fix(cli): apply .env after the built-in local defaults

Loading .env before env_vars meant env.update(env_vars) clobbered any
overlapping key, so a custom REDIS_URL or TEMPORAL_ADDRESS in .env had no
effect. Apply .env after the defaults, below the manifest env block and the
shell, and keep ENVIRONMENT pinned to development; add a regression test.

Claude-Session: https://claude.ai/code/session_01HCVKnA7LeJZ44nxZz1uzF3

Author: michaelxu2288

src/agentex/lib/cli/handlers/run_handlers.py

@@ -413,16 +413,6 @@ def create_agent_environment(manifest: AgentManifest, manifest_dir: Path | None
     # Start with current environment
     env = dict(os.environ)
 
-    # Local development: load the .env next to manifest.yaml into BOTH the ACP and
-    # worker processes (the docs promise this). Variables already set in the shell
-    # win, matching python-dotenv's default. Without this, a value in .env only
-    # reaches a process if some import happens to call load_dotenv() first.
-    if manifest_dir is not None:
-        env_file = Path(manifest_dir) / ".env"
-        if env_file.is_file():
-            for key, value in dotenv_values(env_file).items():
-                if value is not None and key not in env:
-                    env[key] = value
 
     agent_config = manifest.agent
 
@@ -469,6 +459,23 @@ def create_agent_environment(manifest: AgentManifest, manifest_dir: Path | None
 
     env.update(env_vars)
 
+    # Local development: load the .env next to manifest.yaml into BOTH the ACP and
+    # worker processes (the docs promise this). Precedence, highest first: the
+    # manifest's env block, variables already set in the shell, then .env, then
+    # the built-in local defaults above (so .env can point at a custom Redis or
+    # Temporal). ENVIRONMENT stays "development": that is what makes this a
+    # local run. Without this block a value in .env only reaches a process if
+    # some import happens to call load_dotenv() first.
+    if manifest_dir is not None:
+        env_file = Path(manifest_dir) / ".env"
+        if env_file.is_file():
+            manifest_env = agent_config.env or {}
+            for key, value in dotenv_values(env_file).items():
+                if value is None or key == "ENVIRONMENT":
+                    continue
+                if key in os.environ or key in manifest_env:
+                    continue
+                env[key] = value
     return env
 
 

tests/lib/cli/test_run_handlers_env.py

@@ -65,3 +65,17 @@ def test_missing_dotenv_and_no_manifest_dir_are_fine(project_dir: Path, monkeypa
 
     assert "FROM_DOTENV" not in create_agent_environment(manifest, manifest_dir=project_dir)
     assert "FROM_DOTENV" not in create_agent_environment(manifest)
+
+
+def test_dotenv_overrides_builtin_local_defaults_but_not_environment(project_dir: Path, monkeypatch: pytest.MonkeyPatch):
+    """.env may point local runs at a custom Redis/Temporal; ENVIRONMENT stays development."""
+    (project_dir / ".env").write_text("REDIS_URL=redis://custom:6380\nTEMPORAL_ADDRESS=temporal.internal:7233\nENVIRONMENT=production\n")
+    for key in ("REDIS_URL", "TEMPORAL_ADDRESS", "ENVIRONMENT"):
+        monkeypatch.delenv(key, raising=False)
+    manifest = load_agent_manifest(file_path=str(project_dir / "manifest.yaml"))
+
+    env = create_agent_environment(manifest, manifest_dir=project_dir)
+
+    assert env["REDIS_URL"] == "redis://custom:6380"
+    assert env["TEMPORAL_ADDRESS"] == "temporal.internal:7233"
+    assert env["ENVIRONMENT"] == "development"