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/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)