feat: add pour warning for vapor-phase formulas, improve help text, add doctor check

- Add Phase field to Formula type to indicate recommended instantiation phase
- Add warning in 'bd mol pour' when formula has phase="vapor"
- Improve pour/wisp help text with clear comparison of when to use each
- Add CheckPersistentMolIssues doctor check to detect mol- issues in JSONL
- Update beads-release.formula.json with phase="vapor"

This helps prevent accidental persistence of ephemeral workflow issues.

cmd/bd/doctor/maintenance.go

@@ -350,3 +350,78 @@ func resolveBeadsDir(beadsDir string) string {
 
 	return target
 }
+
+// CheckPersistentMolIssues detects mol- prefixed issues that should have been ephemeral.
+// When users run "bd mol pour" on formulas that should use "bd mol wisp", the resulting
+// issues get the "mol-" prefix but persist in JSONL. These should be cleaned up.
+func CheckPersistentMolIssues(path string) DoctorCheck {
+	beadsDir := resolveBeadsDir(filepath.Join(path, ".beads"))
+	jsonlPath := filepath.Join(beadsDir, "issues.jsonl")
+
+	if _, err := os.Stat(jsonlPath); os.IsNotExist(err) {
+		return DoctorCheck{
+			Name:     "Persistent Mol Issues",
+			Status:   StatusOK,
+			Message:  "N/A (no JSONL file)",
+			Category: CategoryMaintenance,
+		}
+	}
+
+	// Read JSONL and count mol- prefixed issues that are not ephemeral
+	file, err := os.Open(jsonlPath) // #nosec G304 - path constructed safely
+	if err != nil {
+		return DoctorCheck{
+			Name:     "Persistent Mol Issues",
+			Status:   StatusOK,
+			Message:  "N/A (unable to read JSONL)",
+			Category: CategoryMaintenance,
+		}
+	}
+	defer file.Close()
+
+	var molCount int
+	var molIDs []string
+	decoder := json.NewDecoder(file)
+
+	for {
+		var issue types.Issue
+		if err := decoder.Decode(&issue); err != nil {
+			break
+		}
+		// Skip deleted issues (tombstones)
+		if issue.DeletedAt != nil {
+			continue
+		}
+		// Look for mol- prefix that shouldn't be in JSONL
+		// (ephemeral issues have Ephemeral=true and don't get exported)
+		if strings.HasPrefix(issue.ID, "mol-") && !issue.Ephemeral {
+			molCount++
+			if len(molIDs) < 3 {
+				molIDs = append(molIDs, issue.ID)
+			}
+		}
+	}
+
+	if molCount == 0 {
+		return DoctorCheck{
+			Name:     "Persistent Mol Issues",
+			Status:   StatusOK,
+			Message:  "No persistent mol- issues",
+			Category: CategoryMaintenance,
+		}
+	}
+
+	detail := fmt.Sprintf("Example: %v", molIDs)
+	if molCount > 3 {
+		detail += fmt.Sprintf(" (+%d more)", molCount-3)
+	}
+
+	return DoctorCheck{
+		Name:     "Persistent Mol Issues",
+		Status:   StatusWarning,
+		Message:  fmt.Sprintf("%d mol- issue(s) in JSONL should be ephemeral", molCount),
+		Detail:   detail,
+		Fix:      "Run 'bd delete <id> --force' to remove, or use 'bd mol wisp' instead of 'bd mol pour'",
+		Category: CategoryMaintenance,
+	}
+}