diff --git a/.claude/settings.json b/.claude/settings.json
index 1d8ef467..971803f1 100644
--- a/.claude/settings.json
+++ b/.claude/settings.json
@@ -7,7 +7,13 @@
     "deny": [
       "EnterPlanMode",
       "Bash(git add -f*)",
-      "Bash(git add --force*)"
+      "Bash(git add --force*)",
+      "Read(/home/patrick/Patrick-Personal/**)",
+      "Edit(/home/patrick/Patrick-Personal/**)",
+      "Write(/home/patrick/Patrick-Personal/**)",
+      "Glob(/home/patrick/Patrick-Personal/**)",
+      "Grep(/home/patrick/Patrick-Personal/**)",
+      "Bash(*Patrick-Personal*)"
     ],
     "defaultMode": "acceptEdits"
   },
diff --git a/src/aipass/ai_mail/apps/handlers/dispatch/wake.py b/src/aipass/ai_mail/apps/handlers/dispatch/wake.py
index 64d29516..6e4aaf80 100644
--- a/src/aipass/ai_mail/apps/handlers/dispatch/wake.py
+++ b/src/aipass/ai_mail/apps/handlers/dispatch/wake.py
@@ -40,6 +40,14 @@ MONITOR_SCRIPT = Path(__file__).parent / "dispatch_monitor.py"
 # Default prompt when no custom message provided
 DEFAULT_PROMPT = "Hi. Check inbox, process new emails, update memories when done."
 
+# Model shorthand mapping
+MODEL_MAP = {
+    "sonnet": "claude-sonnet-4-6",
+    "opus": "claude-opus-4-6",
+    "haiku": "claude-haiku-4-5-20251001",
+}
+DEFAULT_MODEL = "sonnet"
+
 
 # ─── Status Step Tracking ───────────────────────────────
 
@@ -309,14 +317,24 @@ def resolve_branch(branch_email: str) -> Optional[Tuple[Path, str]]:
 
 def wake_branch(branch_email: str, custom_message: Optional[str] = None,
                 fresh: bool = False, auto: bool = False,
-                sender: str = "@devpulse") -> Tuple[DispatchStatus, bool]:
+                sender: str = "@devpulse",
+                model: Optional[str] = None) -> Tuple[DispatchStatus, bool]:
     """
     Spawn a Claude agent at the target branch with step-by-step status.
 
+    Args:
+        branch_email: Target branch email (e.g. "@flow")
+        custom_message: Optional custom prompt (replaces default inbox check)
+        fresh: If True, start fresh session instead of resuming
+        auto: If True, respect autonomous_pause (used by daemon)
+        sender: Return-to-sender for bounce emails
+        model: Model shorthand ("sonnet", "opus", "haiku") or full model ID.
+               Defaults to sonnet (claude-sonnet-4-6).
+
     Returns:
         Tuple of (DispatchStatus with all steps, overall success bool)
     """
-    json_handler.log_operation("wake_branch", {"branch": branch_email, "fresh": fresh, "auto": auto})
+    json_handler.log_operation("wake_branch", {"branch": branch_email, "fresh": fresh, "auto": auto, "model": model or DEFAULT_MODEL})
 
     status = DispatchStatus()
 
@@ -371,6 +389,9 @@ def wake_branch(branch_email: str, custom_message: Optional[str] = None,
     config = _load_config()
     max_turns = config.get("max_turns_per_wake", 100)
 
+    # Resolve model: shorthand -> full ID, or pass through if already a full ID
+    resolved_model = MODEL_MAP.get(model or DEFAULT_MODEL, model or MODEL_MAP[DEFAULT_MODEL])
+
     lock_file_path = str(branch_path / ".ai_mail.local" / ".dispatch.lock")
     if custom_message:
         prompt = f"Hi. {custom_message} "
@@ -382,6 +403,7 @@ def wake_branch(branch_email: str, custom_message: Optional[str] = None,
     if fresh:
         claude_cmd = [
             "claude", "-p", prompt,
+            "--model", resolved_model,
             "--max-turns", str(max_turns),
             "--permission-mode", "bypassPermissions",
             "--output-format", "json"
@@ -389,6 +411,7 @@ def wake_branch(branch_email: str, custom_message: Optional[str] = None,
     else:
         claude_cmd = [
             "claude", "-c", "-p", prompt,
+            "--model", resolved_model,
             "--max-turns", str(max_turns),
             "--permission-mode", "bypassPermissions",
             "--output-format", "json"
@@ -481,13 +504,14 @@ if __name__ == "__main__":
     args = sys.argv[1:]
 
     if not args or args[0] in ("--help", "-h"):
-        print("Usage: wake.py [--fresh] [--auto] [--sender @branch] @branch [\"optional message\"]")
+        print("Usage: wake.py [--fresh] [--auto] [--sender @branch] [--model sonnet|opus] @branch [\"optional message\"]")
         print("  Manually spawn a Claude agent at a branch (daemon not required)")
         print()
         print("Flags:")
         print("  --fresh          Start fresh session (claude -p) instead of resuming (claude -c -p)")
         print("  --auto           Respect autonomous_pause (used by daemon). Manual wake ignores it.")
         print("  --sender @branch Set return-to-sender for bounce emails (default: @devpulse)")
+        print("  --model NAME     Model to use: sonnet (default), opus, haiku, or full model ID")
         print()
         print("Output: Step-by-step status of the dispatch pipeline:")
         print("  ✅ resolve → @branch found at /path/to/branch")
@@ -508,6 +532,7 @@ if __name__ == "__main__":
     use_fresh = "--fresh" in args
     use_auto = "--auto" in args
     use_sender = "@devpulse"
+    use_model = None
 
     if "--sender" in args:
         idx = args.index("--sender")
@@ -515,6 +540,12 @@ if __name__ == "__main__":
             use_sender = args[idx + 1]
             args = args[:idx] + args[idx + 2:]
 
