feat(cli): wire paths + bootstrap + proxy + degraded mode

Also updates test_smoke.py to mock bootstrap/proxy now that main() is
real orchestration rather than a print-and-return stub.

Author: Broccolito

src/codegraphagent/cli.py

@@ -1,16 +1,29 @@
 """CLI entry point for codegraphagent.
 
-This is the [project.scripts] target. It defers the real work to a function
-in this module so that `python -m codegraphagent` and the `codegraphagent`
-command share the same entrypoint.
+Orchestrates the three pieces of the shim:
+  1. paths — resolve the project root and ensure the .biorouter/codegraph
+     state dir + .codegraph symlink exist.
+  2. bootstrap — ensure the vendored engine bundle is downloaded, verified,
+     and extracted.
+  3. proxy — spawn the engine and pump MCP traffic.
+
+If either of the first two fails, hand control to the degraded-mode error
+shim so the agent gets a structured error frame rather than an opaque crash.
 """
 
+from __future__ import annotations
+
+from codegraphagent import bootstrap, error_shim, paths, proxy
+from codegraphagent.errors import CodeGraphAgentError
+
 
 def main() -> int:
-    """Run the CodeGraphAgent MCP server.
+    try:
+        root = paths.resolve_project_root()
+        paths.ensure_layout(root)
+        launcher = bootstrap.ensure_engine()
+    except CodeGraphAgentError as exc:
+        error_shim.serve(exc)
+        return 0
 
-    Returns the process exit code (0 on clean shutdown, non-zero otherwise).
-    Real implementation lands in later tasks; for now this is a stub.
-    """
-    print("codegraphagent: stub — wiring lands in Task E2")
-    return 0
+    return proxy.run(launcher=launcher, cwd=root)

tests/test_cli.py

@@ -0,0 +1,65 @@
+"""cli.main — orchestrates paths.ensure_layout → bootstrap.ensure_engine → proxy.run."""
+
+from __future__ import annotations
+
+from pathlib import Path
+from unittest.mock import patch, MagicMock
+
+import pytest
+
+from codegraphagent import cli
+from codegraphagent.errors import BootstrapError, LayoutConflictError
+
+
+def test_main_happy_path(tmp_path: Path, monkeypatch: pytest.MonkeyPatch):
+    monkeypatch.setenv("BIOROUTER_WORKING_DIR", str(tmp_path))
+    (tmp_path / ".git").mkdir()
+
+    fake_launcher = tmp_path / "fake-launcher"
+    fake_launcher.write_text("")
+
+    proxy_run = MagicMock(return_value=0)
+
+    with patch.object(cli.bootstrap, "ensure_engine", return_value=fake_launcher), \
+         patch.object(cli.proxy, "run", proxy_run):
+        rc = cli.main()
+
+    assert rc == 0
+    proxy_run.assert_called_once()
+    kwargs = proxy_run.call_args.kwargs
+    assert kwargs["launcher"] == fake_launcher
+    assert kwargs["cwd"] == tmp_path.resolve()
+
+
+def test_main_falls_back_to_error_shim_on_bootstrap_error(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+):
+    monkeypatch.setenv("BIOROUTER_WORKING_DIR", str(tmp_path))
+    (tmp_path / ".git").mkdir()
+
+    err = BootstrapError("nope", url="https://example.com/x")
+    error_shim_serve = MagicMock()
+
+    with patch.object(cli.bootstrap, "ensure_engine", side_effect=err), \
+         patch.object(cli.error_shim, "serve", error_shim_serve):
+        rc = cli.main()
+
+    assert rc == 0
+    error_shim_serve.assert_called_once()
+    assert error_shim_serve.call_args.args[0] is err
+
+
+def test_main_falls_back_to_error_shim_on_layout_conflict(
+    tmp_path: Path, monkeypatch: pytest.MonkeyPatch
+):
+    monkeypatch.setenv("BIOROUTER_WORKING_DIR", str(tmp_path))
+    (tmp_path / ".git").mkdir()
+    (tmp_path / ".codegraph").mkdir()
+
+    error_shim_serve = MagicMock()
+    with patch.object(cli.error_shim, "serve", error_shim_serve):
+        rc = cli.main()
+
+    assert rc == 0
+    error_shim_serve.assert_called_once()
+    assert isinstance(error_shim_serve.call_args.args[0], LayoutConflictError)

tests/test_smoke.py

@@ -7,7 +7,20 @@ def test_version_is_set():
     assert codegraphagent.__version__ == "0.1.0"
 
 
-def test_cli_entrypoint_runs():
-    from codegraphagent.cli import main
-    rc = main()
+def test_cli_entrypoint_runs(tmp_path, monkeypatch):
+    """main() returns 0; full bootstrap is mocked to avoid network I/O."""
+    from pathlib import Path
+    from unittest.mock import patch, MagicMock
+    from codegraphagent import cli
+
+    monkeypatch.setenv("BIOROUTER_WORKING_DIR", str(tmp_path))
+    (tmp_path / ".git").mkdir()
+
+    fake_launcher = tmp_path / "fake-launcher"
+    fake_launcher.write_text("")
+
+    with patch.object(cli.bootstrap, "ensure_engine", return_value=fake_launcher), \
+         patch.object(cli.proxy, "run", MagicMock(return_value=0)):
+        rc = cli.main()
+
     assert rc == 0