feat(phase-c): resolve cross-module phase-b TODOs

36 files changed, 184 insertions, 237 deletions

diff --git a/crates/shirabe-php-shim/src/lib.rs b/crates/shirabe-php-shim/src/lib.rs
index f47e221..873f7f4 100644
--- a/crates/shirabe-php-shim/src/lib.rs
+++ b/crates/shirabe-php-shim/src/lib.rs
@@ -2477,3 +2477,16 @@ pub fn date_format_to_strftime(format: &str) -> &'static str {
         other => panic!("Unsupported PHP date format: {other:?}"),
     }
 }
+
+// NOTE: &str matching in const expression does not compile for now.
+pub const PHP_OS: &str = match std::env::consts::OS.as_bytes() {
+    b"linux" => "Linux",
+    b"macos" => "Darwin",
+    b"windows" => "WINNT",
+    b"freebsd" => "FreeBSD",
+    b"openbsd" => "OpenBSD",
+    b"netbsd" => "NetBSD",
+    b"dragonfly" => "DragonFly",
+    b"solaris" | b"illumos" => "SunOS",
+    _ => std::env::consts::OS,
+};
diff --git a/crates/shirabe/src/autoload/autoload_generator.rs b/crates/shirabe/src/autoload/autoload_generator.rs
index 69ecb73..a380763 100644
--- a/crates/shirabe/src/autoload/autoload_generator.rs
+++ b/crates/shirabe/src/autoload/autoload_generator.rs
@@ -438,8 +438,11 @@ impl AutoloadGenerator {
         }
 
         let mut class_map = class_map_generator.take_class_map();
-        // TODO(phase-b): strict_ambiguous should filter vendor path for non-strict mode
-        let ambiguous_classes = class_map.get_ambiguous_classes(None)?;
+        let ambiguous_classes = if strict_ambiguous {
+            class_map.get_ambiguous_classes(None)?
+        } else {
+            class_map.get_ambiguous_classes(Some(r"{/(test|fixture|example|stub)s?/}i"))?
+        };
         for (class_name, ambiguous_paths) in &ambiguous_classes {
             if ambiguous_paths.len() > 1 {
                 self.io.write_error(&format!(
@@ -804,14 +807,17 @@ impl AutoloadGenerator {
         };
         let mut sorted_package_map = self.sort_package_map(package_map);
         sorted_package_map.push(root_package_map);
+        let reverse_sorted_map: Vec<(PackageInterfaceHandle, Option<String>)> =
+            sorted_package_map.iter().rev().cloned().collect();
 
-        // TODO(phase-b): psr-0/4/classmap should use reverse_sorted_map (root first) for correct precedence
+        // reverse-sorted means root first, then dependents, then their dependents, etc.
+        // which makes sense to allow root to override classmap or psr-0/4 entries with higher precedence rules
         let mut psr0 =
-            self.parse_autoloads_type(&sorted_package_map, "psr-0", root_package.clone());
+            self.parse_autoloads_type(&reverse_sorted_map, "psr-0", root_package.clone());
         let mut psr4 =
-            self.parse_autoloads_type(&sorted_package_map, "psr-4", root_package.clone());
+            self.parse_autoloads_type(&reverse_sorted_map, "psr-4", root_package.clone());
         let classmap =
-            self.parse_autoloads_type(&sorted_package_map, "classmap", root_package.clone());
+            self.parse_autoloads_type(&reverse_sorted_map, "classmap", root_package.clone());
 
         // sorted (i.e. dependents first) for files to ensure that dependencies are loaded/available once a file is included
         let files = self.parse_autoloads_type(&sorted_package_map, "files", root_package.clone());
diff --git a/crates/shirabe/src/command/audit_command.rs b/crates/shirabe/src/command/audit_command.rs
index 20532f1..0e050cc 100644
--- a/crates/shirabe/src/command/audit_command.rs
+++ b/crates/shirabe/src/command/audit_command.rs
@@ -181,7 +181,7 @@ impl AuditCommand {
         }
 
