Python: restructure: Python samples into progressive 01-05 layout (#3862)

* restructure: Python samples into progressive 01-05 layout

- 01-get-started/: 6 numbered steps (hello agent → hosting)
- 02-agents/: all agent concept samples (tools, middleware, providers, etc.)
- 03-workflows/: ALL existing workflow samples preserved as-is
- 04-hosting/: azure-functions, durabletask, a2a
- 05-end-to-end/: demos, evaluation, hosted agents
- Old files moved to _to_delete/ for review
- Added AGENTS.md with structure documentation
- autogen-migration/ and semantic-kernel-migration/ preserved at root

* fix: switch to AzureOpenAI Foundry, fix CI failures

- Switch all 01-get-started samples to AzureOpenAIResponsesClient with
  Azure AI Foundry project endpoint (AZURE_AI_PROJECT_ENDPOINT +
  AZURE_OPENAI_RESPONSES_DEPLOYMENT_NAME + AzureCliCredential)
- Add _to_delete/ and 05-end-to-end/ to pyrightconfig.samples.json excludes
- Fix test paths in packages/ that referenced old getting_started/ dirs:
  durabletask conftest + streaming test, azurefunctions conftest,
  devui conftest + capture_messages + openai_sdk_integration
- Fix workflow_as_agent_human_in_the_loop.py import (sibling import)
- Update hosting READMEs and tool comment paths
- Replace root README.md with new structure overview
- Update AGENTS.md to document Azure OpenAI Foundry as default provider

* cleanup: remove _to_delete folder, copy resource files to active dirs

All files in _to_delete/ were either:
- Exact duplicates of files in the new structure (240 files)
- Same file with only comment path updates (100 files)
- One import-fix diff (workflow_as_agent_human_in_the_loop.py)
- One superseded minimal_sample.py

Resource files (sample.pdf, countries.json, employees.pdf, weather.json)
copied to 02-agents/sample_assets/ and 02-agents/resources/ since active
samples reference them.

* fix: address PR review comments, centralize resources, remove root duplicates

- Fix type annotation in 04_memory.py (string union -> proper types)
- Fix old sample paths in observability files
- Fix grammar/spelling in observability samples
- Move sample_assets/ and resources/ to shared/ folder
- Remove 8 duplicate observability files from 02-agents root
- Update resource path references in multimodal_input and provider samples

* fix: update broken links from old getting_started paths to new structure

- Update relative paths in READMEs: getting_started/ → 01-get-started/,
  02-agents/, 03-workflows/, 04-hosting/, 05-end-to-end/
- Fix absolute GitHub URLs in package READMEs
- Fix broken link in ollama package README

* fix: convert absolute GitHub URLs to relative paths for link checker

Absolute URLs to python/samples/ on main branch 404 until PR merges.
Converted to relative paths that linkspector can verify locally.

* fix: update link for handoff sample moved to orchestrations/

* fix: update chatkit-integration README path from demos/ to 05-end-to-end/

* fix: update broken links in orchestrations README to match flat directory structure

python/samples/02-agents/middleware/thread_behavior_middleware.py

@@ -0,0 +1,102 @@
+# Copyright (c) Microsoft. All rights reserved.
+
+import asyncio
+from collections.abc import Awaitable, Callable
+from typing import Annotated
+
+from agent_framework import (
+    AgentContext,
+    ChatMessageStore,
+    tool,
+)
+from agent_framework.azure import AzureOpenAIChatClient
+from azure.identity import AzureCliCredential
+from pydantic import Field
+
+"""
+Thread Behavior MiddlewareTypes Example
+
+This sample demonstrates how middleware can access and track thread state across multiple agent runs.
+The example shows:
+
+- How AgentContext.thread property behaves across multiple runs
+- How middleware can access conversation history through the thread
+- The timing of when thread messages are populated (before vs after call_next() call)
+- How to track thread state changes across runs
+
+Key behaviors demonstrated:
+1. First run: context.messages is populated, context.thread is initially empty (before call_next())
+2. After call_next(): thread contains input message + response from agent
+3. Second run: context.messages contains only current input, thread contains previous history
+4. After call_next(): thread contains full conversation history (all previous + current messages)
+"""
+
+
+# NOTE: approval_mode="never_require" is for sample brevity. Use "always_require" in production; see samples/02-agents/tools/function_tool_with_approval.py and samples/02-agents/tools/function_tool_with_approval_and_threads.py.
+@tool(approval_mode="never_require")
+def get_weather(
+    location: Annotated[str, Field(description="The location to get the weather for.")],
+) -> str:
+    """Get the weather for a given location."""
+    from random import randint
+
+    conditions = ["sunny", "cloudy", "rainy", "stormy"]
+    return f"The weather in {location} is {conditions[randint(0, 3)]} with a high of {randint(10, 30)}°C."
+
+
+async def thread_tracking_middleware(
+    context: AgentContext,
+    call_next: Callable[[], Awaitable[None]],
+) -> None:
+    """MiddlewareTypes that tracks and logs thread behavior across runs."""
+    thread_messages = []
+    if context.thread and context.thread.message_store:
+        thread_messages = await context.thread.message_store.list_messages()
+
+    print(f"[MiddlewareTypes pre-execution] Current input messages: {len(context.messages)}")
+    print(f"[MiddlewareTypes pre-execution] Thread history messages: {len(thread_messages)}")
+
+    # Call call_next to execute the agent
+    await call_next()
+
+    # Check thread state after agent execution
+    updated_thread_messages = []
+    if context.thread and context.thread.message_store:
+        updated_thread_messages = await context.thread.message_store.list_messages()
+
+    print(f"[MiddlewareTypes post-execution] Updated thread messages: {len(updated_thread_messages)}")
+
+
+async def main() -> None:
+    """Example demonstrating thread behavior in middleware across multiple runs."""
+    print("=== Thread Behavior MiddlewareTypes Example ===")
+
+    # For authentication, run `az login` command in terminal or replace AzureCliCredential with preferred
+    # authentication option.
+    agent = AzureOpenAIChatClient(credential=AzureCliCredential()).as_agent(
+        name="WeatherAgent",
+        instructions="You are a helpful weather assistant.",
+        tools=get_weather,
+        middleware=[thread_tracking_middleware],
+        # Configure agent with message store factory to persist conversation history
+        chat_message_store_factory=ChatMessageStore,
+    )
+
+    # Create a thread that will persist messages between runs
+    thread = agent.get_new_thread()
+
+    print("\nFirst Run:")
+    query1 = "What's the weather like in Tokyo?"
+    print(f"User: {query1}")
+    result1 = await agent.run(query1, thread=thread)
+    print(f"Agent: {result1.text}")
+
+    print("\nSecond Run:")
+    query2 = "How about in London?"
+    print(f"User: {query2}")
+    result2 = await agent.run(query2, thread=thread)
+    print(f"Agent: {result2.text}")
+
+
+if __name__ == "__main__":
+    asyncio.run(main())