Address review: chmod ordering, preserve markers, PS1 Python check, YAML key order

- Move ensure_executable_scripts after agent-context extension install
  so extension scripts get execute bits set
- Use preserve_markers=True on reinit to keep user-customized markers
- Add Python 3 version check in PowerShell fallback (matching bash behavior)
- Add sort_keys=False to yaml.safe_dump for stable config output

Author: mnriem

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

@@ -77,8 +77,12 @@ if ($null -eq $Options) {
     $pythonCmd = $null
     foreach ($candidate in @('python3', 'python')) {
         if (Get-Command $candidate -ErrorAction SilentlyContinue) {
-            $pythonCmd = $candidate
-            break
+            # Verify it is Python 3
+            $verOut = & $candidate --version 2>&1
+            if ($verOut -match 'Python 3') {
+                $pythonCmd = $candidate
+                break
+            }
         }
     }
 

src/specify_cli/__init__.py

@@ -342,7 +342,7 @@ def _save_agent_context_config(
     """Persist *config* to the agent-context extension config file."""
     path = project_root / _AGENT_CTX_EXT_CONFIG
     path.parent.mkdir(parents=True, exist_ok=True)
-    path.write_text(yaml.safe_dump(config, default_flow_style=False), encoding="utf-8")
+    path.write_text(yaml.safe_dump(config, default_flow_style=False, sort_keys=False), encoding="utf-8")
 
 
 def _update_agent_context_config_file(

src/specify_cli/commands/init.py

@@ -537,8 +537,6 @@ def init(
                     sanitized_wf = str(wf_err).replace('\n', ' ').strip()
                     tracker.error("workflow", f"install failed: {sanitized_wf[:120]}")
 
-                ensure_executable_scripts(project_path, tracker=tracker)
-
                 init_opts = {
                     "ai": selected_ai,
                     "integration": resolved_integration.key,
@@ -583,9 +581,11 @@ def init(
                     _update_agent_context_config_file(
                         project_path,
                         resolved_integration.context_file,
-                        preserve_markers=False,
+                        preserve_markers=True,
                     )
 
+                ensure_executable_scripts(project_path, tracker=tracker)
+
                 if preset:
                     try:
                         from ..presets import PresetManager, PresetCatalog, PresetError