         let _root_pkg = composer.get_package();
-        // TODO(phase-b): InstalledRepository::new expects Vec<Box<dyn RepositoryInterface>>, but
+        // TODO(phase-c): InstalledRepository::new expects Vec<Box<dyn RepositoryInterface>>, but
         // get_local_repository returns &dyn InstalledRepositoryInterface. Conversion requires
         // either cloning into a Box or restructuring InstalledRepository constructor.
         let _ = RepositoryUtils::filter_required_packages;
diff --git a/crates/shirabe/src/command/base_command.rs b/crates/shirabe/src/command/base_command.rs
index c98bc2b..b1a1837 100644
--- a/crates/shirabe/src/command/base_command.rs
+++ b/crates/shirabe/src/command/base_command.rs
@@ -511,9 +511,8 @@ impl<C: HasBaseCommandData> BaseCommand for C {
         } else {
             crate::factory::DisablePlugins::None
         };
-        // TODO(phase-b): Option<IndexMap<String, PhpMixed>> -> Option<LocalConfigInput> conversion
-        let _ = config;
-        Factory::create(io, None, disable_plugins_kind, disable_scripts).map(|c| c.upcast())
+        let config = config.map(crate::factory::LocalConfigInput::Data);
+        Factory::create(io, config, disable_plugins_kind, disable_scripts).map(|c| c.upcast())
     }
 
     fn get_preferred_install_options(
diff --git a/crates/shirabe/src/command/base_dependency_command.rs b/crates/shirabe/src/command/base_dependency_command.rs
index 9317b31..decfd5b 100644
--- a/crates/shirabe/src/command/base_dependency_command.rs
+++ b/crates/shirabe/src/command/base_dependency_command.rs
@@ -106,17 +106,18 @@ pub trait BaseDependencyCommand: BaseCommand {
 
             repos.push(local_repo);
 
-            let platform_overrides = composer
+            let platform_overrides: IndexMap<String, PhpMixed> = composer
                 .get_config()
                 .borrow()
                 .get("platform")
                 .as_array()
                 .cloned()
-                .unwrap_or_default();
-            // TODO(phase-b): platform_overrides type adjustment; using empty for now
-            let _ = platform_overrides;
+                .unwrap_or_default()
+                .into_iter()
+                .map(|(k, v)| (k, *v))
+                .collect();
             repos.push(crate::repository::RepositoryInterfaceHandle::new(
-                PlatformRepository::new(vec![], IndexMap::new())?,
+                PlatformRepository::new(vec![], platform_overrides)?,
             ));
         }
 
diff --git a/crates/shirabe/src/command/create_project_command.rs b/crates/shirabe/src/command/create_project_command.rs
index c49d2fc..bf00371 100644
--- a/crates/shirabe/src/command/create_project_command.rs
+++ b/crates/shirabe/src/command/create_project_command.rs
@@ -293,7 +293,7 @@ impl CreateProjectCommand {
                 io.clone(),
                 &config,
                 package_name,
-                &*platform_requirement_filter,
+                platform_requirement_filter.clone(),
                 directory.clone(),
                 package_version,
                 stability,
@@ -334,17 +334,10 @@ impl CreateProjectCommand {
                             .get_config()
                             .borrow()
                             .get_repositories();
-                    // TODO(phase-b): generate_repository_name expects existing repos as
-                    // IndexMap<String, Box<dyn RepositoryInterface>>; pass empty placeholder.
-                    let _ = &composer_json_repositories_config;
-                    let placeholder_existing: IndexMap<
-                        String,
-                        crate::repository::RepositoryInterfaceHandle,
-                    > = IndexMap::new();
                     let name = RepositoryFactory::generate_repository_name(
                         &PhpMixed::Int(index as i64),
                         &repo_config,
-                        &placeholder_existing,
+                        &composer_json_repositories_config,
                     );
                     let mut config_source = JsonConfigSource::new(
                         std::rc::Rc::new(std::cell::RefCell::new(JsonFile::new(
@@ -595,7 +588,7 @@ impl CreateProjectCommand {
         io: std::rc::Rc<std::cell::RefCell<dyn IOInterface>>,
         config: &std::rc::Rc<std::cell::RefCell<Config>>,
         package_name: &str,
-        platform_requirement_filter: &dyn PlatformRequirementFilterInterface,
+        platform_requirement_filter: std::rc::Rc<dyn PlatformRequirementFilterInterface>,
         directory: Option<String>,
         mut package_version: Option<String>,
         mut stability: Option<String>,
@@ -850,14 +843,11 @@ impl CreateProjectCommand {
             std::rc::Rc::new(std::cell::RefCell::new(repository_set)),
             Some(&mut platform_repo),
         )?;
-        // TODO(phase-b): platform_requirement_filter is &dyn here but VersionSelector expects
-        // Option<Box<dyn ...>>; pass None as placeholder.
-        let _ = platform_requirement_filter;
         let package = version_selector.find_best_candidate(
             &name,
             package_version.as_deref(),
             &stability,
-            None,
+            Some(platform_requirement_filter.clone()),
             0,
             Some(io.clone()),
             PhpMixed::Bool(true),
diff --git a/crates/shirabe/src/command/package_discovery_trait.rs b/crates/shirabe/src/command/package_discovery_trait.rs
index 32e5e21..b5e6cd5 100644
--- a/crates/shirabe/src/command/package_discovery_trait.rs
+++ b/crates/shirabe/src/command/package_discovery_trait.rs
@@ -852,7 +852,6 @@ pub trait PackageDiscoveryTrait {
         let installed_repo = repository_manager.get_local_repository();
 
