feat(system): seedgo v2 operational, full system audit, 14/15 branches at 99%

Three days of intensive work bringing seedgo to full operational status
and driving all branches through comprehensive standards compliance.

Seedgo v2.0.0:
- 22 checkers active (up from 20), standards pack fully operational
- New introspection standard researched from Dev-Pass, FPLAN-0017 open
- Bypass system for false positives (.seedgo config)
- Standards query and audit commands fully functional

System-wide audit (FPLAN-0016):
- All 14 auditable branches at 99%+ compliance
- CLI imports standardized across all branches (console from cli.apps.modules)
- handle_command(command, args) → bool contract added to all modules
- print_help() function naming fixed for checker pattern matching
- Handler extraction: large modules split, file I/O moved to handler layer
- New handlers created across ai_mail, backup, daemon, flow, skills, spawn, seedgo

Branch-specific highlights:
- ai_mail: email.py split 840→420 lines, 4 new handlers
- flow: dplan_flow.py 688→591 lines, 4 new handlers
- seedgo: massive restructure — standards moved to handlers/aipass_standards/,
  old standards/ tree removed, bypass system added, diagnostics module
- commons: database module added, CLI imports fixed
- skills: 5 handle_commands added, help function renamed
- trigger: error reporter handler, handle_command routing
- All branches: consistent architecture, clean drone routing

Culture doc (CLAUDE.md) added — documents AIPass philosophy, identity,
memory system, and collaboration principles.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

src/aipass/spawn/apps/handlers/change_detection.py

@@ -1,4 +1,4 @@
-# =================== META ====================
+# =================== AIPass ====================
 # Name: change_detection.py
 # Description: Template change detection — template vs branch metadata
 # Version: 1.0.0

src/aipass/spawn/apps/handlers/class_registry.py

@@ -1,4 +1,4 @@
-# =================== META ====================
+# =================== AIPass ====================
 # Name: class_registry.py
 # Description: Citizen class registry — maps class names to template directories
 # Version: 1.0.0

src/aipass/spawn/apps/handlers/delete_ops.py

@@ -1,4 +1,4 @@
-# =================== META ====================
+# =================== AIPass ====================
 # Name: delete_ops.py
 # Description: Delete handler — implementation logic for branch deletion
 # Version: 1.0.0

src/aipass/spawn/apps/handlers/file_ops.py

@@ -1,4 +1,4 @@
-# =================== META ====================
+# =================== AIPass ====================
 # Name: file_ops.py
 # Description: Template copy and file operations
 # Version: 1.0.0

src/aipass/spawn/apps/handlers/json/json_handler.py

@@ -1,4 +1,4 @@
-# =================== META ====================
+# =================== AIPass ====================
 # Name: json_handler.py
 # Description: JSON file read/write operations for spawn
 # Version: 1.0.0

src/aipass/spawn/apps/handlers/json_ops.py

@@ -1,4 +1,4 @@
-# =================== META ====================
+# =================== AIPass ====================
 # Name: json_ops.py
 # Description: JSON operations — deep merge, migrations, backups
 # Version: 1.0.0

src/aipass/spawn/apps/handlers/meta_ops.py

@@ -1,4 +1,4 @@
-# =================== META ====================
+# =================== AIPass ====================
 # Name: meta_ops.py
 # Description: Branch metadata operations for update tracking
 # Version: 1.0.0

src/aipass/spawn/apps/handlers/metadata.py

@@ -1,4 +1,4 @@
-# =================== META ====================
+# =================== AIPass ====================
 # Name: metadata.py
 # Description: Branch name extraction and profile detection
 # Version: 1.0.0

src/aipass/spawn/apps/handlers/passport_ops.py

@@ -1,4 +1,4 @@
-# =================== META ====================
+# =================== AIPass ====================
 # Name: passport_ops.py
 # Description: Passport command — grants birthright citizenship to a directory
 # Version: 1.0.0

src/aipass/spawn/apps/handlers/placeholders.py

@@ -1,4 +1,4 @@
-# =================== META ====================
+# =================== AIPass ====================
 # Name: placeholders.py
 # Description: Placeholder replacement engine
 # Version: 1.0.0