+    if "--model" in args:
+        idx = args.index("--model")
+        if idx + 1 < len(args):
+            use_model = args[idx + 1]
+            args = args[:idx] + args[idx + 2:]
+
     args = [a for a in args if a not in ("--fresh", "--auto")]
 
     if not args:
@@ -525,7 +556,8 @@ if __name__ == "__main__":
     message = args[1] if len(args) > 1 else None
 
     dispatch_status, success = wake_branch(
-        branch, message, fresh=use_fresh, auto=use_auto, sender=use_sender
+        branch, message, fresh=use_fresh, auto=use_auto, sender=use_sender,
+        model=use_model
     )
     print(dispatch_status.format())
     sys.exit(0 if success else 1)
diff --git a/src/aipass/ai_mail/apps/modules/dispatch.py b/src/aipass/ai_mail/apps/modules/dispatch.py
index 958c645d..ec6af82c 100644
--- a/src/aipass/ai_mail/apps/modules/dispatch.py
+++ b/src/aipass/ai_mail/apps/modules/dispatch.py
@@ -39,14 +39,21 @@ COMMANDS:
   dispatch wake @branch               - Wake only (no email sent)
 
 DISPATCH (send + wake):
-  drone @ai_mail dispatch @branch "Subject" "Body"          # Send + continue wake
-  drone @ai_mail dispatch @branch "Subject" "Body" --fresh  # Send + fresh wake
+  drone @ai_mail dispatch @branch "Subject" "Body"                    # Send + continue wake
+  drone @ai_mail dispatch @branch "Subject" "Body" --fresh            # Send + fresh wake
+  drone @ai_mail dispatch @branch "Subject" "Body" --model opus       # Send + wake with Opus
   drone @ai_mail dispatch @branch "Subject" "Body" --no-memory-save
 
 WAKE ONLY:
-  drone @ai_mail dispatch wake @branch            # Wake with default inbox check
-  drone @ai_mail dispatch wake @branch "custom"   # Wake with custom prompt
-  drone wake @branch                              # Shortcut via drone
+  drone @ai_mail dispatch wake @branch                       # Wake with default inbox check
+  drone @ai_mail dispatch wake @branch "custom"              # Wake with custom prompt
+  drone @ai_mail dispatch wake @branch --model opus          # Wake with Opus model
+  drone wake @branch                                         # Shortcut via drone
+
+MODEL OPTIONS:
+  --model sonnet   Claude Sonnet 4.6 (default — cost-effective for most tasks)
+  --model opus     Claude Opus 4.6 (complex tasks needing deeper reasoning)
+  --model haiku    Claude Haiku 4.5 (fastest, simplest tasks)
 
 DAEMON:
   The daemon polls branch inboxes for --dispatch emails and spawns agents.
@@ -156,9 +163,10 @@ def _orchestrate_wake(args: List[str]) -> bool:
         console.print("  Or:    drone wake @branch [\"custom message\"]\n")
         return True
 
-    # Parse --fresh and --sender flags
+    # Parse --fresh, --sender, --model flags
     use_fresh = "--fresh" in args
     use_sender = "@devpulse"
+    use_model = None
     filtered = []
     i = 0
     while i < len(args):
@@ -169,6 +177,10 @@ def _orchestrate_wake(args: List[str]) -> bool:
             use_sender = args[i + 1]
             i += 2
             continue
+        if args[i] == "--model" and i + 1 < len(args):
+            use_model = args[i + 1]
+            i += 2
+            continue
         filtered.append(args[i])
         i += 1
 
@@ -184,7 +196,8 @@ def _orchestrate_wake(args: List[str]) -> bool:
 
     from aipass.ai_mail.apps.handlers.dispatch.wake import wake_branch
     dispatch_status, success = wake_branch(
-        branch_email, custom_message, fresh=use_fresh, sender=use_sender
+        branch_email, custom_message, fresh=use_fresh, sender=use_sender,
+        model=use_model
     )
 
     # Print step-by-step status
@@ -199,6 +212,7 @@ def _orchestrate_dispatch_send(args: List[str]) -> bool:
     use_fresh = False
     no_memory_save = False
     from_branch = None
+    use_model = None
     filtered = []
     i = 0
     while i < len(args):
@@ -214,6 +228,10 @@ def _orchestrate_dispatch_send(args: List[str]) -> bool:
             from_branch = args[i + 1]
             i += 2
             continue
+        if args[i] == "--model" and i + 1 < len(args):
+            use_model = args[i + 1]
+            i += 2
+            continue
         filtered.append(args[i])
         i += 1
 
