fix(agent-context): support multiple context files safely (#2969)

* fix(agent-context): support multiple context files safely

* fix(agent-context): harden context file validation

* fix(agent-context): preserve disabled context target

* fix(agent-context): address review follow-ups

* fix(agent-context): dedupe PowerShell context files

* fix(agent-context): align context file dedupe

* fix(agent-context): align bash context file dedupe

* fix(agent-context): preserve disabled display target

* fix(agent-context): require yaml-capable updater python

* fix(agent-context): preserve context files config

* fix(agent-context): align context file fallbacks

* fix(agent-context): share context file resolution

---------

Co-authored-by: AustinZ21 <AustinZ21@users.noreply.github.com>

tests/extensions/test_extension_agent_context.py

@@ -3,8 +3,13 @@
 from __future__ import annotations
 
 import json
+import os
+import shutil
+import subprocess
+import sys
 from pathlib import Path
 
+import pytest
 import yaml
 
 from specify_cli import (
@@ -13,18 +18,25 @@ from specify_cli import (
     load_init_options,
     save_init_options,
 )
+from specify_cli.agents import CommandRegistrar
 from specify_cli.integrations.base import IntegrationBase
 from specify_cli.integrations.claude import ClaudeIntegration
+from tests.conftest import requires_bash
 
 
 PROJECT_ROOT = Path(__file__).resolve().parent.parent.parent
 EXT_DIR = PROJECT_ROOT / "extensions" / "agent-context"
+BASH = shutil.which("bash")
+POWERSHELL = (
+    shutil.which("pwsh") or shutil.which("powershell.exe") or shutil.which("powershell")
+)
 
 
 def _write_ext_config(project_root: Path, **overrides: object) -> None:
     """Write a minimal agent-context extension config."""
     cfg: dict = {
         "context_file": overrides.get("context_file", ""),
+        "context_files": overrides.get("context_files", []),
         "context_markers": overrides.get(
             "context_markers",
             {
@@ -72,6 +84,14 @@ class TestExtensionLayout:
         assert cmd.is_file()
         assert "agent-context-config.yml" in cmd.read_text(encoding="utf-8")
 
+    def test_command_file_documents_context_file_constraints(self):
+        text = (
+            EXT_DIR / "commands" / "speckit.agent-context.update.md"
+        ).read_text(encoding="utf-8")
+        assert "context file(s)" in text
+        assert "Windows drive paths" in text
+        assert "backslash separators" in text
+
     def test_bundled_scripts_exist(self):
         assert (EXT_DIR / "scripts" / "bash" / "update-agent-context.sh").is_file()
         assert (EXT_DIR / "scripts" / "powershell" / "update-agent-context.ps1").is_file()
@@ -107,6 +127,184 @@ class _CtxIntegration(ClaudeIntegration):
     """Use Claude as a concrete integration with a context_file."""
 