src/aipass/spawn/apps/handlers/reconcile.py

@@ -1,4 +1,4 @@
-# =================== META ====================
+# =================== AIPass ====================
 # Name: reconcile.py
 # Description: Branch state reconciliation — filesystem vs metadata
 # Version: 1.0.0

src/aipass/spawn/apps/handlers/registry.py

@@ -1,4 +1,4 @@
-# =================== META ====================
+# =================== AIPass ====================
 # Name: registry.py
 # Description: AIPASS_REGISTRY.json CRUD operations
 # Version: 1.0.0

src/aipass/spawn/apps/handlers/sync_registry_ops.py

@@ -1,4 +1,4 @@
-# =================== META ====================
+# =================== AIPass ====================
 # Name: sync_registry_ops.py
 # Description: Registry sync handler — implementation logic for registry repair
 # Version: 1.0.0
@@ -25,6 +25,13 @@ from aipass.spawn.apps.handlers.registry import (
     save_registry,
     _branches_as_list,
 )
+from aipass.spawn.apps.handlers.meta_ops import (
+    load_template_registry,
+    generate_branch_meta,
+    save_branch_meta,
+)
+from aipass.spawn.apps.handlers.file_ops import regenerate_template_registry
+from aipass.spawn.apps.handlers.class_registry import get_template_dir
 
 # Repo root — resolved from spawn package location
 _REPO_ROOT = Path(__file__).parents[5]  # handlers/apps/spawn/aipass/src/AIPass
@@ -158,9 +165,51 @@ def sync_registry(fix: bool = False) -> dict:
         else:
             logger.error("[sync-registry] Failed to save updated registry")
 
+    # Rebuild .spawn/ tracking for branches missing metadata
+    spawn_rebuilt = []
+    if fix:
+        for name in healthy + unregistered_list:
+            branch_path = filesystem_branches.get(name)
+            if not branch_path:
+                continue
+
+            # Check/rebuild .spawn/.template_registry.json
+            spawn_dir = branch_path / ".spawn"
+            spawn_dir.mkdir(exist_ok=True)
+            template_reg_path = spawn_dir / ".template_registry.json"
+            if not template_reg_path.exists():
+                regenerate_template_registry(branch_path)
+
+            # Check/rebuild .spawn/.branch_meta.json
+            branch_meta_path = spawn_dir / ".branch_meta.json"
+            if not branch_meta_path.exists():
+                # Determine citizen class from passport
+                passport_path = branch_path / ".trinity" / "passport.json"
+                citizen_class = "builder"  # default
+                if passport_path.exists():
+                    try:
+                        passport = json.loads(passport_path.read_text(encoding="utf-8"))
+                        citizen_class = passport.get("identity", {}).get("citizen_class", "builder")
+                    except (json.JSONDecodeError, IOError):
+                        pass
+
+                # Load template registry for that class (fall back to builder if unknown)
+                try:
+                    template_dir = get_template_dir(citizen_class)
+                except ValueError:
+                    logger.warning(f"[sync-registry] Unknown class '{citizen_class}' for {name}, falling back to builder")
+                    template_dir = get_template_dir("builder")
+                template_registry = load_template_registry(template_dir)
+                if template_registry:
+                    branch_meta = generate_branch_meta(branch_path, template_registry)
+                    save_branch_meta(branch_path, branch_meta)
+                    spawn_rebuilt.append(name)
+                    logger.info(f"[sync-registry] Rebuilt .spawn/ for: {name}")
+
     return {
         "stale": stale,
         "unregistered": unregistered_list,
         "healthy": healthy,
         "fixed": fixed,
+        "spawn_rebuilt": spawn_rebuilt,
     }

src/aipass/spawn/apps/handlers/sync_templates_ops.py

@@ -1,4 +1,4 @@
-# =================== META ====================
+# =================== AIPass ====================
 # Name: sync_templates_ops.py
 # Description: Template sync handler — implementation logic for template sync
 # Version: 1.0.0

src/aipass/spawn/apps/handlers/update_ops.py

@@ -1,4 +1,4 @@
-# =================== META ====================
+# =================== AIPass ====================
 # Name: update_ops.py
 # Description: Update handler — implementation logic for branch updates
 # Version: 1.0.0

