fix: NixOS symlink compatibility for mtime and permission checks (#459)

* fix: use os.Lstat for symlink-safe mtime and permission checks

On NixOS and other systems using symlinks heavily (e.g., home-manager),
os.Stat follows symlinks and returns the target's metadata. This causes:

1. False staleness detection when JSONL is symlinked - mtime of target
   changes unpredictably when symlinks are recreated
2. os.Chmod failing or changing wrong file's permissions when target
   is in read-only location (e.g., /nix/store)
3. os.Chtimes modifying target's times instead of the symlink itself

Changes:
- autoimport.go: Use Lstat for JSONL mtime in CheckStaleness()
- import.go: Use Lstat in TouchDatabaseFile() for JSONL mtime
- export.go: Skip chmod for symlinked files
- multirepo.go: Use Lstat for JSONL mtime cache
- multirepo_export.go: Use Lstat for mtime, skip chmod for symlinks
- doctor/fix/permissions.go: Skip permission fixes for symlinked paths

These changes are safe cross-platform:
- On systems without symlinks, Lstat behaves identically to Stat
- Symlink permission bits are ignored on Unix anyway
- The extra Lstat syscall overhead is negligible

Fixes symlink-related data loss on NixOS. See GitHub issue #379.

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

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

* test: add symlink behavior tests for NixOS compatibility

Add tests that verify symlink handling behavior:
- TestCheckStaleness_SymlinkedJSONL: verifies mtime detection uses
  symlink's own mtime (os.Lstat), not target's mtime (os.Stat)
- TestPermissions_SkipsSymlinkedBeadsDir: verifies chmod is skipped
  for symlinked .beads directories
- TestPermissions_SkipsSymlinkedDatabase: verifies chmod is skipped
  for symlinked database files while still fixing .beads dir perms

Also adds devShell to flake.nix for local development with go, gopls,
golangci-lint, and sqlite tools.

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

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

---------

Co-authored-by: Claude <noreply@anthropic.com>

internal/autoimport/autoimport.go

@@ -289,7 +289,11 @@ func CheckStaleness(ctx context.Context, store storage.Storage, dbPath string) (
 	dbDir := filepath.Dir(dbPath)
 	jsonlPath := utils.FindJSONLInDir(dbDir)
 
-	stat, err := os.Stat(jsonlPath)
+	// Use Lstat to get the symlink's own mtime, not the target's.
+	// This is critical for NixOS and other systems where JSONL may be symlinked.
+	// Using Stat would follow symlinks and return the target's mtime, which can
+	// cause false staleness detection when symlinks are recreated (e.g., by home-manager).
+	stat, err := os.Lstat(jsonlPath)
 	if err != nil {
 		if os.IsNotExist(err) {
 			// JSONL doesn't exist - expected for new repo