 
+class _NoContextIntegration(IntegrationBase):
+    """Minimal integration with no context_file for base-class fallback tests."""
+
+
+def _install_agent_context_config(project_root: Path, **overrides: object) -> None:
+    _write_ext_config(project_root, **overrides)
+
+
+def _bash_posix_path(path: Path) -> str:
+    """Convert a Windows path to the POSIX form used by the available bash."""
+    resolved = str(path.resolve())
+    if os.name != "nt":
+        return resolved
+
+    if BASH:
+        converted = subprocess.run(
+            [
+                BASH,
+                "-lc",
+                "command -v cygpath >/dev/null 2>&1 && cygpath -u \"$1\"",
+                "bash",
+                resolved,
+            ],
+            capture_output=True,
+            text=True,
+            timeout=30,
+        )
+        if converted.returncode == 0 and converted.stdout.strip():
+            return converted.stdout.strip()
+
+    drive = path.drive.rstrip(":").lower()
+    posix = path.as_posix()
+    return f"/mnt/{drive}{posix[2:]}" if drive else posix
+
+
+def _ensure_test_python_on_path(project_root: Path) -> Path:
+    """Create python/python3 shims that run the current pytest interpreter."""
+    shim_dir = project_root / ".test-python-bin"
+    shim_dir.mkdir(exist_ok=True)
+    python_exe = Path(sys.executable).resolve()
+    shell_python = _bash_posix_path(python_exe)
+
+    for name in ("python", "python3"):
+        shell_shim = shim_dir / name
+        shell_shim.write_text(
+            f"#!/usr/bin/env sh\nexec {shlex_quote(shell_python)} \"$@\"\n",
+            encoding="utf-8",
+            newline="\n",
+        )
+        shell_shim.chmod(0o755)
+
+        if os.name == "nt":
+            cmd_shim = shim_dir / f"{name}.cmd"
+            cmd_shim.write_text(
+                f'@echo off\r\n"{python_exe}" %*\r\n',
+                encoding="utf-8",
+            )
+
+    return shim_dir
+
+
+def _current_pythonpath() -> str:
+    """Return sys.path entries needed by child script interpreters."""
+    entries = [
+        entry
+        for entry in sys.path
+        if isinstance(entry, str) and entry
+    ]
+    existing = os.environ.get("PYTHONPATH")
+    if existing:
+        entries.extend(entry for entry in existing.split(os.pathsep) if entry)
+    return os.pathsep.join(dict.fromkeys(entries))
+
+
+def _bundled_script_env(
+    project_root: Path,
+    *,
+    for_bash: bool = False,
+    speckit_python: str | None = None,
+) -> dict[str, str]:
+    env = os.environ.copy()
+    shim_dir = _ensure_test_python_on_path(project_root)
+    env["PATH"] = str(shim_dir) + os.pathsep + env.get("PATH", "")
+    env["SPECKIT_PYTHON"] = (
+        speckit_python
+        if speckit_python is not None
+        else (_bash_posix_path(Path(sys.executable)) if for_bash else sys.executable)
+    )
+    pythonpath = _current_pythonpath()
+    if pythonpath:
+        env["PYTHONPATH"] = pythonpath
+    return env
+
+
+def _run_bash_agent_context_script(
+    project_root: Path,
+    *,
+    speckit_python: str | None = None,
+) -> subprocess.CompletedProcess:
+    script = EXT_DIR / "scripts" / "bash" / "update-agent-context.sh"
+    env = _bundled_script_env(
+        project_root,
+        for_bash=True,
+        speckit_python=speckit_python,
+    )
+    if os.name == "nt":
+        root = _bash_posix_path(project_root)
+        script_path = _bash_posix_path(script)
+        shim_dir = _bash_posix_path(_ensure_test_python_on_path(project_root))
+        command = (
+            f"export PATH={shlex_quote(shim_dir)}:\"$PATH\"; "
+            f"cd {shlex_quote(root)} && {shlex_quote(script_path)}"
+        )
+        return subprocess.run(
+            [BASH, "-lc", command],
+            env=env,
+            capture_output=True,
+            text=True,
+            timeout=30,
+        )
+    return subprocess.run(
+        [BASH, str(script)],
+        cwd=project_root,
+        env=env,
+        capture_output=True,
+        text=True,
+        timeout=30,
+    )
+
+
+def shlex_quote(value: str) -> str:
+    return "'" + value.replace("'", "'\"'\"'") + "'"
+
+
+def _run_powershell_agent_context_script(project_root: Path) -> subprocess.CompletedProcess:
+    script = EXT_DIR / "scripts" / "powershell" / "update-agent-context.ps1"
+    env = _bundled_script_env(project_root)
+    return subprocess.run(
+        [
+            POWERSHELL,
+            "-NoProfile",
+            "-ExecutionPolicy",
+            "Bypass",
+            "-File",
+            str(script),
+        ],
+        cwd=project_root,
+        env=env,
+        capture_output=True,
+        text=True,
+        timeout=30,
+    )
+
+
+def _run_powershell_agent_context_script_with_env(
+    project_root: Path,
+    *,
+    speckit_python: str,
+) -> subprocess.CompletedProcess:
+    script = EXT_DIR / "scripts" / "powershell" / "update-agent-context.ps1"
+    env = _bundled_script_env(project_root, speckit_python=speckit_python)
+    return subprocess.run(
+        [
+            POWERSHELL,
+            "-NoProfile",
+            "-ExecutionPolicy",
+            "Bypass",
+            "-File",
+            str(script),
+        ],
+        cwd=project_root,
+        env=env,
+        capture_output=True,
+        text=True,
+        timeout=30,
+    )
+
+
 class TestContextMarkerResolution:
     def test_defaults_when_ext_config_missing(self, tmp_path):
         i = _CtxIntegration()
@@ -200,6 +398,142 @@ class TestUpsertWithCustomMarkers:
         assert text.startswith("# header\n")
         assert "footer" in text
 
