fix(agents): propagate agent_name into ToolRuntime.context for setup_agent (#2679)

* fix(agents): propagate agent_name into ToolRuntime.context for setup_agent (#2677)

When creating a custom agent via the web UI, SOUL.md was always written
to the global base_dir/SOUL.md instead of agents/<name>/SOUL.md.

Root cause: the bootstrap flow sends agent_name via body.context, but
two layers were broken:

1. services.py only forwarded body.context keys into config["configurable"];
   config["context"] was never populated.
2. worker.py constructed the parent Runtime with a hard-coded
   {thread_id, run_id} context, ignoring config["context"] entirely.

After the langgraph >= 1.1.9 bump (#98a5b34f), ToolRuntime.context no
longer falls back to configurable, so setup_agent's
runtime.context.get("agent_name") returned None and the tool's silent
agent_name=None -> base_dir fallback kicked in, overwriting the global
SOUL.md.

Fix:
- services.py: extract merge_run_context_overrides() and write the
  whitelisted context keys into both configurable (legacy readers) and
  context (langgraph 1.1+ ToolRuntime consumers).
- worker.py: extract _build_runtime_context() and merge config["context"]
  into the Runtime's context (without letting callers override
  thread_id/run_id).

The base_dir fallback in setup_agent_tool.py is left in place because
the IM /bootstrap channel command depends on it. That code path can
be tightened in a follow-up.

Adds regression tests covering both helpers.

* Apply suggestions from code review

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

---------

Co-authored-by: Willem Jiang <willem.jiang@gmail.com>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

backend/tests/test_gateway_services.py

@@ -256,6 +256,37 @@ def test_context_merges_into_configurable():
     assert "thread_id" not in {k for k in context if k in _CONTEXT_CONFIGURABLE_KEYS}
 
 
+def test_merge_run_context_overrides_propagates_to_runtime_context():
+    """Regression for issue #2677: ``agent_name`` (and other whitelisted keys) from
+    ``body.context`` must be propagated into BOTH ``config['configurable']`` and
+    ``config['context']``. Previously only ``configurable`` was populated, so after
+    the LangGraph 1.1.x upgrade removed the fallback from ``configurable``, the
+    ``setup_agent`` tool read ``runtime.context`` with ``agent_name=None`` and
+    silently wrote SOUL.md to the global base_dir.
+    """
+    from app.gateway.services import build_run_config, merge_run_context_overrides
+
+    config = build_run_config("thread-1", None, None)
+    merge_run_context_overrides(config, {"agent_name": "my-agent", "is_bootstrap": True, "thread_id": "ignored"})
+
+    assert config["configurable"]["agent_name"] == "my-agent"
+    assert config["configurable"]["is_bootstrap"] is True
+    assert config["context"]["agent_name"] == "my-agent"
+    assert config["context"]["is_bootstrap"] is True
+    # Non-whitelisted keys are not forwarded.
+    assert "thread_id" not in config["context"]
+
+
+def test_merge_run_context_overrides_noop_for_empty_context():
+    from app.gateway.services import build_run_config, merge_run_context_overrides
+
+    config = build_run_config("thread-1", None, None)
+    before = {k: dict(v) if isinstance(v, dict) else v for k, v in config.items()}
+    merge_run_context_overrides(config, None)
+    merge_run_context_overrides(config, {})
+    assert config == before
+
+
 def test_context_does_not_override_existing_configurable():
     """Values already in config.configurable must NOT be overridden by context."""
     from app.gateway.services import build_run_config