> =>
     ipcRenderer.invoke(IPC_CHANNELS.PROJECT_INITIALIZE, projectId),
 
-  updateProjectAutoBuild: (projectId: string): Promise<IPCResult<InitializationResult>> =>
-    ipcRenderer.invoke(IPC_CHANNELS.PROJECT_UPDATE_AUTOBUILD, projectId),
-
   checkProjectVersion: (projectId: string): Promise<IPCResult<AutoBuildVersionInfo>> =>
     ipcRenderer.invoke(IPC_CHANNELS.PROJECT_CHECK_VERSION, projectId),
 
diff --git a/apps/frontend/src/renderer/components/Sidebar.tsx b/apps/frontend/src/renderer/components/Sidebar.tsx
index e093fb56..d6be635a 100644
--- a/apps/frontend/src/renderer/components/Sidebar.tsx
+++ b/apps/frontend/src/renderer/components/Sidebar.tsx
@@ -40,9 +40,7 @@ import { cn } from '../lib/utils';
 import {
   useProjectStore,
   removeProject,
-  initializeProject,
-  checkProjectVersion,
-  updateProjectAutoBuild
+  initializeProject
 } from '../stores/project-store';
 import { useSettingsStore } from '../stores/settings-store';
 import { AddProjectModal } from './AddProjectModal';
@@ -96,11 +94,9 @@ export function Sidebar({
 
   const [showAddProjectModal, setShowAddProjectModal] = useState(false);
   const [showInitDialog, setShowInitDialog] = useState(false);
-  const [showUpdateDialog, setShowUpdateDialog] = useState(false);
   const [showGitSetupModal, setShowGitSetupModal] = useState(false);
   const [gitStatus, setGitStatus] = useState<GitStatus | null>(null);
   const [pendingProject, setPendingProject] = useState<Project | null>(null);
-  const [_versionInfo, setVersionInfo] = useState<AutoBuildVersionInfo | null>(null);
   const [isInitializing, setIsInitializing] = useState(false);
 
   const selectedProject = projects.find((p) => p.id === selectedProjectId);
@@ -140,20 +136,6 @@ export function Sidebar({
     return () => window.removeEventListener('keydown', handleKeyDown);
   }, [selectedProjectId, onViewChange]);
 
-  // Check for updates when project changes
-  useEffect(() => {
-    const checkUpdates = async () => {
-      if (selectedProjectId && settings.autoUpdateAutoBuild) {
-        const info = await checkProjectVersion(selectedProjectId);
-        if (info?.updateAvailable) {
-          setVersionInfo(info);
-          setShowUpdateDialog(true);
-        }
-      }
-    };
-    checkUpdates();
-  }, [selectedProjectId, settings.autoUpdateAutoBuild]);
-
   // Check git status when project changes
   useEffect(() => {
     const checkGit = async () => {
@@ -211,26 +193,6 @@ export function Sidebar({
     setPendingProject(null);
   };
 
-  const _handleUpdate = async () => {
-    if (!selectedProjectId) return;
-
-    setIsInitializing(true);
-    try {
-      const result = await updateProjectAutoBuild(selectedProjectId);
-      if (result?.success) {
-        setShowUpdateDialog(false);
-        setVersionInfo(null);
-      }
-    } finally {
-      setIsInitializing(false);
-    }
-  };
-
-  const _handleSkipUpdate = () => {
-    setShowUpdateDialog(false);
-    setVersionInfo(null);
-  };
-
   const handleGitInitialized = async () => {
     // Refresh git status after initialization
     if (selectedProject) {
@@ -439,26 +401,6 @@ export function Sidebar({
         </DialogContent>
       </Dialog>
 