         for result in &results {
-            // TODO(phase-b): installed_repo.find_package signature mismatch with FindPackageConstraint
             if installed_repo
                 .find_package(
                     &result.name,
@@ -929,11 +928,14 @@ pub trait PackageDiscoveryTrait {
                 let has_config_platform = platform_extra.contains_key("config.platform");
                 let is_complete = platform_pkg.as_complete().is_some();
                 if has_config_platform && is_complete {
-                    // TODO(phase-b): platform_pkg.get_description() via CompletePackageInterface
                     platform_pkg_version = format!(
                         "{} ({})",
                         platform_pkg_version,
-                        todo!("platform_pkg.get_description()")
+                        platform_pkg
+                            .as_complete()
+                            .unwrap()
+                            .get_description()
+                            .unwrap_or_default()
                     );
                 }
                 details.push(format!(
diff --git a/crates/shirabe/src/command/remove_command.rs b/crates/shirabe/src/command/remove_command.rs
index 1857b17..6cd2424 100644
--- a/crates/shirabe/src/command/remove_command.rs
+++ b/crates/shirabe/src/command/remove_command.rs
@@ -14,6 +14,7 @@ use crate::config::JsonConfigSource;
 use crate::console::input::InputArgument;
 use crate::console::input::InputOption;
 use crate::dependency_resolver::Request;
+use crate::dependency_resolver::UpdateAllowTransitiveDeps;
 use crate::factory::Factory;
 use crate::installer::Installer;
 use crate::io::IOInterface;
@@ -597,7 +598,7 @@ impl RemoveCommand {
                 .unwrap_or(false);
 
         let mut update_allow_transitive_dependencies =
-            Request::UPDATE_LISTED_WITH_TRANSITIVE_DEPS_NO_ROOT_REQUIRE;
+            UpdateAllowTransitiveDeps::UpdateListedWithTransitiveDepsNoRootRequire;
         let mut flags = String::new();
         if input
             .borrow()
@@ -610,7 +611,8 @@ impl RemoveCommand {
                 .as_bool()
                 .unwrap_or(false)
         {
-            update_allow_transitive_dependencies = Request::UPDATE_LISTED_WITH_TRANSITIVE_DEPS;
+            update_allow_transitive_dependencies =
+                UpdateAllowTransitiveDeps::UpdateListedWithTransitiveDeps;
             flags += " --with-all-dependencies";
         } else if input
             .borrow()
@@ -618,7 +620,7 @@ impl RemoveCommand {
             .as_bool()
             .unwrap_or(false)
         {
-            update_allow_transitive_dependencies = Request::UPDATE_ONLY_LISTED;
+            update_allow_transitive_dependencies = UpdateAllowTransitiveDeps::UpdateOnlyListed;
             flags += " --with-dependencies";
         }
 
