fix: Capture stderr instead of suppressing in command execution

Several files were setting cmd.Stderr = nil, which hides potentially
critical error messages:

- prime.go: bd prime, gt mail check, and bd show commands now log
  stderr on failure for debugging
- orphans.go: git fsck now includes stderr in error messages
- patrol_helpers.go: bd list/show/catalog commands now log stderr

Daemon launch cases (up.go, daemon.go, daemon_check.go) correctly
use nil for I/O detachment but now have clarifying comments.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

internal/cmd/orphans.go

@@ -124,14 +124,19 @@ func findOrphanCommits(repoPath string) ([]OrphanCommit, error) {
 	fsckCmd := exec.Command("git", "fsck", "--unreachable", "--no-reflogs")
 	fsckCmd.Dir = repoPath
 
-	var fsckOut bytes.Buffer
+	var fsckOut, fsckErr bytes.Buffer
 	fsckCmd.Stdout = &fsckOut
-	fsckCmd.Stderr = nil // Ignore warnings
+	fsckCmd.Stderr = &fsckErr
 
 	if err := fsckCmd.Run(); err != nil {
 		// git fsck returns non-zero if there are issues, but we still get output
 		// Only fail if we got no output at all
 		if fsckOut.Len() == 0 {
+			// Include stderr in error message for debugging
+			errMsg := strings.TrimSpace(fsckErr.String())
+			if errMsg != "" {
+				return nil, fmt.Errorf("git fsck failed: %w (%s)", err, errMsg)
+			}
 			return nil, fmt.Errorf("git fsck failed: %w", err)
 		}
 	}

internal/cmd/patrol_helpers.go

@@ -3,6 +3,7 @@ package cmd
 import (
 	"bytes"
 	"fmt"
+	"os"
 	"os/exec"
 	"strings"
 
@@ -28,11 +29,15 @@ func findActivePatrol(cfg PatrolConfig) (patrolID, patrolLine string, found bool
 	if cfg.CheckInProgress {
 		cmdList := exec.Command("bd", "--no-daemon", "list", "--status=in_progress", "--type=epic")
 		cmdList.Dir = cfg.BeadsDir
-		var stdoutList bytes.Buffer
+		var stdoutList, stderrList bytes.Buffer
 		cmdList.Stdout = &stdoutList
-		cmdList.Stderr = nil
+		cmdList.Stderr = &stderrList
 
-		if cmdList.Run() == nil {
+		if err := cmdList.Run(); err != nil {
+			if errMsg := strings.TrimSpace(stderrList.String()); errMsg != "" {
+				fmt.Fprintf(os.Stderr, "bd list: %s\n", errMsg)
+			}
+		} else {
 			lines := strings.Split(stdoutList.String(), "\n")
 			for _, line := range lines {
 				if strings.Contains(line, cfg.PatrolMolName) && !strings.Contains(line, "[template]") {
@@ -48,11 +53,15 @@ func findActivePatrol(cfg PatrolConfig) (patrolID, patrolLine string, found bool
 	// Check for open patrols with open children (active wisp)
 	cmdOpen := exec.Command("bd", "--no-daemon", "list", "--status=open", "--type=epic")
 	cmdOpen.Dir = cfg.BeadsDir
-	var stdoutOpen bytes.Buffer
+	var stdoutOpen, stderrOpen bytes.Buffer
 	cmdOpen.Stdout = &stdoutOpen
-	cmdOpen.Stderr = nil
+	cmdOpen.Stderr = &stderrOpen
 
-	if cmdOpen.Run() == nil {
+	if err := cmdOpen.Run(); err != nil {
+		if errMsg := strings.TrimSpace(stderrOpen.String()); errMsg != "" {
+			fmt.Fprintf(os.Stderr, "bd list: %s\n", errMsg)
+		}
+	} else {
 		lines := strings.Split(stdoutOpen.String(), "\n")
 		for _, line := range lines {
 			if strings.Contains(line, cfg.PatrolMolName) && !strings.Contains(line, "[template]") {
@@ -62,10 +71,14 @@ func findActivePatrol(cfg PatrolConfig) (patrolID, patrolLine string, found bool
 					// Check if this molecule has open children
 					cmdShow := exec.Command("bd", "--no-daemon", "show", molID)
 					cmdShow.Dir = cfg.BeadsDir
-					var stdoutShow bytes.Buffer
+					var stdoutShow, stderrShow bytes.Buffer
 					cmdShow.Stdout = &stdoutShow
-					cmdShow.Stderr = nil
-					if cmdShow.Run() == nil {
+					cmdShow.Stderr = &stderrShow
+					if err := cmdShow.Run(); err != nil {
+						if errMsg := strings.TrimSpace(stderrShow.String()); errMsg != "" {
+							fmt.Fprintf(os.Stderr, "bd show: %s\n", errMsg)
+						}
+					} else {
 						showOutput := stdoutShow.String()
 						// Deacon only checks "- open]", witness/refinery also check "- in_progress]"
 						hasOpenChildren := strings.Contains(showOutput, "- open]")
@@ -90,12 +103,16 @@ func autoSpawnPatrol(cfg PatrolConfig) (string, error) {
 	// Find the proto ID for the patrol molecule
 	cmdCatalog := exec.Command("bd", "--no-daemon", "mol", "catalog")
 	cmdCatalog.Dir = cfg.BeadsDir
-	var stdoutCatalog bytes.Buffer
+	var stdoutCatalog, stderrCatalog bytes.Buffer
 	cmdCatalog.Stdout = &stdoutCatalog
-	cmdCatalog.Stderr = nil
+	cmdCatalog.Stderr = &stderrCatalog
 
