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>

10 files changed, 50 insertions, 57 deletions

diff --git a/crates/shirabe/src/command/init_command.rs b/crates/shirabe/src/command/init_command.rs
index 5a3c71b..f8bdad9 100644
--- a/crates/shirabe/src/command/init_command.rs
+++ b/crates/shirabe/src/command/init_command.rs
@@ -426,11 +426,19 @@ impl InitCommand {
 
         if !input.borrow().is_interactive() {
             if input.borrow().get_option("name").is_null() {
-                // TODO(phase-b): input.set_option requires &mut; signature passes &dyn here
+                let name = self.get_default_package_name();
+                input
+                    .borrow_mut()
+                    .set_option("name", PhpMixed::from(name))
+                    .expect("name option is defined");
             }
 
             if input.borrow().get_option("author").is_null() {
-                // TODO(phase-b): input.set_option requires &mut; signature passes &dyn here
+                let author = self.get_default_author();
+                input
+                    .borrow_mut()
+                    .set_option("author", PhpMixed::from(author))
+                    .expect("author option is defined");
             }
         }
     }
diff --git a/crates/shirabe/src/command/require_command.rs b/crates/shirabe/src/command/require_command.rs
index b3ad6cf..d3d17a7 100644
--- a/crates/shirabe/src/command/require_command.rs
+++ b/crates/shirabe/src/command/require_command.rs
@@ -413,9 +413,7 @@ impl RequireCommand {
                         .to_string(),
                     true,
                 ) {
-                    // TODO(phase-b): set_option needs &mut dyn InputInterface, but execute holds
-                    // input as &dyn. Commented out until input is threaded as &mut.
-                    // input.set_option("dev", PhpMixed::Bool(true));
+                    input.borrow_mut().set_option("dev", PhpMixed::Bool(true))?;
                 }
             }
 
@@ -511,9 +509,7 @@ impl RequireCommand {
                         return Ok(0);
                     }
 
-                    // TODO(phase-b): set_option needs &mut dyn InputInterface, but execute holds
-                    // input as &dyn. Commented out until input is threaded as &mut.
-                    // input.set_option("dev", PhpMixed::Bool(true));
+                    input.borrow_mut().set_option("dev", PhpMixed::Bool(true))?;
                     let swap = require_key;
                     require_key = remove_key;
                     remove_key = swap;
@@ -782,21 +778,21 @@ impl RequireCommand {
                     section.shift_remove(package);
                 }
             }
-            // TODO(phase-b): root_package mutation requires &mut RootPackageInterface but
-            // Composer::get_package() exposes only & dyn; needs accessor returning &mut for
-            // the dry-run case to update requires/dev-requires/stability flags/references.
-            let _ = &links;
-            let _ = root_package.get_references().clone();
-            let _ = RootPackageLoader::extract_references(
+            root_package.set_requires(links["require"].clone());
+            root_package.set_dev_requires(links["require-dev"].clone());
+
+            // extract stability flags & references as they weren't present when loading the unmodified composer.json
+            let references = RootPackageLoader::extract_references(
                 requirements,
                 root_package.get_references().clone(),
             );
-            let _ = RootPackageLoader::extract_stability_flags(
+            root_package.set_references(references);
+            let stability_flags = RootPackageLoader::extract_stability_flags(
                 requirements,
                 &root_package.get_minimum_stability(),
                 root_package.get_stability_flags().clone(),
             );
-            // unset($stabilityFlags, $references);
+            root_package.set_stability_flags(stability_flags);
         }
 
         let update_dev_mode = !input
diff --git a/crates/shirabe/src/command/run_script_command.rs b/crates/shirabe/src/command/run_script_command.rs
index cf8b8f1..3fe0855 100644
--- a/crates/shirabe/src/command/run_script_command.rs
+++ b/crates/shirabe/src/command/run_script_command.rs
@@ -144,10 +144,7 @@ impl RunScriptCommand {
             false,
         );
 
-        if let Some(selected) = script.as_string() {
-            // TODO(phase-b): input is std::rc::Rc<std::cell::RefCell<dyn InputInterface>> but set_argument needs &mut.
-            let _ = selected;
-        }
+        input.borrow_mut().set_argument("script", script)?;
 
         Ok(())
     }
diff --git a/crates/shirabe/src/command/self_update_command.rs b/crates/shirabe/src/command/self_update_command.rs
index 9c5ae5a..127661a 100644
--- a/crates/shirabe/src/command/self_update_command.rs
+++ b/crates/shirabe/src/command/self_update_command.rs
@@ -275,7 +275,7 @@ impl SelfUpdateCommand {
         if input.borrow().get_argument("command").as_string() == Some("self")
             && input.borrow().get_argument("version").as_string() == Some("update")
         {
-            // TODO(phase-b): set_argument requires &mut InputInterface; input is &dyn here
+            input.borrow_mut().set_argument("version", PhpMixed::Null)?;
         }
 