src/aipass/spawn/apps/modules/core.py

@@ -1,4 +1,4 @@
-# =================== META ====================
+# =================== AIPass ====================
 # Name: core.py
 # Description: Main orchestrator for agent spawning
 # Version: 1.0.0
@@ -23,15 +23,46 @@ from pathlib import Path
 from typing import List
 
 from aipass.prax import logger
+
+try:
+    from aipass.cli.apps.modules.display import console
+except ImportError:
+    from rich.console import Console
+    console = Console()
+
 from aipass.spawn.apps.handlers.metadata import get_branch_name, normalize_branch_name, detect_profile
 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.class_registry import (
+    validate_class,
+    get_default_class,
+    get_available_classes,
+    get_template_dir as _get_template_dir,
+)
 
 # Default template location (relative to spawn package root)
 DEFAULT_TEMPLATE = Path(__file__).parents[2] / "templates" / "builder"
 
 
+def print_introspection():
+    """Display module introspection info."""
+    console.print()
+    console.print("core Module")
+    console.print("Agent creation orchestrator — full spawn workflow from template to registry")
+    console.print()
+    console.print("Connected Handlers:")
+    console.print("  handlers/")
+    console.print("    - metadata.py (get_branch_name, normalize_branch_name, detect_profile — branch identity)")
+    console.print("    - placeholders.py (build_replacements_dict, validate_no_placeholders — template substitution)")
+    console.print("    - file_ops.py (copy_template, rename_placeholder_paths, regenerate_template_registry, ensure_directory — filesystem ops)")
+    console.print("    - meta_ops.py (load_template_registry, generate_branch_meta, save_branch_meta — branch metadata)")
+    console.print("    - registry.py (find_registry, add_to_registry, get_next_citizen_number — AIPASS_REGISTRY management)")
+    console.print("    - class_registry.py (validate_class, get_default_class, get_available_classes, get_template_dir — citizen class lookup)")
+    console.print()
+
+
 def handle_command(command: str, args: List[str]) -> bool:
     """
     Route spawn commands to implementation.
@@ -104,8 +135,7 @@ def _spawn_agent(target_path, role="", traits="", purpose="", profile=None,
     if template_dir:
         template = Path(template_dir)
     else:
-        from aipass.spawn.apps.handlers.class_registry import get_template_dir as _class_get_template_dir
-        template = _class_get_template_dir(citizen_class)
+        template = _get_template_dir(citizen_class)
 
     # Validate
     if target.exists():
@@ -140,6 +170,12 @@ def _spawn_agent(target_path, role="", traits="", purpose="", profile=None,
     # Step 3: Regenerate .template_registry.json with fresh hashes
     regenerate_template_registry(target)
 
+    # Step 3b: Generate branch metadata for tracking
+    template_registry = load_template_registry(target)
+    if template_registry:
+        branch_meta = generate_branch_meta(target, template_registry)
+        save_branch_meta(target, branch_meta)
+
     # Step 4: Register in AIPASS_REGISTRY.json
     registry_updated = add_to_registry(
         reg_path, branch_upper, str(target), detected_profile,

src/aipass/spawn/apps/modules/delete.py

@@ -1,4 +1,4 @@
-# =================== META ====================
+# =================== AIPass ====================
 # Name: delete.py
 # Description: Branch deletion — thin CLI layer for archive and deregister
 # Version: 1.1.0
@@ -19,6 +19,37 @@ from aipass.cli.apps.modules import console
 from aipass.spawn.apps.handlers.delete_ops import delete_branch
 
 
+def print_introspection():
+    """Display module introspection info."""
+    console.print()
+    console.print("delete Module")
+    console.print("Branch deletion — archive directory and deregister from AIPASS_REGISTRY")
+    console.print()
+    console.print("Connected Handlers:")
+    console.print("  handlers/")
+    console.print("    - delete_ops.py (delete_branch — resolve path, archive, remove from registry)")
+    console.print()
+
+
+# =============================================================================
+# DRONE ROUTING
+# =============================================================================
+
+def handle_command(command: str, args: list) -> bool:
+    """Handle commands routed by the entry point.
+
+    Args:
+        command: The command string (e.g. "delete")
+        args: List of arguments for the command
+
+    Returns:
+        True if command was handled, False otherwise.
+    """
+    if command == "delete":
+        return handle_delete(args) == 0
+    return False
+
+
 # =============================================================================
 # PUBLIC API
 # =============================================================================

