Archive obsolete docs and misc cleanup

- Move lsp-integration.md and secure-console-v3.md to docs/archive-obsolete/
  (these features are now in the Nextra SaaS product)
- Update CLAUDE.md with current project state
- Simplify run_organism.py
- Fix test fixtures for shared backend compatibility
- Minor handler and llm_api cleanups

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

CLAUDE.md

@@ -2,7 +2,7 @@
 
 A tamper-proof nervous system for multi-agent AI systems using XML as the sovereign wire format. AgentServer provides a schema-driven, Turing-complete message bus where agents communicate through validated XML payloads, with automatic XSD generation, handler isolation, and built-in security guarantees against agent misbehavior.
 
-**Version:** 0.2.0
+**Version:** 0.4.0
 
 ## Tech Stack
 
@@ -14,10 +14,11 @@ A tamper-proof nervous system for multi-agent AI systems using XML as the sovere
 | Serialization | xmlable | vendored | Dataclass ↔ XML round-trip with auto-XSD |
 | Config | PyYAML | Latest | Organism configuration (organism.yaml) |
 | Crypto | cryptography | Latest | Ed25519 identity keys for signing |
-| Console | prompt_toolkit | 3.0+ | Interactive TUI console |
 | HTTP | httpx | 0.27+ | LLM backend communication |
 | Case conversion | pyhumps | Latest | Snake/camel case conversion |
 
+> **Note:** TUI console, authentication, and WebSocket server are available in the Nextra SaaS product.
+
 ## Quick Start
 
 ```bash
@@ -38,19 +39,19 @@ pip install -e ".[all]"
 # Or minimal install + specific features
 pip install -e "."                    # Core only
 pip install -e ".[anthropic]"         # + Anthropic SDK
-pip install -e ".[server]"            # + WebSocket server
 
 # Configure environment
 cp .env.example .env
 # Edit .env to add your API keys (XAI_API_KEY, ANTHROPIC_API_KEY, etc.)
 
 # Run the organism
-python run_organism.py config/organism.yaml
-
-# Or use CLI
 xml-pipeline run config/organism.yaml
 xp run config/organism.yaml  # Short alias
 
+# Try the console example
+pip install -e ".[console]"
+python -m examples.console
+
 # Run tests
 pip install -e ".[test]"
 pytest tests/ -v
@@ -61,9 +62,7 @@ pytest tests/ -v
 ```
 xml-pipeline/
 ├── xml_pipeline/              # Main package
-│   ├── auth/                 # Authentication (TOTP, sessions, users)
 │   ├── config/               # Config loading and templates
-│   ├── console/              # TUI console and secure console
 │   ├── listeners/            # Listener implementations and examples
 │   ├── llm/                  # LLM router, backends, token bucket
 │   ├── memory/               # Context buffer for conversation history
@@ -77,21 +76,21 @@ xml-pipeline/
 │   ├── primitives/           # System message types (Boot, TodoUntil, etc.)
 │   ├── prompts/              # System prompts (no_paperclippers, etc.)
 │   ├── schema/               # XSD schema files
-│   ├── server/               # HTTP/WebSocket server
 │   ├── tools/                # Native tools (files, shell, search, etc.)
 │   └── utils/                # Shared utilities
 ├── config/                   # Example organism configurations
 ├── docs/                     # Architecture and design docs
-├── examples/                 # Example MCP servers and integrations
+├── examples/                 # Example console and integrations
 ├── handlers/                 # Example message handlers
 ├── tests/                    # pytest test suite
 ├── third_party/              # Vendored dependencies
 │   └── xmlable/              # XML serialization library
-├── pyproject.toml            # Project metadata and dependencies
+└── pyproject.toml            # Project metadata and dependencies
-├── run_organism.py           # Main entry point with TUI
-└── organism.yaml             # Default organism config (if present)
 ```
 
+> **Note:** Authentication (`auth/`), TUI console (`console/`), and WebSocket server (`server/`)
+> are available in the Nextra SaaS product.
+
 ## Architecture Overview
 
 AgentServer implements a stream-based message pump where all communication flows through validated XML envelopes. The architecture enforces strict isolation between handlers (untrusted code) and the system (trusted zone).
@@ -192,8 +191,7 @@ async def handle_greeting(payload: Greeting, metadata: HandlerMetadata) -> Handl
 | `xml-pipeline check [config]` | Validate config without running |
 | `xml-pipeline version` | Show version and installed features |
 | `xp run [config]` | Short alias for xml-pipeline run |
-| `python run_organism.py [config]` | Run with TUI console |
+| `python -m examples.console` | Run interactive console example |
-| `python run_organism.py --simple [config]` | Run with simple console |
 | `pytest tests/ -v` | Run test suite |
 | `pytest tests/test_pipeline_steps.py -v` | Run specific test file |
 
@@ -304,9 +302,8 @@ pip install xml-pipeline[openai]      # OpenAI SDK
 pip install xml-pipeline[redis]       # Distributed key-value store
 pip install xml-pipeline[search]      # DuckDuckGo search
 
-# Server features
+# Console example
-pip install xml-pipeline[auth]        # TOTP + Argon2 authentication
+pip install xml-pipeline[console]     # prompt_toolkit for examples
-pip install xml-pipeline[server]      # WebSocket server
 
 # Everything
 pip install xml-pipeline[all]
@@ -315,6 +312,8 @@ pip install xml-pipeline[all]
 pip install xml-pipeline[dev]
 ```
 