diff --git a/crates/shirabe/src/command/require_command.rs b/crates/shirabe/src/command/require_command.rs
index 7fa4793..44ab921 100644
--- a/crates/shirabe/src/command/require_command.rs
+++ b/crates/shirabe/src/command/require_command.rs
@@ -20,6 +20,7 @@ use crate::composer::PartialComposerHandle;
 use crate::console::input::InputArgument;
 use crate::console::input::InputOption;
 use crate::dependency_resolver::Request;
+use crate::dependency_resolver::UpdateAllowTransitiveDeps;
 use crate::factory::Factory;
 use crate::installer::Installer;
 use crate::installer::InstallerEvents;
@@ -848,7 +849,7 @@ impl RequireCommand {
                 .as_bool()
                 .unwrap_or(false);
 
-        let mut update_allow_transitive_dependencies = Request::UPDATE_ONLY_LISTED;
+        let mut update_allow_transitive_dependencies = UpdateAllowTransitiveDeps::UpdateOnlyListed;
         let mut flags = String::new();
         if input
             .borrow()
@@ -861,7 +862,8 @@ impl RequireCommand {
                 .as_bool()
                 .unwrap_or(false)
         {
-            update_allow_transitive_dependencies = Request::UPDATE_LISTED_WITH_TRANSITIVE_DEPS;
+            update_allow_transitive_dependencies =
+                UpdateAllowTransitiveDeps::UpdateListedWithTransitiveDeps;
             flags += " --with-all-dependencies";
         } else if input
             .borrow()
@@ -875,7 +877,7 @@ impl RequireCommand {
                 .unwrap_or(false)
         {
             update_allow_transitive_dependencies =
-                Request::UPDATE_LISTED_WITH_TRANSITIVE_DEPS_NO_ROOT_REQUIRE;
+                UpdateAllowTransitiveDeps::UpdateListedWithTransitiveDepsNoRootRequire;
             flags += " --with-dependencies";
         }
 
@@ -1135,7 +1137,8 @@ impl RequireCommand {
                     IndexMap::new(),
                 );
                 let stability_flags_clone = stability_flags.clone();
-                // TODO(phase-b): get_locker_mut needs update_hash with stability flags rewriter.
+                // TODO(phase-c): Locker::update_hash needs the stability-flags rewriter callback;
+                // depends on modeling the closure passed to updateHash.
                 let _ = &stability_flags_clone;
                 todo!("update locker hash with stability flags rewriter");
             }
diff --git a/crates/shirabe/src/command/script_alias_command.rs b/crates/shirabe/src/command/script_alias_command.rs
index 50e7e80..ef95c7e 100644
--- a/crates/shirabe/src/command/script_alias_command.rs
+++ b/crates/shirabe/src/command/script_alias_command.rs
@@ -103,7 +103,7 @@ impl ScriptAliasCommand {
 
         let args = input.borrow().get_arguments();
 
-        // TODO(phase-b): InputInterface has_to_string/get_class_name not modeled in Rust
+        // TODO(phase-c): InputInterface has_to_string/get_class_name not modeled in Rust
         // TODO remove for Symfony 6+ as it is then in the interface
         if false {
             return Err(LogicException {
@@ -122,7 +122,7 @@ impl ScriptAliasCommand {
 
         Platform::put_env("COMPOSER_DEV_MODE", if dev_mode { "1" } else { "0" });
 