@@ -293,7 +311,8 @@ def _orchestrate_dispatch_send(args: List[str]) -> bool:
     from aipass.ai_mail.apps.handlers.dispatch.wake import wake_branch
     dispatch_status, wake_ok = wake_branch(
         target, fresh=use_fresh,
-        sender=user_info.get("email_address", "@ai_mail")
+        sender=user_info.get("email_address", "@ai_mail"),
+        model=use_model
     )
     console.print(dispatch_status.format())
 
diff --git a/src/aipass/ai_mail/tests/test_wake.py b/src/aipass/ai_mail/tests/test_wake.py
index 7cebc7b4..e5d0e214 100644
--- a/src/aipass/ai_mail/tests/test_wake.py
+++ b/src/aipass/ai_mail/tests/test_wake.py
@@ -434,3 +434,28 @@ def _fake_open_factory(real_status_path, mapping):
             return _real_open(mapping[path_str], *args, **kwargs)
         return _real_open(path, *args, **kwargs)
     return _fake_open
+
+
+# --- Model flag tests ---------------------------------------------------
+
+from aipass.ai_mail.apps.handlers.dispatch.wake import MODEL_MAP, DEFAULT_MODEL
+
+
+def test_model_map_has_expected_entries():
+    """MODEL_MAP should contain sonnet, opus, haiku shorthand mappings."""
+    assert "sonnet" in MODEL_MAP
+    assert "opus" in MODEL_MAP
+    assert "haiku" in MODEL_MAP
+    assert "claude-sonnet-4-6" in MODEL_MAP["sonnet"]
+    assert "claude-opus-4-6" in MODEL_MAP["opus"]
+
+
+def test_default_model_is_sonnet():
+    """Default model should be sonnet."""
+    assert DEFAULT_MODEL == "sonnet"
+
+
+def test_model_map_values_are_full_ids():
+    """All MODEL_MAP values should be full claude model IDs."""
+    for key, value in MODEL_MAP.items():
+        assert value.startswith("claude-"), f"{key} -> {value} doesn't start with 'claude-'"
diff --git a/src/aipass/cli/apps/handlers/init/bootstrap.py b/src/aipass/cli/apps/handlers/init/bootstrap.py
index b130813e..6ac3f20b 100644
--- a/src/aipass/cli/apps/handlers/init/bootstrap.py
+++ b/src/aipass/cli/apps/handlers/init/bootstrap.py
@@ -331,6 +331,19 @@ def _claude_settings() -> str:
     ) + "\n"
 
 
+def _with_source(content: str, file_path: Path) -> str:
+    """Prepend a source header to AI prompt file content.
+
+    Args:
+        content: The file content to annotate.
+        file_path: The absolute path where the file will be written.
+
+    Returns:
+        Content with ``<!-- Source: {file_path} -->`` as the first line.
+    """
+    return f"<!-- Source: {file_path} -->\n{content}"
+
+
 def init_project(target: Path, project_name: str | None = None) -> dict:
     """Initialize an AIPass project in the target directory.
 
@@ -391,25 +404,37 @@ def init_project(target: Path, project_name: str | None = None) -> dict:
 
     global_prompt_path = aipass_dir / "aipass_global_prompt.md"
     if not global_prompt_path.exists():
-        global_prompt_path.write_text(_global_prompt_md(name), encoding="utf-8")
+        global_prompt_path.write_text(
+            _with_source(_global_prompt_md(name), global_prompt_path),
+            encoding="utf-8",
+        )
         created.append(str(global_prompt_path))
 
     # 3. CLAUDE.md
     claude_md_path = target / "CLAUDE.md"
     if not claude_md_path.exists():
-        claude_md_path.write_text(_claude_md(name), encoding="utf-8")
+        claude_md_path.write_text(
+            _with_source(_claude_md(name), claude_md_path),
+            encoding="utf-8",
+        )
         created.append(str(claude_md_path))
 
     # 4. AGENTS.md (Codex)
     agents_md_path = target / "AGENTS.md"
     if not agents_md_path.exists():
-        agents_md_path.write_text(_agents_md(name), encoding="utf-8")
+        agents_md_path.write_text(
+            _with_source(_agents_md(name), agents_md_path),
+            encoding="utf-8",
+        )
         created.append(str(agents_md_path))
 
     # 5. GEMINI.md
     gemini_md_path = target / "GEMINI.md"
     if not gemini_md_path.exists():
-        gemini_md_path.write_text(_gemini_md(name), encoding="utf-8")
+        gemini_md_path.write_text(
+            _with_source(_gemini_md(name), gemini_md_path),
+            encoding="utf-8",
+        )
         created.append(str(gemini_md_path))
 