-      {/* Update Auto Claude Dialog - Deprecated, updateAvailable is always false now */}
-      <Dialog open={showUpdateDialog} onOpenChange={setShowUpdateDialog}>
-        <DialogContent>
-          <DialogHeader>
-            <DialogTitle className="flex items-center gap-2">
-              <RefreshCw className="h-5 w-5" />
-              {t('dialogs:update.title')}
-            </DialogTitle>
-            <DialogDescription>
-              {t('dialogs:update.projectInitialized')}
-            </DialogDescription>
-          </DialogHeader>
-          <DialogFooter>
-            <Button variant="outline" onClick={() => setShowUpdateDialog(false)}>
-              {t('common:buttons.close')}
-            </Button>
-          </DialogFooter>
-        </DialogContent>
-      </Dialog>
-
       {/* Add Project Modal */}
       <AddProjectModal
         open={showAddProjectModal}
diff --git a/apps/frontend/src/renderer/components/project-settings/GeneralSettings.tsx b/apps/frontend/src/renderer/components/project-settings/GeneralSettings.tsx
index 81d557e9..7ff89bda 100644
--- a/apps/frontend/src/renderer/components/project-settings/GeneralSettings.tsx
+++ b/apps/frontend/src/renderer/components/project-settings/GeneralSettings.tsx
@@ -31,7 +31,6 @@ interface GeneralSettingsProps {
   isCheckingVersion: boolean;
   isUpdating: boolean;
   handleInitialize: () => Promise<void>;
-  handleUpdate: () => Promise<void>;
 }
 
 export function GeneralSettings({
@@ -41,8 +40,7 @@ export function GeneralSettings({
   versionInfo,
   isCheckingVersion,
   isUpdating,
-  handleInitialize,
-  handleUpdate: _handleUpdate
+  handleInitialize
 }: GeneralSettingsProps) {
   return (
     <>
diff --git a/apps/frontend/src/renderer/components/project-settings/hooks/useProjectSettings.ts b/apps/frontend/src/renderer/components/project-settings/hooks/useProjectSettings.ts
index 4cb47530..448eded7 100644
--- a/apps/frontend/src/renderer/components/project-settings/hooks/useProjectSettings.ts
+++ b/apps/frontend/src/renderer/components/project-settings/hooks/useProjectSettings.ts
@@ -2,8 +2,7 @@ import { useState, useEffect } from 'react';
 import {
   updateProjectSettings,
   checkProjectVersion,
-  initializeProject,
-  updateProjectAutoBuild
+  initializeProject
 } from '../../../stores/project-store';
 import { checkGitHubConnection as checkGitHubConnectionGlobal } from '../../../stores/github';
 import type {
@@ -68,7 +67,6 @@ export interface UseProjectSettingsReturn {
 
   // Actions
   handleInitialize: () => Promise<void>;
-  handleUpdate: () => Promise<void>;
   handleSaveEnv: () => Promise<void>;
   handleClaudeSetup: () => Promise<void>;
   handleSave: (onClose: () => void) => Promise<void>;
@@ -262,24 +260,6 @@ export function useProjectSettings(
     }
   };
 
-  const handleUpdate = async () => {
-    setIsUpdating(true);
-    setError(null);
-    try {
-      const result = await updateProjectAutoBuild(project.id);
-      if (result?.success) {
-        const info = await checkProjectVersion(project.id);
-        setVersionInfo(info);
-      } else {
-        setError(result?.error || 'Failed to update');
-      }
-    } catch (err) {
-      setError(err instanceof Error ? err.message : 'Unknown error');
-    } finally {
-      setIsUpdating(false);
-    }
-  };
-
   const handleSaveEnv = async () => {
     if (!envConfig) return;
 