+    def test_upsert_uses_configured_context_files(self, tmp_path):
+        _write_ext_config(
+            tmp_path,
+            context_file="CLAUDE.md",
+            context_files=["AGENTS.md", "CLAUDE.md"],
+        )
+        i = _CtxIntegration()
+        result = i.upsert_context_section(
+            tmp_path, plan_path="specs/001-foo/plan.md"
+        )
+        assert result == tmp_path / "AGENTS.md"
+        for name in ("AGENTS.md", "CLAUDE.md"):
+            text = (tmp_path / name).read_text(encoding="utf-8")
+            assert IntegrationBase.CONTEXT_MARKER_START in text
+            assert "specs/001-foo/plan.md" in text
+
+    def test_context_files_deduplicate_with_platform_semantics(self, tmp_path):
+        duplicate = "agents.md" if os.name == "nt" else "AGENTS.md"
+        _write_ext_config(
+            tmp_path,
+            context_file="CLAUDE.md",
+            context_files=["AGENTS.md", "CLAUDE.md", duplicate],
+        )
+
+        files = _CtxIntegration()._resolve_context_files(tmp_path)
+
+        assert files == ["AGENTS.md", "CLAUDE.md"]
+
+    def test_empty_context_files_falls_back_to_config_context_file(self, tmp_path):
+        _write_ext_config(
+            tmp_path,
+            context_file="AGENTS.md",
+            context_files=[],
+        )
+
+        files = _CtxIntegration()._resolve_context_files(tmp_path)
+
+        assert files == ["AGENTS.md"]
+
+    def test_config_context_file_takes_precedence_over_class_default(self, tmp_path):
+        _write_ext_config(
+            tmp_path,
+            context_file="AGENTS.md",
+        )
+
+        i = _CtxIntegration()
+        result = i.upsert_context_section(
+            tmp_path, plan_path="specs/001-foo/plan.md"
+        )
+
+        assert result == tmp_path / "AGENTS.md"
+        assert (tmp_path / "AGENTS.md").exists()
+        assert not (tmp_path / "CLAUDE.md").exists()
+
+    def test_config_context_file_fallback_rejects_invalid_path(self, tmp_path):
+        _write_ext_config(
+            tmp_path,
+            context_file="../outside.md",
+            context_files=[],
+        )
+
+        with pytest.raises(ValueError, match="project-relative|must not contain"):
+            _CtxIntegration()._resolve_context_files(tmp_path)
+
+    def test_remove_uses_configured_context_files(self, tmp_path):
+        _write_ext_config(
+            tmp_path,
+            context_file="CLAUDE.md",
+            context_files=["AGENTS.md", "CLAUDE.md"],
+        )
+        i = _CtxIntegration()
+        for name in ("AGENTS.md", "CLAUDE.md"):
+            (tmp_path / name).write_text(
+                f"head\n{IntegrationBase.CONTEXT_MARKER_START}\nbody\n"
+                f"{IntegrationBase.CONTEXT_MARKER_END}\ntail\n",
+                encoding="utf-8",
+            )
+        assert i.remove_context_section(tmp_path) is True
+        for name in ("AGENTS.md", "CLAUDE.md"):
+            text = (tmp_path / name).read_text(encoding="utf-8")
+            assert "body" not in text
+            assert "head" in text
+            assert "tail" in text
+
+    @pytest.mark.parametrize(
+        "bad_path",
+        [
+            "../outside.md",
+            "nested/../../outside.md",
+            "nested\\outside.md",
+            str(Path("/tmp/outside.md")),
+            "C:/tmp/outside.md",
+            "C:tmp/outside.md",
+        ],
+    )
+    def test_upsert_rejects_context_files_outside_project(self, tmp_path, bad_path):
+        _write_ext_config(
+            tmp_path,
+            context_file="CLAUDE.md",
+            context_files=["AGENTS.md", bad_path],
+        )
+        i = _CtxIntegration()
+        with pytest.raises(ValueError, match="project-relative|must not contain"):
+            i.upsert_context_section(tmp_path)
+
+        assert not (tmp_path / "AGENTS.md").exists()
+        assert not (tmp_path.parent / "outside.md").exists()
+
+    @pytest.mark.parametrize(
+        "bad_path",
+        [
+            "../outside.md",
+            "nested\\outside.md",
+            str(Path("/tmp/outside.md")),
+            "C:/tmp/outside.md",
+            "C:tmp/outside.md",
+        ],
+    )
+    def test_remove_rejects_context_files_outside_project(self, tmp_path, bad_path):
+        _write_ext_config(
+            tmp_path,
+            context_file="CLAUDE.md",
+            context_files=["AGENTS.md", bad_path],
+        )
+        outside = tmp_path.parent / "outside.md"
+        outside.write_text(
+            f"{IntegrationBase.CONTEXT_MARKER_START}\nbody\n"
+            f"{IntegrationBase.CONTEXT_MARKER_END}\n",
+            encoding="utf-8",
+        )
+        i = _CtxIntegration()
+        with pytest.raises(ValueError, match="project-relative|must not contain"):
+            i.remove_context_section(tmp_path)
+
+        assert "body" in outside.read_text(encoding="utf-8")
+
     def test_remove_uses_custom_markers(self, tmp_path):
         i = self._setup(
             tmp_path, {"start": "<!-- BEGIN -->", "end": "<!-- END -->"}
@@ -270,6 +604,17 @@ class TestExtensionEnabledGate:
         assert result is None
         assert not (tmp_path / "CLAUDE.md").exists()
 