-        // TODO(phase-b): InputInterface lacks to_string; use a placeholder
+        // TODO(phase-c): InputInterface lacks to_string; use a placeholder until it is modeled.
         let input_as_string = String::new();
         let _ = input;
         let script_alias_input = Preg::replace4(r"{^\S+ ?}", "", &input_as_string, 1)?;
diff --git a/crates/shirabe/src/command/show_command.rs b/crates/shirabe/src/command/show_command.rs
index 1ce91cb..3761b09 100644
--- a/crates/shirabe/src/command/show_command.rs
+++ b/crates/shirabe/src/command/show_command.rs
@@ -610,7 +610,7 @@ impl ShowCommand {
                         .get_option("patch-only")
                         .as_bool()
                         .unwrap_or(false),
-                    &*platform_req_filter,
+                    platform_req_filter.clone(),
                 )?;
             }
             if input.borrow().get_option("outdated").as_bool() == Some(true)
@@ -885,7 +885,7 @@ impl ShowCommand {
                                     show_major_only,
                                     show_minor_only,
                                     show_patch_only,
-                                    &*platform_req_filter,
+                                    platform_req_filter.clone(),
                                 )?;
                                 if latest.is_none() {
                                     continue;
@@ -2639,7 +2639,7 @@ impl ShowCommand {
         major_only: bool,
         minor_only: bool,
         patch_only: bool,
-        platform_req_filter: &dyn PlatformRequirementFilterInterface,
+        platform_req_filter: std::rc::Rc<dyn PlatformRequirementFilterInterface>,
     ) -> anyhow::Result<Option<crate::package::PackageInterfaceHandle>> {
         // find the latest version allowed in this repo set
         let name = package.get_name();
@@ -2738,14 +2738,14 @@ impl ShowCommand {
                 version_compare(&candidate.get_version(), &package_version, "<=")
             });
         }
-        // TODO(phase-b): platform_req_filter needs to be Option<Box<dyn ...>>; current code holds &dyn.
-        let _ = platform_req_filter;
+        // TODO(phase-c): PHP passes $showWarnings (true or a closure) as the last argument, but the
+        // closure form requires modeling a callable inside PhpMixed; hardcoding true until then.
         let _ = show_warnings_box;
         let mut candidate = version_selector.find_best_candidate(
             &name,
             target_version.as_deref(),
             &best_stability,
-            None,
+            Some(platform_req_filter),
             0,
             Some(self.get_io().clone()),
             PhpMixed::Bool(true),
diff --git a/crates/shirabe/src/command/update_command.rs b/crates/shirabe/src/command/update_command.rs
index 751203c..eb618ca 100644
--- a/crates/shirabe/src/command/update_command.rs
+++ b/crates/shirabe/src/command/update_command.rs
@@ -49,7 +49,8 @@ impl UpdateCommand {
             .set_name("update")
             .set_aliases(&["u".to_string(), "upgrade".to_string()])
             .set_description("Updates your dependencies to the latest version according to composer.json, and updates the composer.lock file")
-            // TODO(phase-b): set_definition with InputArgument/InputOption (see PHP UpdateCommand)
+            // TODO(phase-c): populate with InputArgument/InputOption entries (see PHP UpdateCommand);
+            // blocked on the symfony InputDefinition entry modeling.
             .set_definition(&[])
             .set_help(
                 "The <info>update</info> command reads the composer.json file from the\n\
@@ -227,15 +228,10 @@ impl UpdateCommand {
                     "~{}",
                     matches.get(1).cloned().unwrap_or_default()
                 ))?;
-                if temporary_constraints.contains_key(&package.get_name()) {
-                    let existing = temporary_constraints
-                        .get(&package.get_name())
-                        .map(|c| c.clone())
-                        .unwrap();
+                if let Some(existing) = temporary_constraints.get(&package.get_name()) {
                     temporary_constraints.insert(
                         package.get_name(),
-                        // TODO(phase-b): MultiConstraint::create signature
-                        todo!("MultiConstraint::create([existing, constraint], true)"),
+                        MultiConstraint::create(vec![existing.clone(), constraint], true, None)?,
                     );
                 } else {
                     temporary_constraints.insert(package.get_name(), constraint);
@@ -376,14 +372,15 @@ impl UpdateCommand {
                 .as_bool()
                 .unwrap_or(false);
 
-        let mut update_allow_transitive_dependencies: i64 = Request::UPDATE_ONLY_LISTED;
+        let mut update_allow_transitive_dependencies = UpdateAllowTransitiveDeps::UpdateOnlyListed;
         if input
             .borrow()
             .get_option("with-all-dependencies")
             .as_bool()
             .unwrap_or(false)
         {
-            update_allow_transitive_dependencies = Request::UPDATE_LISTED_WITH_TRANSITIVE_DEPS;
+            update_allow_transitive_dependencies =
+                UpdateAllowTransitiveDeps::UpdateListedWithTransitiveDeps;
         } else if input
             .borrow()
             .get_option("with-dependencies")
@@ -391,10 +388,8 @@ impl UpdateCommand {
             .unwrap_or(false)
         {
             update_allow_transitive_dependencies =
-                Request::UPDATE_LISTED_WITH_TRANSITIVE_DEPS_NO_ROOT_REQUIRE;
+                UpdateAllowTransitiveDeps::UpdateListedWithTransitiveDepsNoRootRequire;
         }
-        // Keep `UpdateAllowTransitiveDeps` import alive while still using i64 for the setter.
-        let _ = UpdateAllowTransitiveDeps::UpdateOnlyListed;
 