 	if err := cmdCatalog.Run(); err != nil {
-		return "", fmt.Errorf("failed to list molecule catalog")
+		errMsg := strings.TrimSpace(stderrCatalog.String())
+		if errMsg != "" {
+			return "", fmt.Errorf("failed to list molecule catalog: %s", errMsg)
+		}
+		return "", fmt.Errorf("failed to list molecule catalog: %w", err)
 	}
 
 	// Find patrol molecule in catalog

internal/cmd/prime.go

@@ -429,12 +429,16 @@ func runBdPrime(workDir string) {
 	cmd := exec.Command("bd", "prime")
 	cmd.Dir = workDir
 
-	var stdout bytes.Buffer
+	var stdout, stderr bytes.Buffer
 	cmd.Stdout = &stdout
-	cmd.Stderr = nil // Ignore stderr
+	cmd.Stderr = &stderr
 
 	if err := cmd.Run(); err != nil {
-		// Silently skip if bd prime fails (beads might not be available)
+		// Skip if bd prime fails (beads might not be available)
+		// But log stderr if present for debugging
+		if errMsg := strings.TrimSpace(stderr.String()); errMsg != "" {
+			fmt.Fprintf(os.Stderr, "bd prime: %s\n", errMsg)
+		}
 		return
 	}
 
@@ -521,12 +525,15 @@ func runMailCheckInject(workDir string) {
 	cmd := exec.Command("gt", "mail", "check", "--inject")
 	cmd.Dir = workDir
 
-	var stdout bytes.Buffer
+	var stdout, stderr bytes.Buffer
 	cmd.Stdout = &stdout
-	cmd.Stderr = nil // Ignore stderr
+	cmd.Stderr = &stderr
 
 	if err := cmd.Run(); err != nil {
-		// Silently skip if mail check fails
+		// Skip if mail check fails, but log stderr for debugging
+		if errMsg := strings.TrimSpace(stderr.String()); errMsg != "" {
+			fmt.Fprintf(os.Stderr, "gt mail check: %s\n", errMsg)
+		}
 		return
 	}
 
@@ -947,10 +954,16 @@ func checkSlungWork(ctx RoleContext) bool {
 	// Show bead preview using bd show
 	fmt.Println("**Bead details:**")
 	cmd := exec.Command("bd", "show", hookedBead.ID)
-	var stdout bytes.Buffer
+	var stdout, stderr bytes.Buffer
 	cmd.Stdout = &stdout
-	cmd.Stderr = nil
-	if cmd.Run() == nil {
+	cmd.Stderr = &stderr
+	if err := cmd.Run(); err != nil {
+		if errMsg := strings.TrimSpace(stderr.String()); errMsg != "" {
+			fmt.Fprintf(os.Stderr, "  bd show %s: %s\n", hookedBead.ID, errMsg)
+		} else {
+			fmt.Fprintf(os.Stderr, "  bd show %s: %v\n", hookedBead.ID, err)
+		}
+	} else {
 		lines := strings.Split(stdout.String(), "\n")
 		maxLines := 15
 		if len(lines) > maxLines {

internal/cmd/up.go

@@ -196,6 +196,7 @@ func ensureDaemon(townRoot string) error {
 
 	cmd := exec.Command(gtPath, "daemon", "run")
 	cmd.Dir = townRoot
+	// Detach from parent I/O for background daemon (uses its own logging)
 	cmd.Stdin = nil
 	cmd.Stdout = nil
 	cmd.Stderr = nil

internal/doctor/daemon_check.go

@@ -73,7 +73,7 @@ func (c *DaemonCheck) Fix(ctx *CheckContext) error {
 		return err
 	}
 
-	// Start daemon in background
+	// Start daemon in background (detach from parent I/O - daemon uses its own logging)
 	cmd := exec.Command(gtPath, "daemon", "run")
 	cmd.Dir = ctx.TownRoot
 	cmd.Stdin = nil