fix: deduplicate PyYAML warnings and use self.registry in reconciliation

- Emit PyYAML-missing warning once per function call in bash/PS1 instead
  of per-preset to avoid spamming stderr
- Use self.registry.list_by_priority() in reconciliation methods instead
  of constructing new PresetRegistry instances to avoid redundant I/O
  and potential consistency issues

Author: mnriem

scripts/bash/common.sh

@@ -415,6 +415,7 @@ except Exception:
     sys.exit(1)
 " 2>/dev/null); then
                 if [ -n "$sorted_presets" ]; then
+                    local yaml_warned=false
                     while IFS= read -r preset_id; do
                         # Read strategy and file path from preset manifest
                         local strategy="replace"
@@ -449,9 +450,9 @@ except Exception:
                                 IFS=$'\t' read -r strategy manifest_file <<< "$result"
                                 strategy=$(printf '%s' "$strategy" | tr '[:upper:]' '[:lower:]')
                             fi
-                            # Warn only when PyYAML is explicitly missing
-                            if grep -q 'yaml_missing' "$py_stderr" 2>/dev/null; then
-                                echo "Warning: PyYAML not available; composition strategies in $manifest may be ignored" >&2
+                            if [ "$yaml_warned" = false ] && grep -q 'yaml_missing' "$py_stderr" 2>/dev/null; then
+                                echo "Warning: PyYAML not available; composition strategies may be ignored" >&2
+                                yaml_warned=true
                             fi
                             rm -f "$py_stderr"
                         fi

scripts/powershell/common.ps1

@@ -424,6 +424,7 @@ function Resolve-TemplateContent {
                     }
                 }
             }
+            $yamlWarned = $false
             foreach ($presetId in $sortedPresets) {
                 # Read strategy and file path from preset manifest
                 $strategy = 'replace'
@@ -458,9 +459,9 @@ except Exception:
                             $strategy = $parts[0].ToLowerInvariant()
                             if ($parts.Count -gt 1 -and $parts[1]) { $manifestFilePath = $parts[1] }
                         }
-                        # Warn only when PyYAML is explicitly missing
-                        if ((Test-Path $pyStderrFile) -and (Get-Content $pyStderrFile -Raw -ErrorAction SilentlyContinue) -match 'yaml_missing') {
-                            Write-Warning "PyYAML not available; composition strategies in $manifest may be ignored"
+                        if (-not $yamlWarned -and (Test-Path $pyStderrFile) -and (Get-Content $pyStderrFile -Raw -ErrorAction SilentlyContinue) -match 'yaml_missing') {
+                            Write-Warning "PyYAML not available; composition strategies may be ignored"
+                            $yamlWarned = $true
                         }
                         Remove-Item $pyStderrFile -Force -ErrorAction SilentlyContinue
                     } catch {

src/specify_cli/presets.py

@@ -706,7 +706,7 @@ def _reconcile_composed_commands(self, command_names: List[str]) -> None:
 
         # Cache registry and manifests outside the loop to avoid
         # repeated filesystem reads for each command name.
-        presets_by_priority = list(PresetRegistry(self.presets_dir).list_by_priority()) if self.presets_dir.exists() else []
+        presets_by_priority = list(self.registry.list_by_priority())
 
         for cmd_name in command_names:
             layers = resolver.collect_all_layers(cmd_name, "command")
@@ -956,9 +956,7 @@ def _reconcile_skills(self, command_names: List[str]) -> None:
         skills_dir = self._get_skills_dir()
 
         # Cache registry once to avoid repeated filesystem reads
-        presets_by_priority = list(
-            PresetRegistry(self.presets_dir).list_by_priority()
-        ) if self.presets_dir.exists() else []
+        presets_by_priority = list(self.registry.list_by_priority())
 
         # Group command names by winning preset to batch _register_skills calls
         # while only registering skills for the specific commands being reconciled.