     # 6. README.md
@@ -467,3 +492,93 @@ def init_project(target: Path, project_name: str | None = None) -> dict:
         "target": str(target),
         "created_files": created,
     }
+
+
+def update_project(target: Path) -> dict:
+    """Update managed scaffold files in an existing AIPass project.
+
+    Overwrites managed prompt and config files with the latest templates while
+    leaving all user-owned files (registry, README, STATUS.local.md, .gitignore,
+    hooks/, src/) untouched.
+
+    Args:
+        target: Directory containing the AIPass project to update.
+
+    Returns:
+        dict with project_name, target, updated_files, skipped_files.
+
+    Raises:
+        ValueError: If no ``*_REGISTRY.json`` is found in target (not an AIPass
+            project or init has not been run yet).
+    """
+    target = target.resolve()
+
+    # Locate the project registry to confirm this is an AIPass project and
+    # derive the project name without parsing JSON (filename encodes the name).
+    registry_files = list(target.glob("*_REGISTRY.json"))
+    if not registry_files:
+        raise ValueError(
+            "No AIPass project found — run 'aipass init' first"
+        )
+    registry_path = registry_files[0]
+    name = registry_path.stem.replace("_REGISTRY", "")
+
+    updated: list[str] = []
+    skipped: list[str] = []
+
+    # Managed directories — create if missing (graceful recovery).
+    aipass_dir = target / ".aipass"
+    aipass_dir.mkdir(exist_ok=True)
+
+    claude_dir = target / ".claude"
+    claude_dir.mkdir(exist_ok=True)
+
+    # --- Managed files: always overwrite with latest templates ---
+
+    global_prompt_path = aipass_dir / "aipass_global_prompt.md"
+    global_prompt_path.write_text(
+        _with_source(_global_prompt_md(name), global_prompt_path),
+        encoding="utf-8",
+    )
+    updated.append(str(global_prompt_path))
+
+    settings_path = claude_dir / "settings.json"
+    settings_path.write_text(_claude_settings(), encoding="utf-8")
+    updated.append(str(settings_path))
+
+    claude_md_path = target / "CLAUDE.md"
+    claude_md_path.write_text(
+        _with_source(_claude_md(name), claude_md_path),
+        encoding="utf-8",
+    )
+    updated.append(str(claude_md_path))
+
+    agents_md_path = target / "AGENTS.md"
+    agents_md_path.write_text(
+        _with_source(_agents_md(name), agents_md_path),
+        encoding="utf-8",
+    )
+    updated.append(str(agents_md_path))
+
+    gemini_md_path = target / "GEMINI.md"
+    gemini_md_path.write_text(
+        _with_source(_gemini_md(name), gemini_md_path),
+        encoding="utf-8",
+    )
+    updated.append(str(gemini_md_path))
+
+    # --- User-owned files: always skip ---
+    for skip_name in (
+        str(registry_path),
+        str(target / "README.md"),
+        str(target / "STATUS.local.md"),
+        str(target / ".gitignore"),
+    ):
+        skipped.append(skip_name)
+
+    return {
+        "project_name": name,
+        "target": str(target),
+        "updated_files": updated,
+        "skipped_files": skipped,
+    }
diff --git a/src/aipass/cli/apps/modules/init_project.py b/src/aipass/cli/apps/modules/init_project.py
index f8c50135..d6b45239 100644
--- a/src/aipass/cli/apps/modules/init_project.py
+++ b/src/aipass/cli/apps/modules/init_project.py
@@ -21,7 +21,7 @@ import sys
 from pathlib import Path
 from typing import List
 
-from aipass.cli.apps.handlers.init.bootstrap import init_project
+from aipass.cli.apps.handlers.init.bootstrap import init_project, update_project
 from aipass.cli.apps.modules.display import console, success, error, header
 from aipass.cli.apps.handlers.json import json_handler
 from aipass.prax.apps.modules.logger import system_logger as logger
@@ -56,6 +56,11 @@ def print_introspection():
         "Create an agent in current project",
         "drone @cli aipass init agent my_agent",
     )
+    table.add_row(
+        "init update",
+        "Refresh managed scaffold files",
+        "drone @cli aipass init update",
+    )
 
     console.print(table)
     console.print()
@@ -93,6 +98,7 @@ def print_help():
     console.print("  [green]drone @cli aipass init /path[/green]            [dim]Bootstrap in target directory[/dim]")
     console.print("  [green]drone @cli aipass init /path MyProj[/green]     [dim]Bootstrap with custom name[/dim]")
     console.print("  [green]drone @cli aipass init agent <name>[/green]     [dim]Create an agent in current project[/dim]")
+    console.print("  [green]drone @cli aipass init update[/green]           [dim]Refresh managed scaffold files[/dim]")
     console.print("  [green]drone @cli aipass --help[/green]                [dim]This help message[/dim]")
     console.print()
     console.print("─" * 70)
@@ -159,6 +165,10 @@ def handle_command(command: str, args: List[str]) -> bool:
     if command == "init":
         return _handle_init(args)
 
+    # Direct subcommand shortcut: command="update" → treated as 'init update'
+    if command == "update":
+        return _handle_init(["update"] + args)
+
     # Prefixed command: 'drone @cli aipass init' → command="aipass"
     if command != "aipass":
         return False
@@ -195,6 +205,10 @@ def _handle_init(args: List[str]) -> bool:
         _print_init_help()
         return True
 
+    # Route 'init update' to update handler
+    if args and args[0] == "update":
+        return _handle_init_update(args[1:])
+
     # Route 'init agent <name>' to spawn
     if args and args[0] == "agent":
         return _handle_init_agent(args[1:])
@@ -307,6 +321,95 @@ def _handle_init_agent(args: List[str]) -> bool:
         return True
 