+    def test_upsert_disabled_ignores_bad_context_files_config(self, tmp_path):
+        _write_registry(tmp_path, enabled=False)
+        _write_ext_config(
+            tmp_path,
+            context_file="CLAUDE.md",
+            context_files=["../disabled-upsert-outside.md"],
+        )
+        i = _CtxIntegration()
+        assert i.upsert_context_section(tmp_path) is None
+        assert not (tmp_path.parent / "disabled-upsert-outside.md").exists()
+
     def test_remove_skipped_when_disabled(self, tmp_path):
         _write_registry(tmp_path, enabled=False)
         i = _CtxIntegration()
@@ -283,6 +628,382 @@ class TestExtensionEnabledGate:
         # File must be unchanged when extension is disabled
         assert ctx.read_text(encoding="utf-8") == original
 
+    def test_remove_disabled_ignores_bad_context_files_config(self, tmp_path):
+        _write_registry(tmp_path, enabled=False)
+        _write_ext_config(
+            tmp_path,
+            context_file="CLAUDE.md",
+            context_files=["../disabled-remove-outside.md"],
+        )
+        outside = tmp_path.parent / "disabled-remove-outside.md"
+        outside.write_text(
+            f"{IntegrationBase.CONTEXT_MARKER_START}\nbody\n"
+            f"{IntegrationBase.CONTEXT_MARKER_END}\n",
+            encoding="utf-8",
+        )
+        i = _CtxIntegration()
+        assert i.remove_context_section(tmp_path) is False
+        assert "body" in outside.read_text(encoding="utf-8")
+
+    def test_context_file_display_disabled_uses_config_context_file(
+        self, tmp_path
+    ):
+        _write_registry(tmp_path, enabled=False)
+        _write_ext_config(
+            tmp_path,
+            context_file="AGENTS.md",
+            context_files=["../outside.md"],
+        )
+        i = _CtxIntegration()
+        assert i._context_file_display(tmp_path) == "AGENTS.md"
+
+    def test_context_file_display_disabled_without_context_file_returns_string(
+        self, tmp_path
+    ):
+        _write_registry(tmp_path, enabled=False)
+        i = _NoContextIntegration()
+        assert i._context_file_display(tmp_path) == ""
+
+
+class TestSkillPlaceholderContextValidation:
+    @pytest.mark.parametrize(
+        "bad_path",
+        [
+            "../outside.md",
+            "nested/../../outside.md",
+            "nested\\outside.md",
+            str(Path("/tmp/outside.md")),
+            "C:/tmp/outside.md",
+            "C:tmp/outside.md",
+        ],
+    )
+    def test_context_files_reject_invalid_config_paths(self, tmp_path, bad_path):
+        _write_ext_config(
+            tmp_path,
+            context_file="AGENTS.md",
+            context_files=["AGENTS.md", bad_path],
+        )
+
+        with pytest.raises(ValueError, match="project-relative|must not contain"):
+            CommandRegistrar.resolve_skill_placeholders(
+                "codex",
+                {},
+                "Read __CONTEXT_FILE__",
+                tmp_path,
+            )
+
+    @pytest.mark.parametrize(
+        "bad_path",
+        [
+            "../outside.md",
+            "C:tmp/outside.md",
+        ],
+    )
+    def test_context_file_rejects_invalid_config_path(self, tmp_path, bad_path):
+        _write_ext_config(
+            tmp_path,
+            context_file=bad_path,
+            context_files=[],
+        )
+
+        with pytest.raises(ValueError, match="project-relative|must not contain"):
+            CommandRegistrar.resolve_skill_placeholders(
+                "codex",
+                {},
+                "Read __CONTEXT_FILE__",
+                tmp_path,
+            )
+
+    def test_enabled_extension_rejects_invalid_legacy_init_options_path(
+        self, tmp_path
+    ):
+        save_init_options(tmp_path, {"context_file": "../outside.md"})
+
+        with pytest.raises(ValueError, match="must not contain"):
+            CommandRegistrar.resolve_skill_placeholders(
+                "codex",
+                {},
+                "Read __CONTEXT_FILE__",
+                tmp_path,
+            )
+
+    def test_disabled_extension_ignores_invalid_context_files(self, tmp_path):
+        _write_registry(tmp_path, enabled=False)
+        _write_ext_config(
+            tmp_path,
+            context_file="AGENTS.md",
+            context_files=["../outside.md"],
+        )
+        save_init_options(tmp_path, {"context_file": "AGENTS.md"})
+
+        content = CommandRegistrar.resolve_skill_placeholders(
+            "codex",
+            {},
+            "Read __CONTEXT_FILE__",
+            tmp_path,
+        )
+
+        assert content == "Read AGENTS.md"
+
+    def test_disabled_extension_uses_extension_context_file_before_init_options(
