fix(ci): resolve nightly-install, CI test, and UAT failures

- doctor: change missing config from fail to warn (expected on fresh install)
- test_harness_matrix: add integration marker so 42 agent tests are
  excluded from CI runs (they require tmux + mock agent spawning)
- test_study_integration: pass --agent claude so detect_agents() guard
  is bypassed on runners with no AI agents installed
- harness: capture subprocess/pexpect output in timeout errors for
  UAT diagnostic visibility
- pyproject.toml: register e2e pytest marker at workspace root

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: NetDevAutomate

packages/studyctl/src/studyctl/doctor/core.py

@@ -99,7 +99,7 @@ def check_config_file() -> list[CheckResult]:
             CheckResult(
                 "core",
                 "config_file",
-                "fail",
+                "warn",
                 f"Config not found: {config_path}",
                 "studyctl config init",
                 fix_auto=True,

packages/studyctl/tests/harness/study.py

@@ -110,7 +110,7 @@ def start(
         env.pop("TMUX", None)
         env.pop("TMUX_PANE", None)
 
-        subprocess.run(
+        result = subprocess.run(
             [
                 sys.executable,
                 "-m",
@@ -136,7 +136,12 @@ def start(
         self.tmux.wait_for(
             lambda: self.state.get("study_session_id") is not None,
             timeout=10,
-            msg="session state file not written",
+            msg=(
+                f"session state file not written"
+                f" (exit={result.returncode},"
+                f" stdout={result.stdout[-200:]!r},"
+                f" stderr={result.stderr[-200:]!r})"
+            ),
         )
 
         state = self.state

packages/studyctl/tests/harness/terminal.py

@@ -75,7 +75,16 @@ def spawn_study(
             import time
 
             time.sleep(0.5)
-        raise TimeoutError("Session state file not created after spawn")
+
+        # Capture child output for diagnostics
+        child_output = ""
+        if self._child:
+            before = self._child.before if isinstance(self._child.before, str) else ""
+            after = self._child.after if isinstance(self._child.after, str) else ""
+            child_output = before + after
+        raise TimeoutError(
+            f"Session state file not created after spawn (child output: {child_output[-300:]!r})"
+        )
 
     def attach_and_send_q(self, *, timeout: int = 15) -> bool:
         """Attach to the tmux session and send Q to the sidebar pane.

packages/studyctl/tests/test_doctor_core.py

@@ -72,7 +72,7 @@ def test_config_missing(self, tmp_path: Path):
         missing = tmp_path / "nope.yaml"
         with patch("studyctl.doctor.core._get_config_path", return_value=missing):
             results = check_config_file()
-        assert results[0].status == "fail"
+        assert results[0].status == "warn"
         assert "config init" in results[0].fix_hint
 
     def test_config_invalid_yaml(self, tmp_path: Path):

packages/studyctl/tests/test_harness_matrix.py

@@ -49,6 +49,7 @@
 
 pytestmark = [
     pytest.mark.skipif(not shutil.which("tmux"), reason="tmux not installed"),
+    pytest.mark.integration,
     pytest.mark.e2e,
 ]
 

packages/studyctl/tests/test_study_integration.py

@@ -235,13 +235,21 @@ def _start_session(
     env_overrides = {
         "STUDYCTL_TEST_AGENT_CMD": f"bash {agent_script} {{persona_file}}",
     }
-    args = ["study", topic, "--energy", str(energy)]
+    args = ["study", topic, "--energy", str(energy), "--agent", "claude"]
     if extra_args:
         args.extend(extra_args)
 
-    _studyctl(*args, env_overrides=env_overrides)
+    result = _studyctl(*args, env_overrides=env_overrides)
 
-    _wait_for(STATE_FILE.exists, desc="session-state.json created")
+    _wait_for(
+        STATE_FILE.exists,
+        desc=(
+            f"session-state.json created"
+            f" (exit={result.returncode},"
+            f" stdout={result.stdout[-200:]!r},"
+            f" stderr={result.stderr[-200:]!r})"
+        ),
+    )
     state = _read_state()
     session_name = state.get("tmux_session", "")
     _wait_for(lambda: _session_exists(session_name), desc=f"tmux session {session_name}")

pyproject.toml

@@ -58,4 +58,5 @@ testpaths = ["packages/agent-session-tools/tests", "packages/studyctl/tests"]
 addopts = "--import-mode=importlib"
 markers = [
     "integration: requires external infrastructure (tmux, real DB, network)",
+    "e2e: end-to-end browser tests requiring Playwright + web server",
 ]