Refactor: Clean up obsolete files and organize codebase structure

This commit removes deprecated modules and reorganizes code into logical directories:

Deleted files (superseded by newer systems):
- claude_code_server.py (replaced by agent-sdk direct integration)
- heartbeat.py (superseded by scheduled_tasks.py)
- pulse_brain.py (unused in production)
- config/pulse_brain_config.py (obsolete config)

Created directory structure:
- examples/ (7 example files: example_*.py, demo_*.py)
- tests/ (5 test files: test_*.py)

Updated imports:
- agent.py: Removed heartbeat module and all enable_heartbeat logic
- bot_runner.py: Removed heartbeat parameter from Agent initialization
- llm_interface.py: Updated deprecated claude_code_server message

Preserved essential files:
- hooks.py (for future use)
- adapters/skill_integration.py (for future use)
- All Google integration tools (Gmail, Calendar, Contacts)
- GLM provider code (backward compatibility)

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

examples/example_custom_pulse.py

@@ -0,0 +1,85 @@
+"""
+Example: Pulse & Brain with ONLY YOUR chosen checks.
+
+By default, pulse_brain.py includes example checks.
+This shows how to start with a CLEAN SLATE and only add what YOU want.
+"""
+
+import time
+from pathlib import Path
+
+from agent import Agent
+from pulse_brain import BrainTask, CheckType, PulseCheck, PulseBrain
+
+
+def check_my_file() -> dict:
+    """Check if the important data file exists."""
+    file = Path("important_data.json")
+    return {
+        "status": "ok" if file.exists() else "error",
+        "message": f"File exists: {file.exists()}",
+    }
+
+
+def main() -> None:
+    agent = Agent(provider="claude", enable_heartbeat=False)
+
+    # Create Pulse & Brain with NO automatic checks
+    pb = PulseBrain(agent, pulse_interval=60)
+
+    # Remove all default checks (start clean)
+    pb.pulse_checks = []
+    pb.brain_tasks = []
+
+    print(
+        "Starting with ZERO checks. "
+        "You have complete control.\n"
+    )
+
+    # Add ONLY the checks you want
+    pb.pulse_checks.append(
+        PulseCheck(
+            "my-file", check_my_file,
+            interval_seconds=300,
+        ),
+    )
+
+    pb.brain_tasks.append(
+        BrainTask(
+            name="file-recovery",
+            check_type=CheckType.CONDITIONAL,
+            prompt_template=(
+                "The file important_data.json is missing. "
+                "What should I do to recover it?"
+            ),
+            condition_func=lambda data: (
+                data.get("status") == "error"
+            ),
+        ),
+    )
+
+    print("Added 1 pulse check: my-file")
+    print("Added 1 brain task: file-recovery")
+    print("\nThe agent will ONLY:")
+    print(
+        "  1. Check if important_data.json exists "
+        "(every 5 min, zero cost)"
+    )
+    print(
+        "  2. Ask for recovery help IF it's missing "
+        "(costs tokens)"
+    )
+    print("\nNothing else. You have complete control.\n")
+
+    pb.start()
+
+    try:
+        print("Running... Press Ctrl+C to stop\n")
+        while True:
+            time.sleep(1)
+    except KeyboardInterrupt:
+        pb.stop()
+
+
+if __name__ == "__main__":
+    main()