fix: address fifth round of Copilot PR review feedback

- Reconcile all commands from full priority stack after install so
  install order doesn't determine the winning command file
- Fix bash wrap substitution: use split-and-rejoin (%%/# parameter
  expansion) instead of //pattern/replacement to avoid & expansion
  corrupting content containing ampersands
- Support python/py/py-3 fallbacks in PowerShell Resolve-TemplateContent
  via Get-Python3Command helper, matching Windows environments where
  python3 may not be available
- Reconciliation skips skill-based agents to avoid overwriting properly
  formatted SKILL.md files written by _register_skills()

Author: mnriem

scripts/bash/common.sh

@@ -542,15 +542,25 @@ except Exception:
                 case "$strat" in
                     prepend) content="$(printf '%s\n\n%s' "$layer_content" "$content")" ;;
                     append)  content="$(printf '%s\n\n%s' "$content" "$layer_content")" ;;
-                    wrap)    content="${layer_content//\{CORE_TEMPLATE\}/$content}" ;;
+                    wrap)
+                        # Split on placeholder and rejoin with content to avoid
+                        # bash & expansion in parameter substitution replacement.
+                        local before="${layer_content%%\{CORE_TEMPLATE\}*}"
+                        local after="${layer_content#*\{CORE_TEMPLATE\}}"
+                        content="${before}${content}${after}"
+                        ;;
                 esac
             fi
         else
             case "$strat" in
                 replace) content="$layer_content" ;;
                 prepend) content="$(printf '%s\n\n%s' "$layer_content" "$content")" ;;
                 append)  content="$(printf '%s\n\n%s' "$content" "$layer_content")" ;;
-                wrap)    content="${layer_content//\{CORE_TEMPLATE\}/$content}" ;;
+                wrap)
+                    local before="${layer_content%%\{CORE_TEMPLATE\}*}"
+                    local after="${layer_content#*\{CORE_TEMPLATE\}}"
+                    content="${before}${content}${after}"
+                    ;;
             esac
         fi
     done

scripts/powershell/common.ps1

@@ -287,6 +287,21 @@ function Test-DirHasFiles {
     }
 }
 
+# Find a usable Python 3 executable (python3, python, or py -3).
+# Returns the command/arguments as an array, or $null if none found.
+function Get-Python3Command {
+    if (Get-Command python3 -ErrorAction SilentlyContinue) { return @('python3') }
+    if (Get-Command python -ErrorAction SilentlyContinue) {
+        $ver = & python --version 2>&1
+        if ($ver -match 'Python 3') { return @('python') }
+    }
+    if (Get-Command py -ErrorAction SilentlyContinue) {
+        $ver = & py -3 --version 2>&1
+        if ($ver -match 'Python 3') { return @('py', '-3') }
+    }
+    return $null
+}
+
 # Resolve a template name to a file path using the priority stack:
 #   1. .specify/templates/overrides/
 #   2. .specify/presets/<preset-id>/templates/ (sorted by priority from .registry)
@@ -401,10 +416,11 @@ function Resolve-TemplateContent {
                 $strategy = 'replace'
                 $manifestFilePath = ''
                 $manifest = Join-Path $presetsDir "$presetId/preset.yml"
-                if ((Test-Path $manifest) -and (Get-Command python3 -ErrorAction SilentlyContinue)) {
+                $pyCmd = Get-Python3Command
+                if ((Test-Path $manifest) -and $pyCmd) {
                     try {
-                        # Use python3 to parse YAML manifest for strategy and file path
-                        $stratResult = & python3 -c @"
+                        # Use Python to parse YAML manifest for strategy and file path
+                        $stratResult = & $pyCmd[0] @($pyCmd[1..99]) -c @"
 import sys
 try:
     import yaml

src/specify_cli/presets.py

@@ -646,8 +646,8 @@ def _reconcile_composed_commands(self, command_names: List[str]) -> None:
                                 continue
                             for tmpl in manifest.templates:
                                 if tmpl.get("name") == cmd_name and tmpl.get("type") == "command":
-                                    registrar.register_commands_for_all_agents(
-                                        [tmpl], manifest.id, pack_dir, self.project_root
+                                    self._register_for_non_skill_agents(
+                                        registrar, [tmpl], manifest.id, pack_dir
                                     )
                                     registered = True
                                     break
@@ -681,9 +681,10 @@ def _reconcile_composed_commands(self, command_names: List[str]) -> None:
                             composed_dir.mkdir(parents=True, exist_ok=True)
                             composed_file = composed_dir / f"{cmd_name}.md"
                             composed_file.write_text(composed, encoding="utf-8")
-                            registrar.register_commands_for_all_agents(
+                            self._register_for_non_skill_agents(
+                                registrar,
                                 [{**tmpl, "file": f".composed/{cmd_name}.md"}],
-                                manifest.id, pack_dir, self.project_root,
+                                manifest.id, pack_dir,
                             )
                             registered = True
                             break
@@ -719,10 +720,36 @@ def _register_command_from_path(
             "type": "command",
             "file": cmd_path.name,
         }
-        registrar.register_commands_for_all_agents(
-            [cmd_tmpl], "reconciled", cmd_path.parent, self.project_root
+        self._register_for_non_skill_agents(
+            registrar, [cmd_tmpl], "reconciled", cmd_path.parent
         )
 
+    def _register_for_non_skill_agents(
+        self,
+        registrar: Any,
+        commands: List[Dict[str, Any]],
+        source_id: str,
+        source_dir: Path,
+    ) -> None:
+        """Register commands for all non-skill agents.
+
+        Used during reconciliation to avoid overwriting properly formatted
+        SKILL.md files that were written by _register_skills().
+        """
+        registrar._ensure_configs()
+        for agent_name, agent_config in registrar.AGENT_CONFIGS.items():
+            if agent_config.get("extension") == "/SKILL.md":
+                continue
+            agent_dir = self.project_root / agent_config["dir"]
+            if agent_dir.exists():
+                try:
+                    registrar.register_commands(
+                        agent_name, commands, source_id,
+                        source_dir, self.project_root,
+                    )
+                except (ValueError, Exception):
+                    continue
+
     def _get_skills_dir(self) -> Optional[Path]:
         """Return the active skills directory for preset skill overrides.
 
@@ -1186,6 +1213,14 @@ def install_from_directory(
             self.registry.remove(manifest.id)
             raise
 
+        # Reconcile all affected commands from the full priority stack so that
+        # install order doesn't determine the winning command file.
+        cmd_names = [
+            t["name"] for t in manifest.templates if t.get("type") == "command"
+        ]
+        if cmd_names:
+            self._reconcile_composed_commands(cmd_names)
+
         return manifest
 
     def install_from_zip(