feat(phase-c): resolve &mut-access phase-b TODOs via handle setters

PHP mutator methods that the Phase B port could not call because only
&self / &dyn / Rc access was available. Resolved by the interior-mutation
APIs that already exist: handle &self setters (set_dist/source_reference,
set_requires/dev/references/stability_flags), Rc<RefCell<dyn InputInterface>>
.borrow_mut(), and get_installation_manager().borrow_mut() (build_package_map
passes an empty/canonical package list per upstream). composer.get_package()
returns &RootPackageInterfaceHandle, so the "&dyn" Phase B note was wrong.
factory's set_config_source/set_auth_config_source were already live code;
their stale TODOs are removed.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

1 files changed, 6 insertions, 8 deletions

diff --git a/crates/shirabe/src/command/update_command.rs b/crates/shirabe/src/command/update_command.rs
index e7a7437..efde845 100644
--- a/crates/shirabe/src/command/update_command.rs
+++ b/crates/shirabe/src/command/update_command.rs
@@ -160,17 +160,15 @@ impl UpdateCommand {
         }
 
         let root_package = composer.get_package();
-        // TODO(phase-b): composer.get_package() returns &dyn RootPackageInterface so
-        // set_references/set_stability_flags cannot be called; needs &mut access.
-        let references =
-            RootPackageLoader::extract_references(&reqs, root_package.get_references().clone());
-        let stability_flags = RootPackageLoader::extract_stability_flags(
+        root_package.set_references(RootPackageLoader::extract_references(
+            &reqs,
+            root_package.get_references().clone(),
+        ));
+        root_package.set_stability_flags(RootPackageLoader::extract_stability_flags(
             &reqs,
             &root_package.get_minimum_stability(),
             root_package.get_stability_flags().clone(),
-        );
-        let _ = references;
-        let _ = stability_flags;
+        ));
 
         let parser = VersionParser::new();
         let mut temporary_constraints: IndexMap<String, _> = IndexMap::new();