internal/autoimport/symlink_test.go

@@ -0,0 +1,133 @@
+package autoimport
+
+import (
+	"context"
+	"os"
+	"path/filepath"
+	"testing"
+	"time"
+
+	"github.com/steveyegge/beads/internal/storage/memory"
+)
+
+// TestCheckStaleness_SymlinkedJSONL verifies that mtime detection uses the symlink's
+// own mtime, not the target's mtime. This is critical for NixOS and similar systems
+// where files may be symlinked to read-only locations.
+//
+// Behavior being tested:
+// - When JSONL is a symlink, CheckStaleness should use os.Lstat (symlink mtime)
+// - NOT os.Stat (which would follow the symlink and get target's mtime)
+func TestCheckStaleness_SymlinkedJSONL(t *testing.T) {
+	tmpDir := t.TempDir()
+
+	// Create the target JSONL file with old mtime
+	targetDir := filepath.Join(tmpDir, "target")
+	if err := os.MkdirAll(targetDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+	targetPath := filepath.Join(targetDir, "issues.jsonl")
+	if err := os.WriteFile(targetPath, []byte(`{"id":"test-1"}`), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Set target's mtime to 1 hour ago
+	oldTime := time.Now().Add(-1 * time.Hour)
+	if err := os.Chtimes(targetPath, oldTime, oldTime); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create the .beads directory structure with a symlink to the target
+	beadsDir := filepath.Join(tmpDir, ".beads")
+	if err := os.MkdirAll(beadsDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+
+	symlinkPath := filepath.Join(beadsDir, "issues.jsonl")
+	if err := os.Symlink(targetPath, symlinkPath); err != nil {
+		t.Fatal(err)
+	}
+
+	// The symlink itself was just created (recent mtime)
+	// The target file has old mtime (1 hour ago)
+	// If we use os.Stat (follows symlink), we'd get the target's old mtime
+	// If we use os.Lstat (symlink's own mtime), we'd get the recent mtime
+
+	// Set last_import_time to 30 minutes ago (between target mtime and symlink mtime)
+	importTime := time.Now().Add(-30 * time.Minute)
+	store := memory.New("")
+	ctx := context.Background()
+	store.SetMetadata(ctx, "last_import_time", importTime.Format(time.RFC3339))
+
+	dbPath := filepath.Join(beadsDir, "beads.db")
+
+	// With correct behavior (os.Lstat):
+	// - Symlink mtime: now (just created)
+	// - Import time: 30 min ago
+	// - Result: stale = true (symlink is newer than import)
+	//
+	// With incorrect behavior (os.Stat):
+	// - Target mtime: 1 hour ago
+	// - Import time: 30 min ago
+	// - Result: stale = false (target is older than import) - WRONG!
+	stale, err := CheckStaleness(ctx, store, dbPath)
+	if err != nil {
+		t.Fatalf("CheckStaleness failed: %v", err)
+	}
+
+	if !stale {
+		t.Error("Expected stale=true when symlinked JSONL is newer than last import")
+		t.Error("This indicates os.Stat is being used instead of os.Lstat")
+		t.Error("os.Stat follows the symlink and returns target's mtime (old)")
+		t.Error("os.Lstat returns the symlink's own mtime (recent)")
+	}
+}
+
+// TestCheckStaleness_SymlinkedJSONL_NotStale verifies the inverse case:
+// when the symlink itself is older than the last import, it should not be stale.
+func TestCheckStaleness_SymlinkedJSONL_NotStale(t *testing.T) {
+	tmpDir := t.TempDir()
+
+	// Create target file
+	targetDir := filepath.Join(tmpDir, "target")
+	if err := os.MkdirAll(targetDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+	targetPath := filepath.Join(targetDir, "issues.jsonl")
+	if err := os.WriteFile(targetPath, []byte(`{"id":"test-1"}`), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	// Create symlink
+	beadsDir := filepath.Join(tmpDir, ".beads")
+	if err := os.MkdirAll(beadsDir, 0755); err != nil {
+		t.Fatal(err)
+	}
+	symlinkPath := filepath.Join(beadsDir, "issues.jsonl")
+	if err := os.Symlink(targetPath, symlinkPath); err != nil {
+		t.Fatal(err)
+	}
+
+	// Set symlink's mtime to 1 hour ago
+	oldTime := time.Now().Add(-1 * time.Hour)
+	// Note: os.Chtimes follows symlinks, so we use os.Lchtimes if available
+	// On most systems, symlink mtime is set at creation and can't be changed
+	// So we'll set the import time to be in the future instead
+	_ = oldTime
+
+	// Set last_import_time to just now (after symlink creation)
+	importTime := time.Now().Add(1 * time.Second)
+	store := memory.New("")
+	ctx := context.Background()
+	store.SetMetadata(ctx, "last_import_time", importTime.Format(time.RFC3339))
+
+	dbPath := filepath.Join(beadsDir, "beads.db")
+
+	stale, err := CheckStaleness(ctx, store, dbPath)
+	if err != nil {
+		t.Fatalf("CheckStaleness failed: %v", err)
+	}
+
+	if stale {
+		t.Error("Expected stale=false when last import is after symlink creation")
+	}
+}

internal/storage/sqlite/multirepo.go

@@ -71,7 +71,8 @@ func (s *SQLiteStorage) hydrateFromRepo(ctx context.Context, repoPath, sourceRep
 	jsonlPath := filepath.Join(absRepoPath, ".beads", "issues.jsonl")
 
 	// Check if file exists
-	fileInfo, err := os.Stat(jsonlPath)
+	// Use Lstat to get the symlink's own mtime, not the target's (NixOS fix).
+	fileInfo, err := os.Lstat(jsonlPath)
 	if err != nil {
 		if os.IsNotExist(err) {
 			// No JSONL file - skip this repo

internal/storage/sqlite/multirepo_export.go

@@ -162,13 +162,18 @@ func (s *SQLiteStorage) exportToRepo(ctx context.Context, repoPath string, issue
 	}
 
 	// Set file permissions
-	if err := os.Chmod(jsonlPath, 0644); err != nil { // nolint:gosec // G302: 0644 intentional for git-tracked files
-		// Non-fatal
-		debug.Logf("Debug: failed to set permissions on %s: %v\n", jsonlPath, err)
+	// Skip chmod for symlinks - os.Chmod follows symlinks and would change the target's
+	// permissions, which may be in a read-only location (e.g., /nix/store on NixOS).
+	if info, statErr := os.Lstat(jsonlPath); statErr == nil && info.Mode()&os.ModeSymlink == 0 {
+		if err := os.Chmod(jsonlPath, 0644); err != nil { // nolint:gosec // G302: 0644 intentional for git-tracked files
+			// Non-fatal
+			debug.Logf("Debug: failed to set permissions on %s: %v\n", jsonlPath, err)
+		}
 	}
 
 	// Update mtime cache for this repo
-	fileInfo, err := os.Stat(jsonlPath)
+	// Use Lstat to get the symlink's own mtime, not the target's (NixOS fix).
+	fileInfo, err := os.Lstat(jsonlPath)
 	if err == nil {
 		_, err = s.db.ExecContext(ctx, `
 			INSERT OR REPLACE INTO repo_mtimes (repo_path, jsonl_path, mtime_ns, last_checked)