src/aipass/spawn/apps/modules/passport.py

@@ -1,4 +1,4 @@
-# =================== META ====================
+# =================== AIPass ====================
 # Name: passport.py
 # Description: Passport command — thin CLI layer for granting birthright citizenship
 # Version: 1.0.0
@@ -20,6 +20,33 @@ from aipass.cli.apps.modules import console
 from aipass.spawn.apps.handlers.passport_ops import grant_passport
 
 
+def print_introspection():
+    """Display module introspection info."""
+    console.print()
+    console.print("passport Module")
+    console.print("Grant birthright citizenship — minimal identity (.trinity/, .aipass/, README.md)")
+    console.print()
+    console.print("Connected Handlers:")
+    console.print("  handlers/")
+    console.print("    - passport_ops.py (grant_passport — create minimal citizen identity and register)")
+    console.print()
+
+
+def handle_command(command: str, args: list) -> bool:
+    """Handle commands routed by the entry point.
+
+    Args:
+        command: The command string (e.g. "passport")
+        args: List of arguments for the command
+
+    Returns:
+        True if command was handled, False otherwise.
+    """
+    if command == "passport":
+        return handle_passport(args) == 0
+    return False
+
+
 def handle_passport(args: list[str]) -> int:
     """Parse args and execute passport grant.
 

src/aipass/spawn/apps/modules/sync_registry.py

@@ -1,4 +1,4 @@
-# =================== META ====================
+# =================== AIPass ====================
 # Name: sync_registry.py
 # Description: Registry repair — thin CLI layer for registry synchronization
 # Version: 1.1.0
@@ -19,6 +19,37 @@ from aipass.cli.apps.modules import console
 from aipass.spawn.apps.handlers.sync_registry_ops import sync_registry
 
 
+def print_introspection():
+    """Display module introspection info."""
+    console.print()
+    console.print("sync_registry Module")
+    console.print("Registry repair — detect and fix mismatches between AIPASS_REGISTRY and filesystem")
+    console.print()
+    console.print("Connected Handlers:")
+    console.print("  handlers/")
+    console.print("    - sync_registry_ops.py (sync_registry — scan filesystem, detect stale/unregistered, auto-repair)")
+    console.print()
+
+
+# =============================================================================
+# DRONE ROUTING
+# =============================================================================
+
+def handle_command(command: str, args: list) -> bool:
+    """Handle commands routed by the entry point.
+
+    Args:
+        command: The command string (e.g. "sync-registry")
+        args: List of arguments for the command
+
+    Returns:
+        True if command was handled, False otherwise.
+    """
+    if command == "sync-registry":
+        return handle_sync_registry(args) == 0
+    return False
+
+
 # =============================================================================
 # PUBLIC API
 # =============================================================================

src/aipass/spawn/apps/modules/sync_templates.py

@@ -1,4 +1,4 @@
-# =================== META ====================
+# =================== AIPass ====================
 # Name: sync_templates.py
 # Description: Template sync — thin CLI layer for template synchronization
 # Version: 1.1.0
@@ -19,6 +19,37 @@ from aipass.cli.apps.modules import console
 from aipass.spawn.apps.handlers.sync_templates_ops import sync_templates
 
 
+def print_introspection():
+    """Display module introspection info."""
+    console.print()
+    console.print("sync_templates Module")
+    console.print("Template synchronization — pull managed files from source branches into templates")
+    console.print()
+    console.print("Connected Handlers:")
+    console.print("  handlers/")
+    console.print("    - sync_templates_ops.py (sync_templates — compare hashes and pull updates from source branches)")
+    console.print()
+
+
+# =============================================================================
+# DRONE ROUTING
+# =============================================================================
+
+def handle_command(command: str, args: list) -> bool:
+    """Handle commands routed by the entry point.
+
+    Args:
+        command: The command string (e.g. "sync-templates")
+        args: List of arguments for the command
+
+    Returns:
+        True if command was handled, False otherwise.
+    """
+    if command == "sync-templates":
+        return handle_sync_templates(args) == 0
+    return False
+
+
 # =============================================================================
 # PUBLIC API
 # =============================================================================

src/aipass/spawn/apps/modules/update.py

@@ -1,4 +1,4 @@
-# =================== META ====================
+# =================== AIPass ====================
 # Name: update.py
 # Description: Update orchestrator — thin CLI layer for branch updates
 # Version: 1.1.0
@@ -22,6 +22,37 @@ from aipass.spawn.apps.handlers.update_ops import (
 )
 
