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>

cmd/bd/doctor/fix/permissions.go

@@ -16,11 +16,18 @@ func Permissions(path string) error {
 	beadsDir := filepath.Join(path, ".beads")
 
 	// Check if .beads/ directory exists
-	info, err := os.Stat(beadsDir)
+	// Use Lstat to detect symlinks - we shouldn't chmod symlinked directories
+	// as this would change the target's permissions (problematic on NixOS).
+	info, err := os.Lstat(beadsDir)
 	if err != nil {
 		return fmt.Errorf("failed to stat .beads directory: %w", err)
 	}
 
+	// Skip permission fixes for symlinked .beads directories (common on NixOS with home-manager)
+	if info.Mode()&os.ModeSymlink != 0 {
+		return nil // Symlink permissions are not meaningful on Unix
+	}
+
 	// Ensure .beads directory has exactly 0700 permissions (owner rwx only)
 	expectedDirMode := os.FileMode(0700)
 	if info.Mode().Perm() != expectedDirMode {
@@ -30,8 +37,14 @@ func Permissions(path string) error {
 	}
 
 	// Fix permissions on database file if it exists
+	// Use Lstat to detect symlinks - skip chmod for symlinked database files
 	dbPath := filepath.Join(beadsDir, "beads.db")
-	if dbInfo, err := os.Stat(dbPath); err == nil {
+	if dbInfo, err := os.Lstat(dbPath); err == nil {
+		// Skip permission fixes for symlinked database files (NixOS)
+		if dbInfo.Mode()&os.ModeSymlink != 0 {
+			return nil
+		}
+
 		// Ensure database has exactly 0600 permissions (owner rw only)
 		expectedFileMode := os.FileMode(0600)
 		currentPerms := dbInfo.Mode().Perm()