+> **Note:** Authentication and WebSocket server features are available in the Nextra SaaS product.
+
 ## Native Tools
 
 The project includes built-in tool implementations in `xml_pipeline/tools/`:
@@ -348,15 +347,15 @@ Built-in message types in `xml_pipeline/primitives/`:
 - @docs/message-pump-v2.1.md — Message pump implementation details
 - @docs/handler-contract-v2.1.md — Handler interface specification
 - @docs/llm-router-v2.1.md — LLM backend abstraction
-- @docs/secure-console-v3.md — Console and authentication
 - @docs/platform-architecture.md — Platform-level APIs
 - @docs/native_tools.md — Native tool implementations
 - @docs/primitives.md — System primitives reference (includes thread lifecycle)
 - @docs/configuration.md — Organism configuration reference
-- @docs/lsp-integration.md — LSP editor support for YAML and AssemblyScript
 - @docs/split-config.md — Split configuration architecture
 - @docs/why-not-json.md — Rationale for XML over JSON
 
+> **Note:** Console, authentication, and LSP integration documentation is in the Nextra project.
+
 
 ## Skill Usage Guide
 
@@ -370,7 +369,6 @@ When working on tasks involving these technologies, invoke the corresponding ski
 | cryptography | Implements Ed25519 identity keys for signing and federation auth |
 | httpx | Handles async HTTP requests for LLM backend communication |
 | aiostream | Implements stream-based message pipeline with concurrent fan-out processing |
-| prompt-toolkit | Builds interactive TUI console with password input and command history |
 | lxml | Handles XML processing, XSD validation, C14N normalization, and repair |
 | python | Manages async-first Python 3.11+ codebase with type hints and dataclasses |
 | pytest | Runs async test suite with pytest-asyncio fixtures and markers |

handlers/hello.py

@@ -124,14 +124,6 @@ async def handle_response_print(payload: ShoutedResponse, metadata: HandlerMetad
     """
     Print the final response to the console.
 
-    Routes output to the TUI console if available, otherwise prints to stdout.
+    Note: TUI console is available in Nextra. This handler uses simple stdout.
     """
-    from xml_pipeline.console.console_registry import get_console
+    print(f"\033[36m[response] {payload.message}\033[0m")
-
-    console = get_console()
-
-    if console is not None and hasattr(console, 'on_response'):
-        console.on_response("shouter", payload)
-    else:
-        # Fallback for simple mode or no console
-        print(f"\033[36m[response] {payload.message}\033[0m")

run_organism.py

@@ -1,93 +1,58 @@
 #!/usr/bin/env python3
 """
-run_organism.py — Start the organism with TUI console.
+run_organism.py — Deprecated entry point.
 
-Usage:
+The TUI console and server have been moved to the Nextra SaaS product.
-    python run_organism.py [config.yaml]
+This file is kept for backwards compatibility but will display a helpful message.
-    python run_organism.py --simple [config.yaml]  # Use simple console
 
-This boots the organism with a split-screen terminal UI:
+For the open-source xml-pipeline, use the CLI or programmatic API:
-- Scrolling output area above
-- Status bar separator
-- Input area below
 
-Flow:
+    # CLI
-  1. Bootstrap organism
+    xml-pipeline run config/organism.yaml
-  2. Start pump in background
+
-  3. Run TUI console
+    # Programmatic
-  4. /quit shuts down gracefully
+    from xml_pipeline.message_bus import bootstrap
+    pump = await bootstrap("organism.yaml")
+    await pump.run()
+
+    # Interactive console example
+    pip install xml-pipeline[console]
+    python -m examples.console
+
+For the full TUI console with authentication and WebSocket server,
+see the Nextra project.
 """
 
-import asyncio
 import sys
-from pathlib import Path
-
-from xml_pipeline.message_bus import bootstrap
-from xml_pipeline.console.console_registry import set_console
 
 
-async def run_organism(config_path: str = "config/organism.yaml", use_simple: bool = False):
+def main() -> None:
-    """Boot organism with TUI console."""
+    """Show deprecation message and exit."""
+    print("""
+xml-pipeline: TUI Console Moved to Nextra
+==========================================
 
-    # Bootstrap the pump
+The interactive TUI console with authentication and WebSocket server
-    pump = await bootstrap(config_path)
+has been moved to the Nextra SaaS product (v0.4.0).
 
