Skip missing paths in filesystem sandbox entries (#34598)

## Why

Default read-only protections for project metadata should apply when paths such
as `.git`, `.agents`, and `.codex` exist, without causing sandbox setup to
materialize missing paths as ACL targets.

## What changed

- Add an optional `missing_path_behavior` to filesystem sandbox entries and
  mark default project-metadata protections with `skip`.
- Preserve the behavior through permission transforms and exec/MCP protocol
  serialization while keeping existing path wire variants stable.
- Ignore skip-missing entries when projecting configuration or Windows sandbox
  overrides, while retaining explicit metadata carveouts.

## Testing

- Cover protocol round trips for path and special-path entries.
- Verify default metadata protections and Windows explicit carveout handling.

GitOrigin-RevId: 6df13dadacdd131c44aab9f15a967c81051355c1

codex-rs/app-server-protocol/src/protocol/v2/permissions.rs

@@ -368,6 +368,7 @@ impl TryFrom<FileSystemSandboxEntry> for CoreFileSystemSandboxEntry {
         Ok(Self {
             path: value.path.try_into()?,
             access: value.access.to_core(),
+            missing_path_behavior: None,
         })
     }
 }

codex-rs/app-server-protocol/src/protocol/v2/tests.rs

@@ -591,12 +591,14 @@ fn additional_file_system_permissions_preserves_canonical_entries() {
                     value: CoreFileSystemSpecialPath::Root,
                 },
                 access: CoreFileSystemAccessMode::Write,
+                missing_path_behavior: None,
             },
             CoreFileSystemSandboxEntry {
                 path: CoreFileSystemPath::GlobPattern {
                     pattern: "**/*.env".to_string(),
                 },
                 access: CoreFileSystemAccessMode::Deny,
+                missing_path_behavior: None,
             },
         ],
         glob_scan_max_depth: NonZeroUsize::new(2),