 
+def _handle_init_update(args: List[str]) -> bool:
+    """Handle 'aipass init update' — refresh managed scaffold files."""
+    from rich.panel import Panel
+    from rich.table import Table
+    from rich import box
+
+    if not args or args[0] in ("--help", "-h", "help"):
+        console.print()
+        header("aipass init update — Refresh Scaffold Files")
+        console.print("[dim]Updates managed prompt and config files with the latest templates[/dim]")
+        console.print()
+        console.print("[bold cyan]Usage:[/bold cyan]")
+        console.print("  [green]drone @cli aipass init update[/green]             [dim]Update current directory[/dim]")
+        console.print("  [green]drone @cli aipass init update /path/to/dir[/green]  [dim]Update target directory[/dim]")
+        console.print()
+        console.print("[bold cyan]What gets updated:[/bold cyan]")
+        console.print("  .aipass/aipass_global_prompt.md, .claude/settings.json")
+        console.print("  CLAUDE.md, AGENTS.md, GEMINI.md")
+        console.print()
+        console.print("[bold cyan]What is never touched:[/bold cyan]")
+        console.print("  *_REGISTRY.json, README.md, STATUS.local.md, .gitignore, hooks/, src/")
+        console.print()
+        console.print("[dim]Commands: init update, init update --help[/dim]")
+        console.print()
+        return True
+
+    caller_cwd = os.environ.get("AIPASS_CALLER_CWD", os.getcwd())
+    target_arg = args[0]
+    target = Path(target_arg)
+    if not target.is_absolute():
+        target = Path(caller_cwd) / target
+
+    try:
+        result = update_project(target)
+    except ValueError as exc:
+        logger.warning("Init update validation error: %s", exc)
+        error(str(exc), suggestion="Run 'aipass init' first to create the project")
+        sys.exit(1)
+    except OSError as exc:
+        logger.error("Init update filesystem error: %s", exc)
+        error(f"Filesystem error: {exc}")
+        sys.exit(1)
+
+    # Display results
+    console.print()
+    header("Project Updated")
+
+    summary = (
+        f"[bold]{result['project_name']}[/bold]\n"
+        f"\n"
+        f"  [yellow]Target:[/yellow]   [dim]{result['target']}[/dim]\n"
+        f"  [yellow]Updated:[/yellow]  {len(result['updated_files'])} files\n"
+        f"  [yellow]Skipped:[/yellow]  {len(result['skipped_files'])} files"
+    )
+    console.print(Panel(summary, border_style="green", box=box.ROUNDED))
+
+    # Updated files table
+    updated_table = Table(
+        show_header=True, header_style="bold cyan", border_style="dim", title="Updated"
+    )
+    updated_table.add_column("#", style="green", width=3)
+    updated_table.add_column("File", style="yellow")
+    for i, f in enumerate(result["updated_files"], 1):
+        updated_table.add_row(str(i), f)
+    console.print(updated_table)
+
+    # Skipped files table
+    skipped_table = Table(
+        show_header=True, header_style="bold cyan", border_style="dim", title="Skipped"
+    )
+    skipped_table.add_column("#", style="dim", width=3)
+    skipped_table.add_column("File", style="dim")
+    for i, f in enumerate(result["skipped_files"], 1):
+        skipped_table.add_row(str(i), f)
+    console.print(skipped_table)
+    console.print()
+
+    success(f"Updated {len(result['updated_files'])} files")
+
+    json_handler.log_operation("aipass_init_update", {
+        "project_name": result["project_name"],
+        "target": result["target"],
+        "files_updated": len(result["updated_files"]),
+        "files_skipped": len(result["skipped_files"]),
+    })
+
+    return True
+
+
 def _print_init_help():
     """Display detailed help for the init subcommand."""
     from rich.panel import Panel
@@ -330,6 +433,8 @@ def _print_init_help():
     usage_table.add_row("drone @cli aipass init", "Initialize in current directory")
     usage_table.add_row("drone @cli aipass init /path/to/dir", "Initialize in target directory")
     usage_table.add_row("drone @cli aipass init /path MyProj", "Initialize with custom project name")
+    usage_table.add_row("drone @cli aipass init update", "Refresh managed scaffold files")
+    usage_table.add_row("drone @cli aipass init update /path", "Refresh scaffold in target directory")
     console.print(usage_table)
     console.print()
     console.print("─" * 70)
diff --git a/src/aipass/spawn/apps/handlers/registry.py b/src/aipass/spawn/apps/handlers/registry.py
index 18739c14..b45a501d 100644
--- a/src/aipass/spawn/apps/handlers/registry.py
+++ b/src/aipass/spawn/apps/handlers/registry.py
@@ -12,6 +12,7 @@ import os
 from datetime import datetime
 from pathlib import Path
 
+from aipass.prax.apps.modules.logger import system_logger as logger
 from aipass.spawn.apps.handlers.json import json_handler
 