@@ -397,7 +377,6 @@ export function useProjectSettings(
     linearConnectionStatus,
     isCheckingLinear,
     handleInitialize,
-    handleUpdate,
     handleSaveEnv,
     handleClaudeSetup,
     handleSave
diff --git a/apps/frontend/src/renderer/components/settings/ProjectSettingsContent.tsx b/apps/frontend/src/renderer/components/settings/ProjectSettingsContent.tsx
index d6c0d56c..8500da76 100644
--- a/apps/frontend/src/renderer/components/settings/ProjectSettingsContent.tsx
+++ b/apps/frontend/src/renderer/components/settings/ProjectSettingsContent.tsx
@@ -100,7 +100,6 @@ function ProjectSettingsContentInner({
     linearConnectionStatus,
     isCheckingLinear,
     handleInitialize,
-    handleUpdate,
     handleClaudeSetup,
     error
   } = hook;
@@ -146,7 +145,6 @@ function ProjectSettingsContentInner({
         linearConnectionStatus={linearConnectionStatus}
         isCheckingLinear={isCheckingLinear}
         handleInitialize={handleInitialize}
-        handleUpdate={handleUpdate}
         handleClaudeSetup={handleClaudeSetup}
         onOpenLinearImport={() => setShowLinearImportModal(true)}
       />
diff --git a/apps/frontend/src/renderer/components/settings/sections/SectionRouter.tsx b/apps/frontend/src/renderer/components/settings/sections/SectionRouter.tsx
index 73894391..710de08f 100644
--- a/apps/frontend/src/renderer/components/settings/sections/SectionRouter.tsx
+++ b/apps/frontend/src/renderer/components/settings/sections/SectionRouter.tsx
@@ -35,7 +35,6 @@ interface SectionRouterProps {
   linearConnectionStatus: LinearSyncStatus | null;
   isCheckingLinear: boolean;
   handleInitialize: () => Promise<void>;
-  handleUpdate: () => Promise<void>;
   handleClaudeSetup: () => Promise<void>;
   onOpenLinearImport: () => void;
 }
@@ -71,7 +70,6 @@ export function SectionRouter({
   linearConnectionStatus,
   isCheckingLinear,
   handleInitialize,
-  handleUpdate,
   handleClaudeSetup,
   onOpenLinearImport
 }: SectionRouterProps) {
@@ -90,7 +88,6 @@ export function SectionRouter({
             isCheckingVersion={isCheckingVersion}
             isUpdating={isUpdating}
             handleInitialize={handleInitialize}
-            handleUpdate={handleUpdate}
           />
         </SettingsSection>
       );
diff --git a/apps/frontend/src/renderer/components/settings/utils/hookProxyFactory.ts b/apps/frontend/src/renderer/components/settings/utils/hookProxyFactory.ts
index dcc071b6..0f7ae8bb 100644
--- a/apps/frontend/src/renderer/components/settings/utils/hookProxyFactory.ts
+++ b/apps/frontend/src/renderer/components/settings/utils/hookProxyFactory.ts
@@ -47,7 +47,6 @@ export function createHookProxy(
     get linearConnectionStatus() { return hookRef.current.linearConnectionStatus; },
     get isCheckingLinear() { return hookRef.current.isCheckingLinear; },
     get handleInitialize() { return hookRef.current.handleInitialize; },
-    get handleUpdate() { return hookRef.current.handleUpdate; },
     get handleSaveEnv() { return hookRef.current.handleSaveEnv; },
     get handleClaudeSetup() { return hookRef.current.handleClaudeSetup; },
     get handleSave() { return hookRef.current.handleSave; },
diff --git a/apps/frontend/src/renderer/components/terminal/useTerminalEvents.ts b/apps/frontend/src/renderer/components/terminal/useTerminalEvents.ts
index ded05f23..92c61305 100644
--- a/apps/frontend/src/renderer/components/terminal/useTerminalEvents.ts
+++ b/apps/frontend/src/renderer/components/terminal/useTerminalEvents.ts
@@ -1,5 +1,6 @@
 import { useEffect } from 'react';
 import { useTerminalStore } from '../../stores/terminal-store';
+import { terminalBufferManager } from '../../lib/terminal-buffer-manager';
 
 interface UseTerminalEventsOptions {
   terminalId: string;
@@ -20,7 +21,7 @@ export function useTerminalEvents({
   useEffect(() => {
     const cleanup = window.electronAPI.onTerminalOutput((id, data) => {
       if (id === terminalId) {
-        useTerminalStore.getState().appendOutput(terminalId, data);
+        terminalBufferManager.append(terminalId, data);
         onOutput?.(data);
       }
     });
diff --git a/apps/frontend/src/renderer/lib/mocks/project-mock.ts b/apps/frontend/src/renderer/lib/mocks/project-mock.ts
index 38f63bd8..b1dded3d 100644
--- a/apps/frontend/src/renderer/lib/mocks/project-mock.ts
+++ b/apps/frontend/src/renderer/lib/mocks/project-mock.ts
@@ -33,11 +33,6 @@ export const projectMock = {
     data: { success: true, version: '1.0.0', wasUpdate: false }
   }),
 
