feat(agency): complete WP-0002 Part 3 — E2E tests, docs, sys-medic cross-refs, bugfix

T25: add tests/test_e2e_agency_framework.py — 16 E2E tests covering the full
memory lifecycle (init, show, brief, clear) and protocol list/show commands.

T26: replace agency-framework.md protocols placeholder with full documentation —
location convention, frontmatter schema, CLI reference, sys-medic memory
extensions, and protocols table.

T27: add Related Documents footer to agent-sys-medic.md linking to the k3s
protocol runbook, ADR-002, ADR-003, and agency-framework.md.

Fix: rename CLI command function list() → list_agents() to stop it shadowing
Python's built-in list(). The shadow caused memory_brief() to invoke the
agent-list command instead of constructing a list from dict keys, producing
the agent list as output on every `memory brief` invocation.

All 27 WP-0002 tasks complete. Test suite: 51 passed, 1 skipped.

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

tests/test_e2e_agency_framework.py

@@ -0,0 +1,262 @@
+"""
+End-to-end tests for the agency framework: memory lifecycle and coach orientation.
+
+Tests the full workflow:
+  1. memory init — scaffold a memory file in a test project
+  2. Populate memory with realistic content (simulating sessions)
+  3. memory show — verify content is readable
+  4. memory brief — verify orientation brief includes own memory and cross-agent context
+  5. protocols list / show — verify protocol discovery works
+  6. memory clear — verify wipe works
+"""
+
+import textwrap
+from pathlib import Path
+
+import pytest
+from click.testing import CliRunner
+
+from kaizen_agentic.cli import cli
+
+
+# ---------------------------------------------------------------------------
+# Helpers
+# ---------------------------------------------------------------------------
+
+def _sys_medic_memory() -> str:
+    """Realistic sys-medic memory after two simulated sessions."""
+    return textwrap.dedent("""\
+        ---
+        agent: sys-medic
+        project: test-cluster
+        last_updated: 2026-03-18
+        session_count: 2
+        ---
+
+        ## Project Context
+        k3s single-node cluster on an ARM64 host (tegpi-01).
+        No external load balancer. Traefik ingress. Longhorn storage.
+
+        ## Accumulated Findings
+        - kubelet log rotation was disabled; logs grew to 2.1 GB
+        - containerd image GC threshold was set too high (98%)
+
+        ## What Worked
+        - `journalctl --vacuum-size=500M` recovered ~1.8 GB without restart
+        - Lowering GC threshold to 80% in containerd config resolved disk pressure
+
+        ## Watch Points
+        - inotify watch limit hits ceiling under heavy Longhorn load
+        - node has only 4 GB RAM; memory pressure risk during backup windows
+
+        ## Open Threads
+        - Check whether kube-system namespace daemonsets have resource limits set
+
+        ## Node Profiles
+        tegpi-01 | load avg ~0.6 at idle | inotify-limited under load | 2026-03-18
+
+        ## Recurring Findings
+        - kubelet log growth · first seen 2026-03-10 · 2 occurrences
+
+        ## Cleared Issues
+        - containerd GC disk pressure · adjusted config 2026-03-18 · resolved
+
+        ## Session Log
+        2026-03-10 · tegpi-01 initial assessment · found log bloat + GC issue · recommendations documented
+        2026-03-18 · tegpi-01 follow-up · verified GC fix; inotify limit noted · watch
+    """)
+
+
+def _project_management_memory() -> str:
+    """Minimal project-management agent memory."""
+    return textwrap.dedent("""\
+        ---
+        agent: project-management
+        project: test-cluster
+        last_updated: 2026-03-15
+        session_count: 1
+        ---
+
+        ## Project Context
+        Operational runbook project for the k3s home cluster.
+
+        ## Accumulated Findings
+        - Infra tasks are better tracked in Gitea issues than in TODO files
+
+        ## Session Log
+        2026-03-15 · initial planning session · task structure agreed
+    """)
+
+
+# ---------------------------------------------------------------------------
+# Fixtures
+# ---------------------------------------------------------------------------
+
+@pytest.fixture
+def project(tmp_path):
+    """A temporary 'project' directory with a name."""
+    p = tmp_path / "test-cluster"
+    p.mkdir()
+    return p
+
+
+# ---------------------------------------------------------------------------
+# Tests
+# ---------------------------------------------------------------------------
+
+class TestMemoryInit:
+    def test_init_creates_file(self, project):
+        runner = CliRunner()
+        result = runner.invoke(cli, ["memory", "init", "sys-medic", "--target", str(project)])
+        assert result.exit_code == 0, result.output
+        assert "Initialized memory" in result.output
+
+        memory_file = project / ".kaizen" / "agents" / "sys-medic" / "memory.md"
+        assert memory_file.exists()
+
+    def test_init_file_content_has_required_sections(self, project):
+        runner = CliRunner()
+        runner.invoke(cli, ["memory", "init", "sys-medic", "--target", str(project)])
+
+        memory_file = project / ".kaizen" / "agents" / "sys-medic" / "memory.md"
+        content = memory_file.read_text()
+
+        assert "agent: sys-medic" in content
+        assert "project: test-cluster" in content
+        assert "session_count: 0" in content
+        assert "## Project Context" in content
+        assert "## Accumulated Findings" in content
+        assert "## What Worked" in content
+        assert "## Watch Points" in content
+        assert "## Open Threads" in content
+        assert "## Session Log" in content
+