         install
             .set_dry_run(
@@ -456,13 +451,7 @@ impl UpdateCommand {
                     .as_bool()
                     .unwrap_or(false),
             )
-            // TODO(phase-b): VersionParser::parse_constraints returns Arc<dyn ...> but
-            // Installer::set_temporary_constraints expects IndexMap<String, Box<dyn ...>>;
-            // bridge the constraint storage types later.
-            .set_temporary_constraints({
-                let _ = &temporary_constraints;
-                IndexMap::new()
-            })
+            .set_temporary_constraints(temporary_constraints)
             .set_audit_config(
                 self.create_audit_config(&mut *composer.get_config().borrow_mut(), input.clone())?,
             )
@@ -548,7 +537,6 @@ impl UpdateCommand {
         );
 
         let filter: Option<String> = if packages.len() > 0 {
-            // TODO(phase-b): base_package::package_names_to_regexp signature
             Some(base_package::package_names_to_regexp(&packages, "%s"))
         } else {
             None
@@ -682,11 +670,21 @@ impl UpdateCommand {
 
     fn create_version_selector(&self, composer: &PartialComposerHandle) -> Result<VersionSelector> {
         let composer = crate::command::composer_full(composer);
+        let root_aliases: Vec<crate::repository::RootAliasInput> = composer
+            .get_package()
+            .get_aliases()
+            .into_iter()
+            .map(|alias| crate::repository::RootAliasInput {
+                package: alias.get("package").cloned().unwrap_or_default(),
+                version: alias.get("version").cloned().unwrap_or_default(),
+                alias: alias.get("alias").cloned().unwrap_or_default(),
+                alias_normalized: alias.get("alias_normalized").cloned().unwrap_or_default(),
+            })
+            .collect();
         let mut repository_set = RepositorySet::new(
             &composer.get_package().get_minimum_stability(),
             composer.get_package().get_stability_flags().clone(),
-            // TODO(phase-b): collect root aliases from composer.get_package().get_aliases()
-            Vec::new(),
+            root_aliases,
             composer.get_package().get_references().clone(),
             IndexMap::new(),
             IndexMap::new(),
diff --git a/crates/shirabe/src/dependency_resolver/decisions.rs b/crates/shirabe/src/dependency_resolver/decisions.rs
index 3b82883..81f0088 100644
--- a/crates/shirabe/src/dependency_resolver/decisions.rs
+++ b/crates/shirabe/src/dependency_resolver/decisions.rs
@@ -11,7 +11,6 @@ pub struct Decisions {
     pub(crate) pool: std::rc::Rc<std::cell::RefCell<Pool>>,
     pub(crate) decision_map: IndexMap<i64, i64>,
     pub(crate) decision_queue: Vec<(i64, std::rc::Rc<std::cell::RefCell<Rule>>)>,
-    iterator_cursor: Option<usize>,
 }
 
 impl std::fmt::Debug for Decisions {
@@ -32,7 +31,6 @@ impl Decisions {
             pool,
             decision_map: IndexMap::new(),
             decision_queue: Vec::new(),
-            iterator_cursor: None,
         }
     }
 