 
@@ -212,3 +213,57 @@ def add_to_registry(registry_path, branch_name, branch_path, profile, email, pur
     json_handler.log_operation("registry_updated", data={"branch": branch_name})
 
     return save_registry(registry_path, registry)
+
+
+def fix_passport_registry_id(branch_dir: Path, registry_path: Path) -> bool:
+    """Update passport.json registry_id if it doesn't match the current registry.
+
+    Call when adopting an existing agent or during sync-registry --fix to repair
+    registry_id mismatches caused by registry recreation.
+
+    Args:
+        branch_dir: Path to the branch directory (containing .trinity/passport.json)
+        registry_path: Path to the project registry (*_REGISTRY.json)
+
+    Returns:
+        True if passport was updated, False if already correct or failed.
+    """
+    passport_path = branch_dir / ".trinity" / "passport.json"
+    if not passport_path.exists():
+        return False
+    if not registry_path.exists():
+        return False
+
+    try:
+        registry_data = json_handler.read_json(registry_path)
+        if registry_data is None:
+            return False
+        current_id = registry_data.get("metadata", {}).get("id", "")
+    except Exception as e:
+        logger.warning("[registry] Cannot read registry_id from %s: %s", registry_path.name, e)
+        return False
+
+    if not current_id:
+        return False
+
+    try:
+        passport = json_handler.read_json(passport_path)
+        if passport is None:
+            return False
+        old_id = passport.get("citizenship", {}).get("registry_id", "")
+        if old_id == current_id:
+            return False  # Already correct, no update needed
+
+        passport.setdefault("citizenship", {})["registry_id"] = current_id
+        success = json_handler.write_json(passport_path, passport)
+        if success:
+            logger.info(
+                "[registry] Fixed registry_id for %s: %s → %s",
+                branch_dir.name,
+                old_id[:8] if old_id else "empty",
+                current_id[:8],
+            )
+        return success
+    except Exception as e:
+        logger.warning("[registry] Failed to fix registry_id for %s: %s", branch_dir.name, e)
+        return False
diff --git a/src/aipass/spawn/apps/handlers/sync_registry_ops.py b/src/aipass/spawn/apps/handlers/sync_registry_ops.py
index 7c413518..71939f3b 100644
--- a/src/aipass/spawn/apps/handlers/sync_registry_ops.py
+++ b/src/aipass/spawn/apps/handlers/sync_registry_ops.py
@@ -27,6 +27,7 @@ from aipass.spawn.apps.handlers.registry import (
     load_registry,
     save_registry,
     _branches_as_list,
+    fix_passport_registry_id,
 )
 from aipass.spawn.apps.handlers.meta_ops import (
     load_template_registry,
@@ -243,6 +244,17 @@ def sync_registry(fix: bool = False) -> dict:
                     spawn_rebuilt.append(name)
                     logger.info(f"[sync-registry] Rebuilt .spawn/ for: {name}")
 
+    # Fix registry_id mismatches in passports for all known branches
+    ids_fixed = []
+    if fix:
+        all_known = list(healthy) + list(unregistered_list)
+        for name in all_known:
+            branch_path = filesystem_branches.get(name)
+            if branch_path:
+                was_fixed = fix_passport_registry_id(branch_path, registry_path)
+                if was_fixed:
+                    ids_fixed.append(name)
+
     json_handler.log_operation("registry_scanned")
 
     return {
@@ -251,4 +263,5 @@ def sync_registry(fix: bool = False) -> dict:
         "healthy": healthy,
         "fixed": fixed,
         "spawn_rebuilt": spawn_rebuilt,
+        "ids_fixed": ids_fixed,
     }
diff --git a/src/aipass/spawn/apps/modules/core.py b/src/aipass/spawn/apps/modules/core.py
index d14eeff5..25c2b122 100644
--- a/src/aipass/spawn/apps/modules/core.py
+++ b/src/aipass/spawn/apps/modules/core.py
@@ -35,7 +35,7 @@ from aipass.spawn.apps.handlers.metadata import get_branch_name, normalize_branc
 from aipass.spawn.apps.handlers.placeholders import build_replacements_dict, validate_no_placeholders
 from aipass.spawn.apps.handlers.file_ops import copy_template, rename_placeholder_paths, regenerate_template_registry, ensure_directory
 from aipass.spawn.apps.handlers.meta_ops import load_template_registry, generate_branch_meta, save_branch_meta
-from aipass.spawn.apps.handlers.registry import find_registry, add_to_registry, get_next_citizen_number
+from aipass.spawn.apps.handlers.registry import find_registry, add_to_registry, get_next_citizen_number, fix_passport_registry_id
 from aipass.spawn.apps.handlers.class_registry import (
     get_template_dir as _get_template_dir,
     validate_class as validate_class,
@@ -230,9 +230,13 @@ def _spawn_agent(target_path, role="", traits="", purpose="", profile=None,
 def _adopt_existing(target, purpose, profile, registry_path):
     """Register an existing directory that already has a passport.
 
-    Used when 'aipass init agent' targets a directory the user already
+    Enhanced to also:
+    - Fix registry_id mismatch in passport (caused by registry recreation)
+    - Run template update to sync scaffolding files
+
+    Used when 'spawn create @existing' targets a directory the user already
     moved code into. Instead of failing with "Target already exists",
-    we register it in the project registry.
+    we register it and sync its template files.
 