-    if use_simple:
+For the open-source xml-pipeline, use:
-        # Use old SecureConsole for compatibility
-        from xml_pipeline.console import SecureConsole
-        console = SecureConsole(pump)
-        if not await console.authenticate():
-            print("Authentication failed.")
-            return
-        set_console(None)
 
-        pump_task = asyncio.create_task(pump.run())
+  1. CLI command:
-        try:
+     xml-pipeline run config/organism.yaml
-            await console.run_command_loop()
-        finally:
-            pump_task.cancel()
-            try:
-                await pump_task
-            except asyncio.CancelledError:
-                pass
-            await pump.shutdown()
-        print("Goodbye!")
-    else:
-        # Use new TUI console
-        from xml_pipeline.console.tui_console import TUIConsole
-        console = TUIConsole(pump)
-        set_console(console)  # Register for handlers to find
 
-        # Start pump in background
+  2. Programmatic API:
-        pump_task = asyncio.create_task(pump.run())
+     from xml_pipeline.message_bus import bootstrap
+     pump = await bootstrap("organism.yaml")
+     await pump.run()
 
-        try:
+  3. Console example (for testing):
-            await console.run()
+     pip install xml-pipeline[console]
-        finally:
+     python -m examples.console
-            pump_task.cancel()
-            try:
-                await pump_task
-            except asyncio.CancelledError:
-                pass
-            await pump.shutdown()
 
-
+For full TUI console, authentication, and WebSocket server features,
-def main():
+see the Nextra project.
-    args = sys.argv[1:]
+""")
-    use_simple = "--simple" in args
+    sys.exit(1)
-    if use_simple:
-        args.remove("--simple")
-
-    config_path = args[0] if args else "config/organism.yaml"
-
-    if not Path(config_path).exists():
-        print(f"Config not found: {config_path}")
-        sys.exit(1)
-
-    try:
-        asyncio.run(run_organism(config_path, use_simple=use_simple))
-    except KeyboardInterrupt:
-        print("\nInterrupted")
 
 
 if __name__ == "__main__":

tests/test_pump_integration.py

@@ -147,15 +147,8 @@ class TestFullPipelineFlow:
         handler_calls = []
         original_handler = pump.listeners["greeter"].handler
 
-        # Mock the LLM call since we don't have a real API key in tests
+        # Mock platform.complete since handle_greeting uses platform API
-        from xml_pipeline.llm.backend import LLMResponse
+        mock_response = "Hello, World!"
-
-        mock_response = LLMResponse(
-            content="Hello, World!",
-            model="mock",
-            usage={"total_tokens": 10},
-            finish_reason="stop",
-        )
 
         async def tracking_handler(payload, metadata):
             handler_calls.append((payload, metadata))
@@ -164,7 +157,7 @@ class TestFullPipelineFlow:
 
         pump.listeners["greeter"].handler = tracking_handler
 
-        with patch('xml_pipeline.llm.complete', new=AsyncMock(return_value=mock_response)):
+        with patch('xml_pipeline.platform.complete', new=AsyncMock(return_value=mock_response)):
             # Create and inject a Greeting message
             thread_id = str(uuid.uuid4())
             envelope = make_envelope(
@@ -235,17 +228,10 @@ class TestFullPipelineFlow:
 
         pump._reinject_responses = capture_reinject
 
-        # Mock the LLM call since we don't have a real API key in tests
+        # Mock platform.complete since handle_greeting uses platform API (not llm directly)
-        from xml_pipeline.llm.backend import LLMResponse
+        mock_response = "Hello, Alice!"
 