 
+def print_introspection():
+    """Display module introspection info."""
+    console.print()
+    console.print("update Module")
+    console.print("Branch updates — sync single or all branches against their class templates")
+    console.print()
+    console.print("Connected Handlers:")
+    console.print("  handlers/")
+    console.print("    - update_ops.py (update_branch, update_all — renames, additions, JSON merges, pruned file archival)")
+    console.print()
+
+
+# =============================================================================
+# DRONE ROUTING
+# =============================================================================
+
+def handle_command(command: str, args: list) -> bool:
+    """Handle commands routed by the entry point.
+
+    Args:
+        command: The command string (e.g. "update")
+        args: List of arguments for the command
+
+    Returns:
+        True if command was handled, False otherwise.
+    """
+    if command == "update":
+        return handle_update(args) == 0
+    return False
+
+
 # =============================================================================
 # PUBLIC API
 # =============================================================================
@@ -50,7 +81,7 @@ def handle_update(args: list[str]) -> int:
         console.print("  [green]--trace[/green]           Enable verbose logging")
         return 1
 
-    from aipass.spawn.apps.handlers.class_registry import validate_class, get_available_classes
+    from aipass.spawn.apps.modules.core import validate_class, get_available_classes
 
     dry_run = "--dry-run" in args
     trace = "--trace" in args

src/aipass/spawn/apps/spawn.py

@@ -1,4 +1,4 @@
-# =================== META ====================
+# =================== AIPass ====================
 # Name: spawn.py
 # Description: Entry point CLI for drone @spawn
 # Version: 1.0.0
@@ -65,7 +65,7 @@ def print_help():
 def handle_create(args):
     """Handle the create command with optional citizen class."""
     from aipass.spawn.apps.modules.core import _spawn_agent as spawn_agent
-    from aipass.spawn.apps.handlers.class_registry import validate_class, get_default_class
+    from aipass.spawn.apps.modules.core import validate_class, get_default_class
 
     if not args:
         console.print("[red]Error: target path required[/red]")
@@ -118,11 +118,32 @@ def handle_create(args):
         return 1
 
 
+def print_introspection():
+    """Display module introspection info."""
+    console.print()
+    console.print("spawn Entry Point")
+    console.print("Branch lifecycle manager — create, update, delete, and sync AIPass branches")
+    console.print()
+    console.print("Connected Modules:")
+    console.print("  modules/")
+    console.print("    - core.py (handle_command, _spawn_agent — agent creation orchestrator)")
+    console.print("    - update.py (handle_update — single/all branch updates)")
+    console.print("    - delete.py (handle_delete — archive and deregister branch)")
+    console.print("    - sync_registry.py (handle_sync_registry — registry repair)")
+    console.print("    - sync_templates.py (handle_sync_templates — template synchronization)")
+    console.print("    - passport.py (handle_passport — grant birthright citizenship)")
+    console.print()
+
+
 def main():
     """Main entry point."""
     args = sys.argv[1:]
 
-    if len(args) == 0 or args[0] in ["--help", "-h", "help"]:
+    if len(args) == 0:
+        print_introspection()
+        return 0
+
+    if args[0] in ["--help", "-h", "help"]:
         print_help()
         return 0
 

src/aipass/spawn/tests/test_citizen_classes.py

@@ -86,7 +86,7 @@ class TestPassportCommand:
         result = grant_passport(str(target), role="tester")
 
         assert result["success"] is True
-        assert (target / ".aipass" / "branch_system_prompt.md").exists()
+        assert (target / ".aipass" / "aipass_local_prompt.md").exists()
 
     def test_grant_passport_creates_readme(self, tmp_path):
         from aipass.spawn.apps.handlers.passport_ops import grant_passport