fix(agent-context): preserve disabled context target

Author: AustinZ21

src/specify_cli/agents.py

@@ -398,18 +398,19 @@ def resolve_skill_placeholders(
 
         body = body.replace("{ARGS}", "$ARGUMENTS").replace("__AGENT__", agent_name)
 
-        # Resolve __CONTEXT_FILE__ from the agent-context extension config
-        # when enabled. Fall back to init-options.json for projects that
-        # haven't migrated or that explicitly disabled the extension.
+        # Resolve __CONTEXT_FILE__ from the agent-context extension config.
+        # When disabled, ignore stale context_files but keep the singular
+        # context_file value so generated commands still point at the agent
+        # context file managed before the extension was disabled.
         context_file = ""
         from .integrations.base import IntegrationBase
 
-        if IntegrationBase._agent_context_extension_enabled(project_root):
-            # Local import: _load_agent_context_config lives in __init__.py which
-            # imports agents.py, so a top-level import would be circular.
-            from . import _load_agent_context_config
+        # Local import: _load_agent_context_config lives in __init__.py which
+        # imports agents.py, so a top-level import would be circular.
+        from . import _load_agent_context_config
 
-            ac_cfg = _load_agent_context_config(project_root)
+        ac_cfg = _load_agent_context_config(project_root)
+        if IntegrationBase._agent_context_extension_enabled(project_root):
             context_files = ac_cfg.get("context_files")
             if isinstance(context_files, list):
                 context_file_values = []
@@ -435,6 +436,10 @@ def resolve_skill_placeholders(
                         context_file = IntegrationBase._validate_context_file_path(
                             project_root, candidate
                         )
+        else:
+            configured_context_file = ac_cfg.get("context_file")
+            if isinstance(configured_context_file, str):
+                context_file = configured_context_file.strip()
         if not context_file:
             context_file = init_opts.get("context_file") or ""
         body = body.replace("__CONTEXT_FILE__", context_file)

tests/extensions/test_extension_agent_context.py

@@ -6,6 +6,7 @@
 import os
 import shutil
 import subprocess
+import sys
 from pathlib import Path
 
 import pytest
@@ -155,6 +156,8 @@ def shlex_quote(value: str) -> str:
 
 def _run_powershell_agent_context_script(project_root: Path) -> subprocess.CompletedProcess:
     script = EXT_DIR / "scripts" / "powershell" / "update-agent-context.ps1"
+    env = os.environ.copy()
+    env["PATH"] = str(Path(sys.executable).parent) + os.pathsep + env.get("PATH", "")
     return subprocess.run(
         [
             POWERSHELL,
@@ -165,6 +168,7 @@ def _run_powershell_agent_context_script(project_root: Path) -> subprocess.Compl
             str(script),
         ],
         cwd=project_root,
+        env=env,
         capture_output=True,
         text=True,
         timeout=30,
@@ -540,6 +544,26 @@ def test_disabled_extension_ignores_invalid_context_files(self, 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"
+
 
 class TestBundledUpdaterPathValidation:
     def test_bash_script_contains_resolved_containment_check(self):