     Args:
         target: Path to the existing directory with .trinity/passport.json
@@ -262,6 +266,9 @@ def _adopt_existing(target, purpose, profile, registry_path):
             logger.warning("Failed to read passport for purpose: %s", e)
             purpose = "Adopted agent"
 
+    # Fix registry_id in passport if it doesn't match the current registry
+    fix_passport_registry_id(target, reg_path)
+
     # Store path relative to registry location
     try:
         registry_branch_path = str(target.relative_to(reg_path.parent))
@@ -277,11 +284,24 @@ def _adopt_existing(target, purpose, profile, registry_path):
     json_handler.log_operation("branch_adopted", data={"branch": branch_upper})
     logger.info("[spawn] Adopted existing branch: %s (registered in %s)", branch_upper, reg_path.name)
 
+    # Run template update to sync scaffolding files.
+    # Preserves: .trinity/, .ai_mail.local/, memories, all .py files.
+    # Only adds missing template files and merges JSON configs.
+    update_additions = 0
+    try:
+        from aipass.spawn.apps.handlers.update_ops import update_branch
+        update_result = update_branch(branch_lower)
+        update_additions = update_result.get("additions", 0)
+        if update_result.get("errors"):
+            logger.warning("[spawn] Template update had errors for %s: %s", branch_upper, update_result["errors"])
+    except Exception as exc:
+        logger.warning("[spawn] Template update failed for %s (adoption succeeded): %s", branch_upper, exc)
+
     return {
         "success": True,
         "branch_name": branch_upper,
         "path": str(target),
-        "files_copied": 0,
+        "files_copied": update_additions,
         "dirs_created": 0,
         "files_skipped": 0,
         "renamed": [],
diff --git a/src/aipass/spawn/apps/modules/sync_registry.py b/src/aipass/spawn/apps/modules/sync_registry.py
index 70ccf452..e9e5f5d7 100644
--- a/src/aipass/spawn/apps/modules/sync_registry.py
+++ b/src/aipass/spawn/apps/modules/sync_registry.py
@@ -134,9 +134,12 @@ def _print_summary(result: dict) -> None:
         console.print("  [green]No unregistered branches[/green]")
 
     # Fix status
-    if fixed:
+    ids_fixed = result.get("ids_fixed", [])
+    if fixed or ids_fixed:
         console.print()
         console.print("  [green]Registry has been repaired.[/green]")
+        if ids_fixed:
+            console.print(f"  [green]Fixed registry_id in {len(ids_fixed)} passport(s): {', '.join(sorted(ids_fixed))}[/green]")
     elif stale or unregistered:
         console.print()
         console.print("  [dim]Run with --fix to auto-repair.[/dim]")
diff --git a/src/aipass/spawn/tests/test_lifecycle.py b/src/aipass/spawn/tests/test_lifecycle.py
index d06ee40a..c263a5e4 100644
--- a/src/aipass/spawn/tests/test_lifecycle.py
+++ b/src/aipass/spawn/tests/test_lifecycle.py
@@ -525,6 +525,192 @@ class TestAdoptExisting:
         entry = next(b for b in reg["branches"] if b["name"] == "SMART_AGENT")
         assert entry["description"] == "Process reports daily"
 