         let latest = versions_util.get_latest(None)??;
diff --git a/crates/shirabe/src/command/show_command.rs b/crates/shirabe/src/command/show_command.rs
index 53f3ac4..f324a5c 100644
--- a/crates/shirabe/src/command/show_command.rs
+++ b/crates/shirabe/src/command/show_command.rs
@@ -634,10 +634,11 @@ impl ShowCommand {
                 self.get_io().write_no_newline(&package.get_name());
                 let path = {
                     let composer_ref = composer.as_ref().unwrap();
-                    // TODO(phase-b): get_installation_manager wants &mut Composer; PHP shares
-                    // by reference. Skipping the install path lookup keeps compile clean.
-                    let _ = composer_ref;
-                    None::<String>
+                    composer_ref
+                        .borrow_partial()
+                        .get_installation_manager()
+                        .borrow_mut()
+                        .get_install_path(package.clone().into())
                 };
                 if let Some(path) = path {
                     let real = realpath(&path).unwrap_or_default();
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();
diff --git a/crates/shirabe/src/console/application.rs b/crates/shirabe/src/console/application.rs
index 124cc9b..0ff2893 100644
--- a/crates/shirabe/src/console/application.rs
+++ b/crates/shirabe/src/console/application.rs
@@ -638,14 +638,13 @@ impl Application {
                                         let generator = composer.get_autoload_generator().clone();
                                         let generator = generator.borrow();
 
-                                        // TODO(phase-b): build_package_map needs &mut InstallationManager
-                                        // but get_composer returns &Composer; skip until shared ownership is settled.
-                                        let package_map: Vec<(
-                                            crate::package::PackageInterfaceHandle,
-                                            Option<String>,
-                                        )> = todo!(
-                                            "build_package_map requires &mut InstallationManager"
-                                        );
+                                        let installation_manager =
+                                            composer.get_installation_manager();
+                                        let package_map = generator.build_package_map(
+                                            &mut installation_manager.borrow_mut(),
+                                            root_package.clone(),
+                                            vec![],
+                                        )?;
                                         let map = generator.parse_autoloads(
                                             package_map,
                                             root_package.clone(),
diff --git a/crates/shirabe/src/downloader/git_downloader.rs b/crates/shirabe/src/downloader/git_downloader.rs
index 078ac3a..7dace1b 100644
--- a/crates/shirabe/src/downloader/git_downloader.rs
+++ b/crates/shirabe/src/downloader/git_downloader.rs
@@ -1000,11 +1000,9 @@ impl VcsDownloader for GitDownloader {
             self.update_to_commit(package.clone(), &path, &r#ref, &pretty_version)?
         {
             if package.get_dist_reference() == package.get_source_reference() {
-                // TODO(phase-b): set_dist_reference requires &mut PackageInterface
-                // package.set_dist_reference(Some(new_ref.clone()));
+                package.set_dist_reference(Some(new_ref.clone()));
             }
-            // package.set_source_reference(Some(new_ref));
-            let _ = new_ref;
+            package.set_source_reference(Some(new_ref));
         }
 
         Ok(None)
@@ -1125,11 +1123,9 @@ impl VcsDownloader for GitDownloader {
             self.update_to_commit(target.clone(), &path, &r#ref, &pretty_version)?
         {
             if target.get_dist_reference() == target.get_source_reference() {
-                // TODO(phase-b): set_dist_reference requires &mut PackageInterface
-                // target.set_dist_reference(Some(new_ref.clone()));
+                target.set_dist_reference(Some(new_ref.clone()));
             }
-            // target.set_source_reference(Some(new_ref));
-            let _ = new_ref;
+            target.set_source_reference(Some(new_ref));
         }
 
         let mut update_origin_url = false;
diff --git a/crates/shirabe/src/event_dispatcher/event_dispatcher.rs b/crates/shirabe/src/event_dispatcher/event_dispatcher.rs
index bea2e76..797083c 100644
--- a/crates/shirabe/src/event_dispatcher/event_dispatcher.rs
+++ b/crates/shirabe/src/event_dispatcher/event_dispatcher.rs
@@ -1278,12 +1278,12 @@ impl EventDispatcher {
 
         self.previous_hash = Some(hash_value);
 
-        // TODO(phase-b): build_package_map needs &mut InstallationManager and returns Result;
-        // Composer is &Composer here so we cannot take a mut borrow. Defer until shared ownership.
-        let _ = &generator;
-        let _ = packages;
-        let package_map: Vec<(crate::package::PackageInterfaceHandle, Option<String>)> =
-            todo!("build_package_map requires &mut InstallationManager");
+        let installation_manager = composer.get_installation_manager();
+        let package_map = generator.build_package_map(
+            &mut installation_manager.borrow_mut(),
+            package.clone(),
+            packages,
+        )?;
         // TODO(phase-b): parse_autoloads also expects the filtered dev packages list
         // (PhpMixed in this port).
         let map = generator.parse_autoloads(
diff --git a/crates/shirabe/src/factory.rs b/crates/shirabe/src/factory.rs
index c099777..ac7c055 100644
--- a/crates/shirabe/src/factory.rs
+++ b/crates/shirabe/src/factory.rs
@@ -289,7 +289,6 @@ impl Factory {
             let file_path_owned = file.get_path().to_string();
             config.merge(&read_data, &file_path_owned);
         }
-        // TODO(phase-b): set_config_source takes Box<dyn ConfigSourceInterface>
         config.set_config_source(Box::new(JsonConfigSource::new(
             std::rc::Rc::new(std::cell::RefCell::new(file)),
             false,
@@ -355,7 +354,6 @@ impl Factory {
             let auth_path_owned = auth_file.get_path().to_string();
             config.merge(&wrapped, &auth_path_owned);
         }
-        // TODO(phase-b): set_auth_config_source takes Box<dyn ConfigSourceInterface>
         config.set_auth_config_source(Box::new(JsonConfigSource::new(
             std::rc::Rc::new(std::cell::RefCell::new(auth_file)),
             true,