Fix follow-up agent-context review issues

Author: Copilot

extensions/agent-context/agent-context-config.yml

@@ -5,7 +5,7 @@
 # Path (relative to the project root) to the coding agent context file
 # managed by this extension (e.g. CLAUDE.md, AGENTS.md,
 # .github/copilot-instructions.md). Set automatically from the active
-# integration; edit to override.
+# integration and regenerated during `specify init` or integration switches.
 context_file: ""
 
 # Delimiters for the managed Spec Kit section.

extensions/agent-context/scripts/bash/update-agent-context.sh

@@ -41,17 +41,25 @@ fi
 
 # Parse extension config once; emit three newline-separated fields:
 # context_file, context_markers.start, context_markers.end
-_raw_opts="$("$_python" - "$EXT_CONFIG" <<'PY'
+if ! _raw_opts="$("$_python" - "$EXT_CONFIG" <<'PY'
 import sys
 try:
     import yaml
 except ImportError:
-    yaml = None
+    print(
+        "agent-context: PyYAML is required to parse extension config; cannot update context.",
+        file=sys.stderr,
+    )
+    sys.exit(2)
 try:
     with open(sys.argv[1], "r", encoding="utf-8") as fh:
-        data = yaml.safe_load(fh) if yaml else {}
-except Exception:
-    data = {}
+        data = yaml.safe_load(fh)
+except Exception as exc:
+    print(
+        f"agent-context: unable to parse {sys.argv[1]} ({exc}); cannot update context.",
+        file=sys.stderr,
+    )
+    sys.exit(2)
 if not isinstance(data, dict):
     data = {}
 def get_str(obj, *keys):
@@ -66,7 +74,10 @@ print(get_str(data, "context_file"))
 print(get_str(data, "context_markers", "start"))
 print(get_str(data, "context_markers", "end"))
 PY
-)"
+)"; then
+  echo "agent-context: failed to read extension config; skipping update." >&2
+  exit 0
+fi
 
 {
   IFS= read -r CONTEXT_FILE

extensions/agent-context/scripts/powershell/update-agent-context.ps1

@@ -16,6 +16,25 @@ param(
     [string]$PlanPath
 )
 
+function Get-ConfigValue {
+    param(
+        [AllowNull()][object]$Object,
+        [Parameter(Mandatory = $true)][string]$Key
+    )
+
+    if ($null -eq $Object) {
+        return $null
+    }
+    if ($Object -is [System.Collections.IDictionary]) {
+        return $Object[$Key]
+    }
+    $prop = $Object.PSObject.Properties[$Key]
+    if ($prop) {
+        return $prop.Value
+    }
+    return $null
+}
+
 $ErrorActionPreference = 'Stop'
 $DefaultStart = '<!-- SPECKIT START -->'
 $DefaultEnd   = '<!-- SPECKIT END -->'
@@ -47,22 +66,30 @@ import json
 import sys
 try:
     import yaml
-except Exception:
-    yaml = None
+except ImportError:
+    print(
+        "agent-context: PyYAML is required to parse extension config; cannot update context.",
+        file=sys.stderr,
+    )
+    sys.exit(2)
 
 try:
     with open(sys.argv[1], "r", encoding="utf-8") as fh:
-        data = yaml.safe_load(fh) if yaml else {}
-except Exception:
-    data = {}
+        data = yaml.safe_load(fh)
+except Exception as exc:
+    print(
+        f"agent-context: unable to parse {sys.argv[1]} ({exc}); cannot update context.",
+        file=sys.stderr,
+    )
+    sys.exit(2)
 
 if not isinstance(data, dict):
     data = {}
 
 print(json.dumps(data))
 '@ $ExtConfig
             if ($LASTEXITCODE -eq 0 -and $jsonOut) {
-                $Options = $jsonOut | ConvertFrom-Json -AsHashtable -ErrorAction Stop
+                $Options = $jsonOut | ConvertFrom-Json -ErrorAction Stop
             }
         } catch {
             $Options = $null
@@ -75,21 +102,23 @@ print(json.dumps(data))
     }
 }
 
-$ContextFile = $Options['context_file']
+$ContextFile = Get-ConfigValue -Object $Options -Key 'context_file'
 if (-not $ContextFile) {
     Write-Host 'agent-context: context_file not set in extension config; nothing to do.'
     exit 0
 }
 
 $MarkerStart = $DefaultStart
 $MarkerEnd   = $DefaultEnd
-$cm = $Options['context_markers']
+$cm = Get-ConfigValue -Object $Options -Key 'context_markers'
 if ($cm) {
-    if ($cm['start'] -is [string] -and $cm['start']) {
-        $MarkerStart = $cm['start']
+    $cmStart = Get-ConfigValue -Object $cm -Key 'start'
+    if ($cmStart -is [string] -and $cmStart) {
+        $MarkerStart = $cmStart
     }
-    if ($cm['end'] -is [string] -and $cm['end']) {
-        $MarkerEnd = $cm['end']
+    $cmEnd = Get-ConfigValue -Object $cm -Key 'end'
+    if ($cmEnd -is [string] -and $cmEnd) {
+        $MarkerEnd = $cmEnd
     }
 }
 

src/specify_cli/__init__.py

@@ -1549,20 +1549,24 @@ def _clear_init_options_for_integration(project_root: Path, integration_key: str
     no stale path is left behind when the integration is uninstalled.
     """
     opts = load_init_options(project_root)
+    has_legacy_context_keys = ("context_file" in opts) or ("context_markers" in opts)
+    # Remove legacy fields that older versions may have written.
+    opts.pop("context_file", None)
+    opts.pop("context_markers", None)
+
     if opts.get("integration") == integration_key or opts.get("ai") == integration_key:
         opts.pop("integration", None)
         opts.pop("ai", None)
         opts.pop("ai_skills", None)
-        # Remove legacy fields that older versions may have written.
-        opts.pop("context_file", None)
-        opts.pop("context_markers", None)
         save_init_options(project_root, opts)
         # Clear context_file in the extension config too.
         ext_cfg_path = project_root / _AGENT_CTX_EXT_CONFIG
         if ext_cfg_path.exists():
             _update_agent_context_config_file(
                 project_root, "", preserve_markers=True
             )
+    elif has_legacy_context_keys:
+        save_init_options(project_root, opts)
 
 
 def _remove_integration_json(project_root: Path) -> None:

tests/extensions/test_extension_agent_context.py

@@ -294,6 +294,27 @@ def test_clear_init_options_clears_ext_config_context_file(self, tmp_path):
         cfg = _load_agent_context_config(tmp_path)
         assert cfg.get("context_file") == ""
 
+    def test_clear_init_options_removes_legacy_context_keys_even_when_not_active(
+        self, tmp_path
+    ):
+        from specify_cli import _clear_init_options_for_integration
+
+        save_init_options(
+            tmp_path,
+            {
+                "integration": "copilot",
+                "ai": "copilot",
+                "context_file": "CLAUDE.md",
+                "context_markers": {"start": "<!-- X -->", "end": "<!-- Y -->"},
+            },
+        )
+        _clear_init_options_for_integration(tmp_path, "claude")
+        opts = load_init_options(tmp_path)
+        assert opts["integration"] == "copilot"
+        assert opts["ai"] == "copilot"
+        assert "context_file" not in opts
+        assert "context_markers" not in opts
+
     def test_update_init_options_writes_context_file_to_ext_config(self, tmp_path):
         from specify_cli import _update_init_options_for_integration