+    def test_adopt_existing_fixes_registry_id(self, tmp_path):
+        """Adoption fixes mismatched registry_id in passport."""
+        from aipass.spawn.apps.modules.core import _spawn_agent
+
+        agent = tmp_path / "id_agent"
+        agent.mkdir()
+        (agent / ".trinity").mkdir()
+        (agent / ".trinity" / "passport.json").write_text(json.dumps({
+            "branch_info": {"branch_name": "id_agent"},
+            "identity": {"citizen_class": "builder", "purpose": "Test"},
+            "citizenship": {"registry_id": "old-uuid-1234"},
+        }))
+
+        reg_path = tmp_path / "TEST_REGISTRY.json"
+        reg_path.write_text(json.dumps({
+            "metadata": {
+                "id": "new-uuid-5678",
+                "version": "1.0.0",
+                "last_updated": "2026-04-11",
+                "total_branches": 0,
+            },
+            "branches": [],
+        }))
+
+        result = _spawn_agent(str(agent), registry_path=str(reg_path))
+
+        assert result["success"] is True
+        passport = json.loads((agent / ".trinity" / "passport.json").read_text())
+        assert passport["citizenship"]["registry_id"] == "new-uuid-5678"
+
+    def test_adopt_skips_registry_id_fix_when_already_correct(self, tmp_path):
+        """Adoption does not modify passport when registry_id already matches."""
+        from aipass.spawn.apps.modules.core import _spawn_agent
+
+        agent = tmp_path / "matched_agent"
+        agent.mkdir()
+        (agent / ".trinity").mkdir()
+        (agent / ".trinity" / "passport.json").write_text(json.dumps({
+            "branch_info": {"branch_name": "matched_agent"},
+            "identity": {"citizen_class": "builder", "purpose": "Test"},
+            "citizenship": {"registry_id": "correct-uuid-9999"},
+        }))
+
+        reg_path = tmp_path / "TEST_REGISTRY.json"
+        reg_path.write_text(json.dumps({
+            "metadata": {
+                "id": "correct-uuid-9999",
+                "version": "1.0.0",
+                "last_updated": "2026-04-11",
+                "total_branches": 0,
+            },
+            "branches": [],
+        }))
+
+        # Get mtime before adoption to detect writes
+        before_mtime = (agent / ".trinity" / "passport.json").stat().st_mtime
+
+        result = _spawn_agent(str(agent), registry_path=str(reg_path))
+
+        assert result["success"] is True
+        after_mtime = (agent / ".trinity" / "passport.json").stat().st_mtime
+        # File should NOT have been rewritten (ids already match)
+        assert before_mtime == after_mtime
+
+
+# ---------------------------------------------------------------------------
+# FIX PASSPORT REGISTRY ID Tests
+# ---------------------------------------------------------------------------
+
+class TestFixPassportRegistryId:
+    """Tests for fix_passport_registry_id() in registry.py."""
+
+    def test_fixes_mismatched_id(self, tmp_path):
+        """Updates passport when registry_id doesn't match."""
+        from aipass.spawn.apps.handlers.registry import fix_passport_registry_id
+
+        branch = tmp_path / "myagent"
+        branch.mkdir()
+        (branch / ".trinity").mkdir()
+        (branch / ".trinity" / "passport.json").write_text(json.dumps({
+            "citizenship": {"registry_id": "old-id"},
+        }))
+
+        reg = tmp_path / "TEST_REGISTRY.json"
+        reg.write_text(json.dumps({"metadata": {"id": "new-id"}, "branches": []}))
+
+        result = fix_passport_registry_id(branch, reg)
+
+        assert result is True
+        passport = json.loads((branch / ".trinity" / "passport.json").read_text())
+        assert passport["citizenship"]["registry_id"] == "new-id"
+
+    def test_skips_when_already_correct(self, tmp_path):
+        """Returns False when ids already match (no write needed)."""
+        from aipass.spawn.apps.handlers.registry import fix_passport_registry_id
+
+        branch = tmp_path / "myagent"
+        branch.mkdir()
+        (branch / ".trinity").mkdir()
+        (branch / ".trinity" / "passport.json").write_text(json.dumps({
+            "citizenship": {"registry_id": "same-id"},
+        }))
+
+        reg = tmp_path / "TEST_REGISTRY.json"
+        reg.write_text(json.dumps({"metadata": {"id": "same-id"}, "branches": []}))
+
+        result = fix_passport_registry_id(branch, reg)
+
+        assert result is False
+
+    def test_handles_missing_passport(self, tmp_path):
+        """Returns False gracefully when passport doesn't exist."""
+        from aipass.spawn.apps.handlers.registry import fix_passport_registry_id
+
+        branch = tmp_path / "npassport"
+        branch.mkdir()
+
+        reg = tmp_path / "TEST_REGISTRY.json"
+        reg.write_text(json.dumps({"metadata": {"id": "some-id"}, "branches": []}))
+
+        result = fix_passport_registry_id(branch, reg)
+        assert result is False
+
+    def test_handles_registry_with_no_id(self, tmp_path):
+        """Returns False when registry has no metadata.id."""
+        from aipass.spawn.apps.handlers.registry import fix_passport_registry_id
+
+        branch = tmp_path / "myagent"
+        branch.mkdir()
+        (branch / ".trinity").mkdir()
+        (branch / ".trinity" / "passport.json").write_text(json.dumps({
+            "citizenship": {"registry_id": "old-id"},
+        }))
+
+        reg = tmp_path / "TEST_REGISTRY.json"
+        reg.write_text(json.dumps({"metadata": {}, "branches": []}))  # No id field
+
+        result = fix_passport_registry_id(branch, reg)
+        assert result is False
+
+    def test_sync_registry_fix_repairs_ids(self, tmp_path, monkeypatch):
+        """sync_registry --fix calls fix_passport_registry_id on healthy branches."""
+        from aipass.spawn.apps.handlers.sync_registry_ops import sync_registry
+
+        # Set up a project with one healthy branch that has wrong registry_id
+        project = tmp_path / "project"
+        project.mkdir()
+
+        reg_path = project / "TEST_REGISTRY.json"
+        reg_path.write_text(json.dumps({
+            "metadata": {
+                "id": "correct-uuid-abc",
+                "version": "1.0.0",
+                "last_updated": "2026-04-11",
+                "total_branches": 1,
+            },
+            "branches": [
+                {
+                    "name": "MYAGENT",
+                    "path": "myagent",
+                    "profile": "library",
+                    "description": "Test",
+                    "email": "@myagent",
+                    "status": "active",
+                    "created": "2026-04-11",
+                    "last_active": "2026-04-11",
+                }
+            ],
+        }))
+
+        agent_dir = project / "myagent"
+        agent_dir.mkdir()
+        (agent_dir / ".trinity").mkdir()
+        passport_path = agent_dir / ".trinity" / "passport.json"
+        passport_path.write_text(json.dumps({
+            "citizenship": {"registry_id": "old-stale-uuid"},
+        }))
+
+        monkeypatch.chdir(project)
+
+        result = sync_registry(fix=True)
+
+        assert "myagent" in result.get("ids_fixed", [])
+        passport = json.loads(passport_path.read_text())
+        assert passport["citizenship"]["registry_id"] == "correct-uuid-abc"
+
 
 # ---------------------------------------------------------------------------
 # SYNC TEMPLATES Tests