+        self, tmp_path
+    ):
+        _write_registry(tmp_path, enabled=False)
+        _write_ext_config(
+            tmp_path,
+            context_file="AGENTS.md",
+            context_files=["CLAUDE.md"],
+        )
+        save_init_options(tmp_path, {"context_file": "LEGACY.md"})
+
+        content = CommandRegistrar.resolve_skill_placeholders(
+            "codex",
+            {},
+            "Read __CONTEXT_FILE__",
+            tmp_path,
+        )
+
+        assert content == "Read AGENTS.md"
+
+    def test_context_files_deduplicate_with_platform_semantics(self, tmp_path):
+        duplicate = "agents.md" if os.name == "nt" else "AGENTS.md"
+        _write_ext_config(
+            tmp_path,
+            context_file="AGENTS.md",
+            context_files=["AGENTS.md", "CLAUDE.md", duplicate],
+        )
+
+        content = CommandRegistrar.resolve_skill_placeholders(
+            "codex",
+            {},
+            "Read __CONTEXT_FILE__",
+            tmp_path,
+        )
+
+        assert content == "Read AGENTS.md, CLAUDE.md"
+
+
+class TestBundledUpdaterPathValidation:
+    def test_bundled_script_env_makes_yaml_importable(self, tmp_path):
+        env = _bundled_script_env(tmp_path)
+
+        result = subprocess.run(
+            [env["SPECKIT_PYTHON"], "-c", "import yaml"],
+            env=env,
+            capture_output=True,
+            text=True,
+            timeout=30,
+        )
+
+        assert result.returncode == 0, result.stderr + result.stdout
+
+    @requires_bash
+    def test_bash_script_trims_context_file_fallback(self, tmp_path):
+        project = tmp_path / "project"
+        project.mkdir()
+        _install_agent_context_config(
+            project,
+            context_file="  AGENTS.md  ",
+            context_files=[],
+        )
+
+        result = _run_bash_agent_context_script(project)
+
+        assert result.returncode == 0, result.stderr + result.stdout
+        assert "agent-context: updated AGENTS.md" in (result.stderr + result.stdout)
+        assert (project / "AGENTS.md").exists()
+        assert not (project / "  AGENTS.md  ").exists()
+
+    @requires_bash
+    def test_bash_script_rejects_symlink_escape(self, tmp_path):
+        project = tmp_path / "project"
+        outside = tmp_path / "outside"
+        project.mkdir()
+        outside.mkdir()
+        _install_agent_context_config(
+            project,
+            context_file="AGENTS.md",
+            context_files=["link/out.md"],
+        )
+
+        if os.name == "nt":
+            root = _bash_posix_path(tmp_path)
+            create_link = subprocess.run(
+                [
+                    BASH,
+                    "-lc",
+                    f"ln -s {shlex_quote(root + '/outside')} "
+                    f"{shlex_quote(root + '/project/link')}",
+                ],
+                capture_output=True,
+                text=True,
+                timeout=30,
+            )
+            if create_link.returncode != 0:
+                pytest.skip(f"symlink unavailable: {create_link.stderr}")
+        else:
+            try:
+                (project / "link").symlink_to(outside, target_is_directory=True)
+            except OSError as exc:
+                pytest.skip(f"symlink unavailable: {exc}")
+
+        result = _run_bash_agent_context_script(project)
+
+        assert result.returncode == 1
+        assert "resolves outside the project root" in result.stderr
+        assert not (outside / "out.md").exists()
+
+    @requires_bash
+    def test_bash_script_deduplicates_context_files_in_order(self, tmp_path):
+        project = tmp_path / "project"
+        project.mkdir()
+        duplicate = "agents.md" if os.name == "nt" else "AGENTS.md"
+        _install_agent_context_config(
+            project,
+            context_file="AGENTS.md",
+            context_files=["AGENTS.md", "CLAUDE.md", duplicate],
+        )
+
+        result = _run_bash_agent_context_script(project)
+
+        assert result.returncode == 0, result.stderr + result.stdout
+        output = result.stderr + result.stdout
+        assert output.count("agent-context: updated AGENTS.md") == 1
+        assert output.count("agent-context: updated CLAUDE.md") == 1
+        assert "agent-context: updated agents.md" not in output
+
+    @requires_bash
+    def test_bash_script_falls_back_from_invalid_speckit_python(self, tmp_path):
+        project = tmp_path / "project"
+        project.mkdir()
+        _install_agent_context_config(
+            project,
+            context_file="AGENTS.md",
+            context_files=["AGENTS.md"],
+        )
+