@@ -154,33 +152,6 @@ impl Decisions {
         self.decision_queue.len()
     }
 
-    pub fn rewind(&mut self) {
-        if self.decision_queue.is_empty() {
-            self.iterator_cursor = None;
-        } else {
-            self.iterator_cursor = Some(self.decision_queue.len() - 1);
-        }
-    }
-
-    pub fn current(&self) -> Option<&(i64, std::rc::Rc<std::cell::RefCell<Rule>>)> {
-        self.iterator_cursor
-            .and_then(|cursor| self.decision_queue.get(cursor))
-    }
-
-    pub fn key(&self) -> Option<usize> {
-        self.iterator_cursor
-    }
-
-    pub fn next(&mut self) {
-        self.iterator_cursor = self
-            .iterator_cursor
-            .and_then(|cursor| if cursor > 0 { Some(cursor - 1) } else { None });
-    }
-
-    pub fn valid(&self) -> bool {
-        self.iterator_cursor.is_some() && self.current().is_some()
-    }
-
     pub fn is_empty(&self) -> bool {
         self.decision_queue.is_empty()
     }
@@ -227,6 +198,11 @@ impl Decisions {
 
         str
     }
+
+    // Reverse iteration: newest-first.
+    pub fn iter(&self) -> impl Iterator<Item = &(i64, std::rc::Rc<std::cell::RefCell<Rule>>)> {
+        self.decision_queue.iter().rev()
+    }
 }
 
 impl fmt::Display for Decisions {
diff --git a/crates/shirabe/src/dependency_resolver/problem.rs b/crates/shirabe/src/dependency_resolver/problem.rs
index 47cf3b5..7841946 100644
--- a/crates/shirabe/src/dependency_resolver/problem.rs
+++ b/crates/shirabe/src/dependency_resolver/problem.rs
@@ -92,7 +92,6 @@ impl Problem {
             }
 
             let reason_data = rule_ref.get_reason_data();
-            // TODO(phase-b): reason_data for RULE_ROOT_REQUIRE; extract via ReasonData::RootRequire variant.
             let (package_name, constraint): (String, Option<&AnyConstraint>) = match reason_data {
                 rule::ReasonData::RootRequire {
                     package_name,
@@ -144,27 +143,23 @@ impl Problem {
                 rule::ReasonData::RootRequire { package_name, .. } => package_name.clone(),
                 _ => String::new(),
             },
-            rule::RULE_FIXED => {
-                // TODO(phase-b): reason_data for RULE_FIXED is `array{package: BasePackage}`.
-                // PHP: (string) $rule->getReasonData()['package']
-                match rule.get_reason_data() {
-                    rule::ReasonData::Fixed { package } => package.get_pretty_string(),
-                    _ => String::new(),
-                }
-            }
+            rule::RULE_FIXED => match rule.get_reason_data() {
+                rule::ReasonData::Fixed { package } => package.get_unique_name(),
+                _ => String::new(),
+            },
             rule::RULE_PACKAGE_CONFLICT | rule::RULE_PACKAGE_REQUIRES => {
-                // TODO(phase-b): reason_data is a Link.
                 let source = rule.get_source_package(pool).unwrap();
                 let link_pretty = match rule.get_reason_data() {
                     rule::ReasonData::Link(link) => link.get_pretty_string(source.clone()),
                     _ => String::new(),
                 };
-                format!("{}//{}", source.get_pretty_string(), link_pretty)
+                format!("{}//{}", source.get_unique_name(), link_pretty)
             }
             rule::RULE_PACKAGE_SAME_NAME
             | rule::RULE_PACKAGE_ALIAS
             | rule::RULE_PACKAGE_INVERSE_ALIAS => {
-                // TODO(phase-b): convert ReasonData to PhpMixed for php_to_string
+                // TODO(phase-c): PHP returns (string) $rule->getReasonData(), but the alias rules'
+                // reason_data is still a placeholder pending the RuleSetGenerator reason_data wiring.
                 format!("{:?}", rule.get_reason_data())
             }
             rule::RULE_LEARNED => implode(
@@ -807,7 +802,7 @@ impl Problem {
             }
 
             if pool.is_security_removed_package_version(package_name, constraint) {
-                // TODO(phase-b): get_matching_security_advisories needs Vec<PackageInterfaceHandle>
+                // TODO(phase-c): get_matching_security_advisories needs Vec<PackageInterfaceHandle>
                 // and SecurityAdvisory.inner.advisory_id is on the private inner field.
                 // Convert packages to PackageInterfaceHandle and adjust SecurityAdvisory accessor first.
                 let _ = repository_set;
diff --git a/crates/shirabe/src/dependency_resolver/request.rs b/crates/shirabe/src/dependency_resolver/request.rs
index 88957f2..83efb9b 100644
--- a/crates/shirabe/src/dependency_resolver/request.rs
+++ b/crates/shirabe/src/dependency_resolver/request.rs
@@ -28,13 +28,15 @@ impl Request {
     pub const UPDATE_LISTED_WITH_TRANSITIVE_DEPS: i64 = UPDATE_LISTED_WITH_TRANSITIVE_DEPS;
 }
 