-        mock_response = LLMResponse(
+        with patch('xml_pipeline.platform.complete', new=AsyncMock(return_value=mock_response)):
-            content="Hello, Alice!",
-            model="mock",
-            usage={"total_tokens": 10},
-            finish_reason="stop",
-        )
-
-        with patch('xml_pipeline.llm.complete', new=AsyncMock(return_value=mock_response)):
             # Inject a Greeting
             thread_id = str(uuid.uuid4())
             envelope = make_envelope(
@@ -479,13 +465,8 @@ class TestThreadRoutingFlow:
         pump.listeners["shouter"].handler = trace_shouter
         pump.listeners["response-handler"].handler = trace_response
 
-        # Mock LLM response
+        # Mock platform.complete since handle_greeting uses platform API
-        mock_llm = LLMResponse(
+        mock_response = "Hello there, friend!"
-            content="Hello there, friend!",
-            model="mock",
-            usage={"total_tokens": 10},
-            finish_reason="stop",
-        )
 
         # Capture final output (response-handler sends to console, but console isn't registered)
         final_outputs = []
@@ -498,7 +479,7 @@ class TestThreadRoutingFlow:
 
         pump._reinject_responses = capture_reinject
 
-        with patch('xml_pipeline.llm.complete', new=AsyncMock(return_value=mock_llm)):
+        with patch('xml_pipeline.platform.complete', new=AsyncMock(return_value=mock_response)):
             # Inject ConsoleInput (simulating: user typed "@greeter TestUser")
             # Note: xmlify converts field names to PascalCase for XML elements
             thread_id = str(uuid.uuid4())
@@ -642,15 +623,10 @@ class TestThreadRoutingFlow:
                     pass
                 pump._reinject_responses = noop_reinject
 
-                # Mock LLM
+                # Mock platform.complete since handle_greeting uses platform API
-                mock_llm = LLMResponse(
+                mock_response = "Hello!"
-                    content="Hello!",
-                    model="mock",
-                    usage={"total_tokens": 5},
-                    finish_reason="stop",
-                )
 
-                with patch('xml_pipeline.llm.complete', new=AsyncMock(return_value=mock_llm)):
+                with patch('xml_pipeline.platform.complete', new=AsyncMock(return_value=mock_response)):
                     # Inject initial message
                     thread_id = str(uuid.uuid4())
                     envelope = make_envelope(

tests/test_todo_registry.py

@@ -411,7 +411,6 @@ class TestGreeterTodoFlow:
         """
         from handlers.hello import Greeting, GreetingResponse, handle_greeting
         from handlers.console import ShoutedResponse
-        from xml_pipeline.llm.backend import LLMResponse
 
         # Clear registry
         todo_registry = get_todo_registry()
@@ -419,15 +418,10 @@ class TestGreeterTodoFlow:
 
         thread_id = str(uuid.uuid4())
 
-        # Mock LLM
+        # Mock platform.complete (not llm.complete) since handle_greeting uses platform API
-        mock_llm = LLMResponse(
+        mock_response = "Hello there!"
-            content="Hello there!",
-            model="mock",
-            usage={"total_tokens": 5},
-            finish_reason="stop",
-        )
 
-        with patch('xml_pipeline.llm.complete', new=AsyncMock(return_value=mock_llm)):
+        with patch('xml_pipeline.platform.complete', new=AsyncMock(return_value=mock_response)):
             # Call greeter handler
             metadata = HandlerMetadata(
                 thread_id=thread_id,
@@ -466,7 +460,6 @@ class TestGreeterTodoFlow:
         When greeter is called again with raised todos, it should close them.
         """
         from handlers.hello import Greeting, GreetingResponse, handle_greeting
-        from xml_pipeline.llm.backend import LLMResponse
 
         # Clear registry
         todo_registry = get_todo_registry()
@@ -485,19 +478,14 @@ class TestGreeterTodoFlow:
         # Verify eyebrow is raised
         assert todo_registry._by_id[watcher_id].eyebrow_raised is True
 
-        # Mock LLM
+        # Mock platform.complete (not llm.complete) since handle_greeting uses platform API
-        mock_llm = LLMResponse(
+        mock_response = "Hello again!"
-            content="Hello again!",
-            model="mock",
-            usage={"total_tokens": 5},
-            finish_reason="stop",
-        )
 
         # Format the nudge as the pump would
         raised = todo_registry.get_raised_for(thread_id, "greeter")
         nudge = todo_registry.format_nudge(raised)
 
-        with patch('xml_pipeline.llm.complete', new=AsyncMock(return_value=mock_llm)):
+        with patch('xml_pipeline.platform.complete', new=AsyncMock(return_value=mock_response)):
             # Call greeter with the nudge
             metadata = HandlerMetadata(
                 thread_id=thread_id,

xml_pipeline/platform/llm_api.py

@@ -99,7 +99,8 @@ async def complete(
         context_buffer = get_context_buffer()
         history = context_buffer.get_thread(thread_id)
 
-        for slot in history:
+        # get_thread returns None if thread doesn't exist yet
+        for slot in history or []:
             # Determine role: assistant if from this agent, user otherwise
             role = "assistant" if slot.from_id == agent_name else "user"