FPLAN-0410 repo cleanup + integration test bug fixes

VERA cleanup (FPLAN-0410):
- Remove all /home/aipass hardcoded paths (portability)
- Remove internal Telegram bot code from public repo (6k+ lines)
- Remove runtime logs, .claude/settings.local.json, stale files
- Clean READMEs across all branches
- Restructure spawn handlers into proper 3-layer architecture
- Add __init__.py files for proper package imports
- Update seedgo standards for public repo context
- Add log_structure standard to seedgo

Integration test bug fixes:
- Fix double @@ display in drone introspection output
- Fix spawn registry resolving to wrong file (walk up from package root)
- Fix email sender identity always showing as @ai_mail (pass AIPASS_CALLER_CWD)
- Fix branch_detection.py relative path resolution against CWD instead of registry dir
- Add .trinity/passport.json detection for spawned agents
- Archive duplicate json_ops.py, update imports to canonical json_handler
- Update .gitignore for runtime logs and .claude/ dirs

Tested end-to-end in Docker container (aipass-test:latest):
- Spawn → register → send email → receive → reply all verified working

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

src/aipass/cli/.claude/settings.local.json

@@ -1,8 +0,0 @@
-{
-  "permissions": {
-    "allow": [],
-    "deny": [],
-    "ask": []
-  },
-  "enabledMcpjsonServers": []
-}

src/aipass/cli/.seed/bypass.json

@@ -1,7 +1,7 @@
 {
   "metadata": {
     "version": "1.0.0",
-    "created": "2026-03-06T03:16:10.906535",
+    "created": "2026-03-06T14:27:34.810230",
     "description": "Standards bypass configuration for this branch"
   },
   "bypass": [],

src/aipass/cli/README.md

@@ -1,51 +1,50 @@
 # CLI
 
-**Purpose:** Terminal display formatting - headers, success, error, warning helpers
-**Module:** `aipass.cli`
-**Created:** 2026-03-05
+Display and output formatting service for AIPass modules. Provides consistent terminal output — headers, success/error/warning messages, section breaks, and operation templates — so every module looks the same without duplicating Rich formatting code.
 
----
+## Usage
 
-## Overview
+```python
+from aipass.cli import header, success, error, warning, section
 
-### What I Do
+header("Creating Branch", {"Name": "feature", "Type": "module"})
+success("Files created", items=12, time="2.3s")
+error("Path not found", suggestion="Check spelling")
+warning("Config missing, using defaults")
+section("Results")
+```
 
+### Operation Templates
 
-### How I Work
-- **Entry Point:** `apps/cli.py`
-- **Pattern:** Auto-discovers and routes to modules
+```python
+from aipass.cli import operation_start, operation_complete
 
----
+operation_start("Processing", count=10)
+# ... do work ...
+operation_complete(created=5, skipped=3, failed=0)
+```
+
+### Direct Console Access
+
+```python
+from aipass.cli import console
+
+console.print("[bold cyan]Custom Rich output[/bold cyan]")
+```
 
 ## Architecture
 
 ```
-CLI/
+cli/
 ├── apps/
-│   ├── cli.py       # Entry point
-│   ├── modules/            # Business logic
-│   ├── handlers/           # Implementation
-│   └── plugins/            # Extensions
-├── docs/
-├── tests/
-├── passport.json           # Identity
-├── local.json              # Session history
-├── observations.json       # Collaboration patterns
-└── README.md
+│   ├── cli.py                  # Entry point
+│   ├── modules/
+│   │   ├── display.py          # header, success, error, warning, section
+│   │   └── templates.py        # operation_start, operation_complete
+│   └── handlers/
+│       └── json/               # JSON file management
+└── tests/
 ```
 
----
-
-## Commands
-
-*Configure after initialization*
-
----
-
-## Integration Points
-
-### Depends On
-
-
-### Provides To
-
+- `apps/modules/` — Public API. Import from here.
+- `apps/handlers/` — Internal implementation. Don't import directly.

src/aipass/cli/apps/handlers/__init__.py

@@ -64,7 +64,7 @@ def _find_real_caller():
 
 def _extract_branch_name(filepath: str) -> str:
     """Extract branch name from a file path."""
-    parts = filepath.split("/")
+    parts = Path(filepath).parts
     for i, part in enumerate(parts):
         if part == "aipass":
             if i + 1 < len(parts):

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

@@ -15,15 +15,27 @@
 #   - No Prax imports (handler tier 3)
 # =============================================
 
+"""JSON Auto-Creating Handler - manages CLI JSON files with templates and auto-rotation."""
+
 import json
 from pathlib import Path
 from datetime import datetime
-from typing import Dict, List, Any, Optional
-import sys
+from typing import Dict, Any, Optional
 import inspect
+from aipass.prax.apps.modules.logger import system_logger as logger
 
-# Constants — package-relative paths (portable across any machine)
-CLI_ROOT = Path(__file__).resolve().parents[3]  # json_handler.py -> json -> handlers -> apps -> cli
+def _find_repo_root() -> Path:
+    """Walk up from this file to find the repo root (contains pyproject.toml or AIPASS_REGISTRY.json)."""
+    current = Path(__file__).resolve().parent
+    for parent in [current] + list(current.parents):
+        if (parent / "pyproject.toml").exists() or (parent / "AIPASS_REGISTRY.json").exists():
+            return parent
+    return Path.cwd()
+
+
+# Constants — resolved via repo root walk-up (portable across any machine)
+_REPO_ROOT = _find_repo_root()
+CLI_ROOT = _REPO_ROOT / "src" / "aipass" / "cli"
 CLI_JSON_DIR = CLI_ROOT / "cli_json"
 JSON_TEMPLATES_DIR = CLI_ROOT / "apps" / "json_templates"
 
@@ -108,9 +120,8 @@ def ensure_json_exists(module_name: str, json_type: str) -> bool:
             if validate_json_structure(data, json_type):
                 return True
             # If corrupted, fall through to regenerate
-        except Exception:
-            # If unreadable, fall through to regenerate
-            pass
+        except Exception as exc:
+            logger.warning("JSON unreadable at %s, regenerating: %s", json_path, exc)
 
     template = load_template(json_type, module_name)