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/export.go

@@ -455,8 +455,12 @@ Examples:
 			}
 
 			// Set appropriate file permissions (0600: rw-------)
-			if err := os.Chmod(finalPath, 0600); err != nil {
-			fmt.Fprintf(os.Stderr, "Warning: failed to set file permissions: %v\n", 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, err := os.Lstat(finalPath); err == nil && info.Mode()&os.ModeSymlink == 0 {
+				if err := os.Chmod(finalPath, 0600); err != nil {
+					fmt.Fprintf(os.Stderr, "Warning: failed to set file permissions: %v\n", err)
+				}
 			}
 
 		// Verify JSONL file integrity after export