-  updateProjectAutoBuild: async () => ({
-    success: true,
-    data: { success: true, version: '1.0.0', wasUpdate: true }
-  }),
-
   checkProjectVersion: async () => ({
     success: true,
     data: {
diff --git a/apps/frontend/src/renderer/stores/project-store.ts b/apps/frontend/src/renderer/stores/project-store.ts
index 1aecf74c..5d95d6e1 100644
--- a/apps/frontend/src/renderer/stores/project-store.ts
+++ b/apps/frontend/src/renderer/stores/project-store.ts
@@ -453,24 +453,3 @@ export async function initializeProject(
     return null;
   }
 }
-
-/**
- * Update auto-claude in a project
- */
-export async function updateProjectAutoBuild(
-  projectId: string
-): Promise<InitializationResult | null> {
-  const store = useProjectStore.getState();
-
-  try {
-    const result = await window.electronAPI.updateProjectAutoBuild(projectId);
-    if (result.success && result.data) {
-      return result.data;
-    }
-    store.setError(result.error || 'Failed to update auto-claude');
-    return null;
-  } catch (error) {
-    store.setError(error instanceof Error ? error.message : 'Unknown error');
-    return null;
-  }
-}
diff --git a/apps/frontend/src/renderer/stores/terminal-store.ts b/apps/frontend/src/renderer/stores/terminal-store.ts
index 5e03779d..92171069 100644
--- a/apps/frontend/src/renderer/stores/terminal-store.ts
+++ b/apps/frontend/src/renderer/stores/terminal-store.ts
@@ -45,8 +45,6 @@ interface TerminalState {
   setClaudeMode: (id: string, isClaudeMode: boolean) => void;
   setClaudeSessionId: (id: string, sessionId: string) => void;
   setAssociatedTask: (id: string, taskId: string | undefined) => void;
-  appendOutput: (id: string, data: string) => void;
-  clearOutputBuffer: (id: string) => void;
   clearAllTerminals: () => void;
   setHasRestoredSessions: (value: boolean) => void;
 
@@ -187,18 +185,6 @@ export const useTerminalStore = create<TerminalState>((set, get) => ({
     }));
   },
 
-  // DEPRECATED: Use terminalBufferManager.append() directly
-  // Kept for backward compatibility, but does NOT trigger React re-renders
-  appendOutput: (id: string, data: string) => {
-    terminalBufferManager.append(id, data);
-    // No React state update - this is the key performance improvement!
-  },
-
-  // DEPRECATED: Use terminalBufferManager.clear() directly
-  clearOutputBuffer: (id: string) => {
-    terminalBufferManager.clear(id);
-  },
-
   clearAllTerminals: () => {
     set({ terminals: [], activeTerminalId: null, hasRestoredSessions: false });
   },
diff --git a/apps/frontend/src/shared/constants/ipc.ts b/apps/frontend/src/shared/constants/ipc.ts
index 261b3e8e..40c5bde2 100644
--- a/apps/frontend/src/shared/constants/ipc.ts
+++ b/apps/frontend/src/shared/constants/ipc.ts
@@ -10,7 +10,6 @@ export const IPC_CHANNELS = {
   PROJECT_LIST: 'project:list',
   PROJECT_UPDATE_SETTINGS: 'project:updateSettings',
   PROJECT_INITIALIZE: 'project:initialize',
-  PROJECT_UPDATE_AUTOBUILD: 'project:updateAutoBuild',
   PROJECT_CHECK_VERSION: 'project:checkVersion',
 
   // Tab state operations (persisted in main process)
diff --git a/apps/frontend/src/shared/types/ipc.ts b/apps/frontend/src/shared/types/ipc.ts
index 48e69a0e..90ca97bc 100644
--- a/apps/frontend/src/shared/types/ipc.ts
+++ b/apps/frontend/src/shared/types/ipc.ts
@@ -123,7 +123,6 @@ export interface ElectronAPI {
   getProjects: () => Promise<IPCResult<Project[]>>;
   updateProjectSettings: (projectId: string, settings: Partial<ProjectSettings>) => Promise<IPCResult>;
   initializeProject: (projectId: string) => Promise<IPCResult<InitializationResult>>;
-  updateProjectAutoBuild: (projectId: string) => Promise<IPCResult<InitializationResult>>;
   checkProjectVersion: (projectId: string) => Promise<IPCResult<AutoBuildVersionInfo>>;
 
   // Tab State (persisted in main process for reliability)
diff --git a/tests/test_agent_architecture.py b/tests/test_agent_architecture.py
index 54262880..1b97d706 100644
--- a/tests/test_agent_architecture.py
+++ b/tests/test_agent_architecture.py
@@ -303,19 +303,6 @@ class TestElectronToolScoping:
 class TestSubtaskTerminology:
     """Verify subtask terminology is used consistently."""
 