+    def test_init_idempotent(self, project):
+        runner = CliRunner()
+        runner.invoke(cli, ["memory", "init", "sys-medic", "--target", str(project)])
+        result = runner.invoke(cli, ["memory", "init", "sys-medic", "--target", str(project)])
+        assert result.exit_code == 0
+        assert "already exists" in result.output
+
+
+class TestMemoryShow:
+    def test_show_returns_content(self, project):
+        memory_file = project / ".kaizen" / "agents" / "sys-medic" / "memory.md"
+        memory_file.parent.mkdir(parents=True, exist_ok=True)
+        memory_file.write_text(_sys_medic_memory())
+
+        runner = CliRunner()
+        result = runner.invoke(cli, ["memory", "show", "sys-medic", "--target", str(project)])
+        assert result.exit_code == 0
+        assert "Node Profiles" in result.output
+        assert "tegpi-01" in result.output
+
+    def test_show_missing_prints_guidance(self, project):
+        runner = CliRunner()
+        result = runner.invoke(cli, ["memory", "show", "sys-medic", "--target", str(project)])
+        assert result.exit_code == 0
+        assert "No memory found" in result.output
+        assert "memory init" in result.output
+
+
+class TestMemoryBrief:
+    def _populate(self, project):
+        """Write both agent memories into the project."""
+        sm_dir = project / ".kaizen" / "agents" / "sys-medic"
+        sm_dir.mkdir(parents=True, exist_ok=True)
+        (sm_dir / "memory.md").write_text(_sys_medic_memory())
+
+        pm_dir = project / ".kaizen" / "agents" / "project-management"
+        pm_dir.mkdir(parents=True, exist_ok=True)
+        (pm_dir / "memory.md").write_text(_project_management_memory())
+
+    def test_brief_includes_own_memory(self, project):
+        self._populate(project)
+        runner = CliRunner()
+        result = runner.invoke(cli, ["memory", "brief", "sys-medic", "--target", str(project)])
+        assert result.exit_code == 0
+        assert "Orientation Brief for: sys-medic" in result.output
+        assert "Your Memory" in result.output
+        assert "tegpi-01" in result.output  # content from sys-medic memory
+
+    def test_brief_includes_cross_agent_context(self, project):
+        self._populate(project)
+        runner = CliRunner()
+        result = runner.invoke(cli, ["memory", "brief", "sys-medic", "--target", str(project)])
+        assert result.exit_code == 0
+        assert "Context From Other Agents" in result.output
+        assert "project-management" in result.output
+
+    def test_brief_coach_tip_present(self, project):
+        self._populate(project)
+        runner = CliRunner()
+        result = runner.invoke(cli, ["memory", "brief", "sys-medic", "--target", str(project)])
+        assert result.exit_code == 0
+        assert "agent-coach" in result.output
+
+    def test_brief_no_memory_gives_guidance(self, project):
+        runner = CliRunner()
+        result = runner.invoke(cli, ["memory", "brief", "sys-medic", "--target", str(project)])
+        assert result.exit_code == 0
+        assert "No agent memory files found" in result.output
+
+    def test_brief_raw_flag_skips_header(self, project):
+        self._populate(project)
+        runner = CliRunner()
+        result = runner.invoke(cli, ["memory", "brief", "sys-medic", "--target", str(project), "--raw"])
+        assert result.exit_code == 0
+        assert "=== sys-medic ===" in result.output
+        # Raw mode should not include the orientation header
+        assert "Orientation Brief for:" not in result.output
+
+
+class TestMemoryClear:
+    def test_clear_removes_file(self, project):
+        memory_file = project / ".kaizen" / "agents" / "sys-medic" / "memory.md"
+        memory_file.parent.mkdir(parents=True, exist_ok=True)
+        memory_file.write_text(_sys_medic_memory())
+
+        runner = CliRunner()
+        result = runner.invoke(
+            cli, ["memory", "clear", "sys-medic", "--target", str(project)], input="y\n"
+        )
+        assert result.exit_code == 0
+        assert not memory_file.exists()
+
+    def test_clear_missing_is_graceful(self, project):
+        runner = CliRunner()
+        result = runner.invoke(
+            cli, ["memory", "clear", "sys-medic", "--target", str(project)], input="y\n"
+        )
+        assert result.exit_code == 0
+        assert "nothing to clear" in result.output
+
+
+class TestProtocolsCommand:
+    def test_protocols_list_finds_sys_medic(self):
+        """Protocols list against the real agents dir should include sys-medic k3s protocol."""
+        runner = CliRunner()
+        result = runner.invoke(cli, ["protocols", "list"])
+        assert result.exit_code == 0
+        assert "sys-medic" in result.output
+        assert "k3s-node-health-assessment" in result.output.replace("-", "-")
+
+    def test_protocols_list_filtered_by_agent(self):
+        runner = CliRunner()
+        result = runner.invoke(cli, ["protocols", "list", "sys-medic"])
+        assert result.exit_code == 0
+        assert "k3s" in result.output.lower()
+
+    def test_protocols_show_outputs_content(self):
+        runner = CliRunner()
+        result = runner.invoke(cli, ["protocols", "show", "sys-medic", "k3s-node-health-assessment"])
+        assert result.exit_code == 0
+        # Protocol should contain key structural sections
+        assert "k3s" in result.output.lower()
+        assert "Prerequisites" in result.output or "Scope" in result.output
+
+    def test_protocols_list_unknown_agent_no_crash(self):
+        runner = CliRunner()
+        result = runner.invoke(cli, ["protocols", "list", "nonexistent-agent"])
+        assert result.exit_code == 0
+        assert "No protocols found" in result.output