+        result = _run_bash_agent_context_script(
+            project,
+            speckit_python="/definitely/missing/python",
+        )
+
+        assert result.returncode == 0, result.stderr + result.stdout
+        assert "agent-context: updated AGENTS.md" in (result.stderr + result.stdout)
+        assert (project / "AGENTS.md").exists()
+
+    @pytest.mark.skipif(POWERSHELL is None, reason="PowerShell not available")
+    def test_powershell_script_rejects_backslash_context_files(self, tmp_path):
+        project = tmp_path / "project"
+        project.mkdir()
+        _install_agent_context_config(
+            project,
+            context_file="AGENTS.md",
+            context_files=["nested\\AGENTS.md"],
+        )
+
+        result = _run_powershell_agent_context_script(project)
+
+        assert result.returncode == 1
+        assert "must not contain backslash separators" in (
+            result.stderr + result.stdout
+        )
+        assert not (project / "nested" / "AGENTS.md").exists()
+
+    @pytest.mark.skipif(POWERSHELL is None, reason="PowerShell not available")
+    def test_powershell_script_rejects_drive_qualified_context_files(self, tmp_path):
+        project = tmp_path / "project"
+        project.mkdir()
+        _install_agent_context_config(
+            project,
+            context_file="AGENTS.md",
+            context_files=["C:tmp/outside.md"],
+        )
+
+        result = _run_powershell_agent_context_script(project)
+
+        assert result.returncode == 1
+        assert "must be project-relative paths" in (result.stderr + result.stdout)
+        assert not (project / "tmp" / "outside.md").exists()
+
+    @pytest.mark.skipif(POWERSHELL is None, reason="PowerShell not available")
+    def test_powershell_script_deduplicates_context_files_in_order(self, tmp_path):
+        project = tmp_path / "project"
+        project.mkdir()
+        duplicate = "agents.md" if os.name == "nt" else "AGENTS.md"
+        _install_agent_context_config(
+            project,
+            context_file="AGENTS.md",
+            context_files=["AGENTS.md", "CLAUDE.md", duplicate],
+        )
+
+        result = _run_powershell_agent_context_script(project)
+
+        assert result.returncode == 0, result.stderr + result.stdout
+        output = result.stderr + result.stdout
+        assert output.count("agent-context: updated AGENTS.md") == 1
+        assert output.count("agent-context: updated CLAUDE.md") == 1
+        assert "agent-context: updated agents.md" not in output
+
+    @pytest.mark.skipif(POWERSHELL is None, reason="PowerShell not available")
+    def test_powershell_script_falls_back_from_invalid_speckit_python(self, tmp_path):
+        project = tmp_path / "project"
+        project.mkdir()
+        _install_agent_context_config(
+            project,
+            context_file="AGENTS.md",
+            context_files=["AGENTS.md"],
+        )
+
+        result = _run_powershell_agent_context_script_with_env(
+            project,
+            speckit_python=str(project / "missing-python"),
+        )
+
+        assert result.returncode == 0, result.stderr + result.stdout
+        assert "agent-context: updated AGENTS.md" in (result.stderr + result.stdout)
+        assert (project / "AGENTS.md").exists()
+
+    @pytest.mark.skipif(
+        POWERSHELL is None or os.name != "nt",
+        reason="Windows PowerShell junction test requires Windows",
+    )
+    def test_powershell_script_rejects_junction_escape(self, tmp_path):
+        project = tmp_path / "project"
+        outside = tmp_path / "outside"
+        project.mkdir()
+        outside.mkdir()
+        _install_agent_context_config(
+            project,
+            context_file="AGENTS.md",
+            context_files=["link/out.md"],
+        )
+
+        create_link = subprocess.run(
+            [
+                POWERSHELL,
+                "-NoProfile",
+                "-ExecutionPolicy",
+                "Bypass",
+                "-Command",
+                (
+                    "New-Item -ItemType Junction "
+                    f"-Path {str(project / 'link')!r} "
+                    f"-Target {str(outside)!r} | Out-Null"
+                ),
+            ],
+            capture_output=True,
+            text=True,
+            timeout=30,
+        )
+        if create_link.returncode != 0:
+            pytest.skip(f"junction unavailable: {create_link.stderr}")
+
+        result = _run_powershell_agent_context_script(project)
+
+        assert result.returncode == 1
+        assert "resolves outside the project root" in (result.stderr + result.stdout)
+        assert not (outside / "out.md").exists()
+
 