-    def test_implementation_plan_uses_subtask_class(self):
-        """Implementation plan uses Subtask class."""
-        impl_plan_path = Path(__file__).parent.parent / "apps" / "backend" / "implementation_plan" / "main.py"
-        content = impl_plan_path.read_text()
-
-        # Check that it re-exports or imports Subtask and SubtaskStatus
-        assert "Subtask" in content, (
-            "implementation_plan/main.py should reference 'Subtask'"
-        )
-        assert "SubtaskStatus" in content, (
-            "implementation_plan/main.py should reference SubtaskStatus enum"
-        )
-
     def test_progress_uses_subtask_terminology(self):
         """Progress module uses subtask terminology."""
         progress_path = Path(__file__).parent.parent / "apps" / "backend" / "core" / "progress.py"
diff --git a/tests/test_spec_complexity.py b/tests/test_spec_complexity.py
index 48b09220..36944477 100644
--- a/tests/test_spec_complexity.py
+++ b/tests/test_spec_complexity.py
@@ -587,18 +587,6 @@ class TestSaveAssessment:
         assert "phases_to_run" in data
         assert "discovery" in data["phases_to_run"]
 
-    def test_saves_dev_mode_flag(self, spec_dir: Path):
-        """Saves dev_mode flag in output."""
-        assessment = ComplexityAssessment(
-            complexity=Complexity.STANDARD,
-            confidence=0.8,
-        )
-
-        save_assessment(spec_dir, assessment, dev_mode=True)
-        data = json.loads((spec_dir / "complexity_assessment.json").read_text())
-
-        assert data["dev_mode"] is True
-
     def test_saves_timestamp(self, spec_dir: Path):
         """Saves created_at timestamp."""
         assessment = ComplexityAssessment(
diff --git a/tests/test_spec_pipeline.py b/tests/test_spec_pipeline.py
index a6778cd9..a606bb31 100644
--- a/tests/test_spec_pipeline.py
+++ b/tests/test_spec_pipeline.py
@@ -122,17 +122,6 @@ class TestGetSpecsDir:
 
             mock_init.assert_called_once_with(temp_dir)
 
-    def test_dev_mode_param_ignored(self, temp_dir: Path):
-        """dev_mode parameter is deprecated and ignored."""
-        with patch('spec.pipeline.init_auto_claude_dir') as mock_init:
-            mock_init.return_value = (temp_dir / ".auto-claude", False)
-
-            result1 = get_specs_dir(temp_dir, dev_mode=False)
-            result2 = get_specs_dir(temp_dir, dev_mode=True)
-
-            assert result1 == result2
-
-
 class TestSpecOrchestratorInit:
     """Tests for SpecOrchestrator initialization."""
 
@@ -574,35 +563,6 @@ class TestComplexityOverride:
             assert orchestrator.use_ai_assessment is False
 
 
-class TestSpecOrchestratorDevMode:
-    """Tests for dev mode configuration."""
-
-    def test_default_dev_mode_false(self, temp_dir: Path):
-        """Dev mode is False by default."""
-        with patch('spec.pipeline.init_auto_claude_dir') as mock_init:
-            mock_init.return_value = (temp_dir / ".auto-claude", False)
-            specs_dir = temp_dir / ".auto-claude" / "specs"
-            specs_dir.mkdir(parents=True, exist_ok=True)
-
-            orchestrator = SpecOrchestrator(project_dir=temp_dir)
-
-            assert orchestrator.dev_mode is False
-
-    def test_enable_dev_mode(self, temp_dir: Path):
-        """Can enable dev mode."""
-        with patch('spec.pipeline.init_auto_claude_dir') as mock_init:
-            mock_init.return_value = (temp_dir / ".auto-claude", False)
-            specs_dir = temp_dir / ".auto-claude" / "specs"
-            specs_dir.mkdir(parents=True, exist_ok=True)
-
-            orchestrator = SpecOrchestrator(
-                project_dir=temp_dir,
-                dev_mode=True,
-            )
-
-            assert orchestrator.dev_mode is True
-
-
 class TestSpecOrchestratorValidator:
     """Tests for SpecValidator integration."""