fix(repository): resolve remaining late-binding hazards from the audit

Three fixes for the ComposerRepository/FilesystemRepository/PlatformRepository
hazards where inner-composition delegation skipped PHP's late-bound virtual
dispatch:

- ComposerRepository::has_package now builds its packageMap through the
  late-bound getPackages() equivalent, so lazy-providers repos surface the
  LogicException and available-packages repos load their package list, as in
  PHP, instead of silently answering false from the raw array.

- RepositoryInterface::get_repo_name returns anyhow::Result<String>: PHP's
  getRepoName() counts through the late-bound initialize(), which is fallible
  in file-reading subclasses. FilesystemRepository and PackageRepository now
  run that initialization instead of freezing the inner array repository to an
  empty state (which also made a later write() truncate installed.json).
  Supporting changes keep the initialization chain callable from &self:
  JsonFile::read takes &self (indent moved into a RefCell), FilesystemRepository
  dev_mode became a Cell, and WritableArrayRepository dev_package_names a
  RefCell.

- PlatformRepository::new routes constructor packages through its own
  add_package so the override handling and full platform initialization run
  as they do via PHP's parent constructor; the inner find_package/add_package
  delegations inside add_package (and ComposerRepository::add_package) gained
  the same is_initialized guard, since the constructor path would otherwise
  freeze the repository.

Same defect class as 7db937af, 97b5211a and 3e367f78.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

5 files changed, 7 insertions, 5 deletions

diff --git a/crates/shirabe/src/command/bump_command.rs b/crates/shirabe/src/command/bump_command.rs
index 78b1f627..a4518b0b 100644
--- a/crates/shirabe/src/command/bump_command.rs
+++ b/crates/shirabe/src/command/bump_command.rs
@@ -72,7 +72,7 @@ impl BumpCommand {
             return Ok(Self::ERROR_GENERIC);
         }
 
-        let mut composer_json = JsonFile::new(composer_json_path.clone(), None, None)?;
+        let composer_json = JsonFile::new(composer_json_path.clone(), None, None)?;
         let contents = match file_get_contents(composer_json.get_path()) {
             Some(c) => c,
             None => {
diff --git a/crates/shirabe/src/command/config_command.rs b/crates/shirabe/src/command/config_command.rs
index 7e8b82e9..129b6614 100644
--- a/crates/shirabe/src/command/config_command.rs
+++ b/crates/shirabe/src/command/config_command.rs
@@ -1569,7 +1569,7 @@ impl ConfigCommand {
             let mut config = Factory::create_config(None, None)?;
 
             // load configuration
-            let mut config_file = JsonFile::new(
+            let config_file = JsonFile::new(
                 this.get_composer_config_file(input_handle.clone(), &config)?,
                 None,
                 None,
@@ -1581,7 +1581,7 @@ impl ConfigCommand {
             }
 
             // load auth-configuration
-            let mut auth_config_file = JsonFile::new(
+            let auth_config_file = JsonFile::new(
                 this.get_auth_config_file(input_handle.clone(), &config)?,
                 None,
                 None,
diff --git a/crates/shirabe/src/command/package_discovery_trait.rs b/crates/shirabe/src/command/package_discovery_trait.rs
index 229d84e9..cfd2d302 100644
--- a/crates/shirabe/src/command/package_discovery_trait.rs
+++ b/crates/shirabe/src/command/package_discovery_trait.rs
@@ -589,10 +589,12 @@ pub trait PackageDiscoveryTrait: BaseCommand {
                             all_repos_package
                                 .get_repository()
                                 .map(|r| r.get_repo_name())
+                                .transpose()?
                                 .unwrap_or_default(),
                             package
                                 .get_repository()
                                 .map(|r| r.get_repo_name())
+                                .transpose()?
                                 .unwrap_or_default(),
                         ),
                         code: 0,
diff --git a/crates/shirabe/src/command/remove_command.rs b/crates/shirabe/src/command/remove_command.rs
index e611542f..77deaf14 100644
--- a/crates/shirabe/src/command/remove_command.rs
+++ b/crates/shirabe/src/command/remove_command.rs
@@ -285,7 +285,7 @@ impl Command for RemoveCommand {
 
         let file = Factory::get_composer_file()?;
 
-        let mut json_file = JsonFile::new(file.clone(), None, None)?;
+        let json_file = JsonFile::new(file.clone(), None, None)?;
         let composer_data = json_file.read()?;
         let composer_backup = std::fs::read_to_string(json_file.get_path())?;
 
diff --git a/crates/shirabe/src/command/repository_command.rs b/crates/shirabe/src/command/repository_command.rs
index d23e114c..ab2cf2d4 100644
--- a/crates/shirabe/src/command/repository_command.rs
+++ b/crates/shirabe/src/command/repository_command.rs
@@ -165,7 +165,7 @@ impl RepositoryCommand {
                 >,
             > = std::rc::Rc::new(std::cell::RefCell::new(input.clone()));
             let config = crate::factory::Factory::create_config(None, None)?;
-            let mut config_file = JsonFile::new(
+            let config_file = JsonFile::new(
                 this.get_composer_config_file(input_handle, &config)?,
                 None,
                 None,