feat: enhance interrupt handling and container resource configuration

- Introduced a shared interrupt signaling mechanism to allow tools to check for user interrupts during long-running operations.
- Updated the AIAgent to handle interrupts more effectively, ensuring in-progress tool calls are canceled and multiple interrupt messages are combined into one prompt.
- Enhanced the CLI configuration to include container resource limits (CPU, memory, disk) and persistence options for Docker, Singularity, and Modal environments.
- Improved documentation to clarify interrupt behaviors and container resource settings, providing users with better guidance on configuration and usage.

tools/interrupt.py

@@ -0,0 +1,28 @@
+"""Shared interrupt signaling for all tools.
+
+Provides a global threading.Event that any tool can check to determine
+if the user has requested an interrupt. The agent's interrupt() method
+sets this event, and tools poll it during long-running operations.
+
+Usage in tools:
+    from tools.interrupt import is_interrupted
+    if is_interrupted():
+        return {"output": "[interrupted]", "returncode": 130}
+"""
+
+import threading
+
+_interrupt_event = threading.Event()
+
+
+def set_interrupt(active: bool) -> None:
+    """Called by the agent to signal or clear the interrupt."""
+    if active:
+        _interrupt_event.set()
+    else:
+        _interrupt_event.clear()
+
+
+def is_interrupted() -> bool:
+    """Check if an interrupt has been requested. Safe to call from any thread."""
+    return _interrupt_event.is_set()