 # ── Extension config writers ─────────────────────────────────────────────────
 
@@ -349,6 +1070,65 @@ class TestExtensionConfigWriters:
         assert cfg["context_file"] == i.context_file
         assert "context_markers" in cfg
 
+    def test_update_init_options_preserves_context_files(self, tmp_path):
+        from specify_cli import _update_init_options_for_integration
+
+        _write_ext_config(
+            tmp_path,
+            context_file="AGENTS.md",
+            context_files=["AGENTS.md", "CLAUDE.md"],
+        )
+        i = _CtxIntegration()
+        _update_init_options_for_integration(tmp_path, i, script_type="sh")
+        cfg = _load_agent_context_config(tmp_path)
+        assert cfg["context_file"] == i.context_file
+        assert cfg["context_files"] == ["AGENTS.md", "CLAUDE.md"]
+
+    def test_update_init_options_preserves_empty_context_files(self, tmp_path):
+        from specify_cli import _update_init_options_for_integration
+
+        _write_ext_config(
+            tmp_path,
+            context_file="AGENTS.md",
+            context_files=[],
+        )
+        i = _CtxIntegration()
+        _update_init_options_for_integration(tmp_path, i, script_type="sh")
+        cfg = _load_agent_context_config(tmp_path)
+        assert cfg["context_file"] == i.context_file
+        assert cfg["context_files"] == []
+
+    def test_update_init_options_normalizes_invalid_context_files(self, tmp_path):
+        from specify_cli import _update_init_options_for_integration
+
+        _write_ext_config(tmp_path, context_file="AGENTS.md")
+        cfg = _load_agent_context_config(tmp_path)
+        cfg["context_files"] = "AGENTS.md"
+        _save_agent_context_config(tmp_path, cfg)
+
+        i = _CtxIntegration()
+        _update_init_options_for_integration(tmp_path, i, script_type="sh")
+        cfg = _load_agent_context_config(tmp_path)
+        assert cfg["context_file"] == i.context_file
+        assert cfg["context_files"] == []
+
+    def test_clear_init_options_clears_context_files(self, tmp_path):
+        from specify_cli import _clear_init_options_for_integration
+
+        save_init_options(
+            tmp_path,
+            {"integration": "claude", "ai": "claude"},
+        )
+        _write_ext_config(
+            tmp_path,
+            context_file="CLAUDE.md",
+            context_files=["AGENTS.md", "CLAUDE.md"],
+        )
+        _clear_init_options_for_integration(tmp_path, "claude")
+        cfg = _load_agent_context_config(tmp_path)
+        assert cfg.get("context_file") == ""
+        assert "context_files" not in cfg
+
     def test_update_init_options_preserves_custom_markers(self, tmp_path):
         from specify_cli import _update_init_options_for_integration