-/// Represents the value of updateAllowTransitiveDependencies, which is false|UPDATE_* in PHP.
-#[derive(Debug, Clone, PartialEq)]
+#[derive(Debug, Clone, Copy, PartialEq, Eq)]
 pub enum UpdateAllowTransitiveDeps {
-    /// Corresponds to PHP false (initial value)
+    /// Corresponds to PHP false.
     False,
+    /// \Composer\DependencyResolver\Request::UPDATE_ONLY_LISTED
     UpdateOnlyListed,
+    /// \Composer\DependencyResolver\Request::UPDATE_LISTED_WITH_TRANSITIVE_DEPS_NO_ROOT_REQUIRE
     UpdateListedWithTransitiveDepsNoRootRequire,
+    /// \Composer\DependencyResolver\Request::UPDATE_LISTED_WITH_TRANSITIVE_DEPS
     UpdateListedWithTransitiveDeps,
 }
 
diff --git a/crates/shirabe/src/dependency_resolver/rule.rs b/crates/shirabe/src/dependency_resolver/rule.rs
index 7804b99..4e5a920 100644
--- a/crates/shirabe/src/dependency_resolver/rule.rs
+++ b/crates/shirabe/src/dependency_resolver/rule.rs
@@ -229,7 +229,9 @@ impl Rule {
                 if PlatformRepository::is_platform_package(link.get_target()) {
                     return false;
                 }
-                // TODO(phase-b): Request::get_locked_repository() signature
+                // TODO(phase-c): request.get_locked_repository() exists, but its get_packages()
+                // returns Result while is_caused_by_lock returns bool; resolving needs the bool
+                // chain (also via Problem/SolverProblemsException, itself phase-c) to carry Result.
                 let locked_repo: Option<()> = todo!("request.get_locked_repository()");
                 if let Some(_locked_repo) = locked_repo {
                     let packages: Vec<BasePackageHandle> = todo!("locked_repo.get_packages()");
@@ -269,7 +271,9 @@ impl Rule {
                 if PlatformRepository::is_platform_package(package_name) {
                     return false;
                 }
-                // TODO(phase-b): Request::get_locked_repository() signature
+                // TODO(phase-c): request.get_locked_repository() exists, but its get_packages()
+                // returns Result while is_caused_by_lock returns bool; resolving needs the bool
+                // chain (also via Problem/SolverProblemsException, itself phase-c) to carry Result.
                 let locked_repo: Option<()> = todo!("request.get_locked_repository()");
                 if let Some(_locked_repo) = locked_repo {
                     let packages: Vec<BasePackageHandle> = todo!("locked_repo.get_packages()");
diff --git a/crates/shirabe/src/dependency_resolver/solver.rs b/crates/shirabe/src/dependency_resolver/solver.rs
index 3d2113e..03dd575 100644
--- a/crates/shirabe/src/dependency_resolver/solver.rs
+++ b/crates/shirabe/src/dependency_resolver/solver.rs
@@ -239,10 +239,8 @@ impl Solver {
         self.io
             .write_error3("Generating rules", true, crate::io::DEBUG);
         let mut rule_set_generator = RuleSetGenerator::new(self.policy.clone(), self.pool.clone());
-        // TODO(phase-b): get_rules_for takes Option<Rc<dyn PlatformRequirementFilterInterface>>;
-        // PHP passes the filter directly. Forwarding `None` here keeps the call typecheckable.
-        let _ = platform_requirement_filter.as_ref();
-        self.rules = rule_set_generator.get_rules_for(request, None)?;
+        self.rules =
+            rule_set_generator.get_rules_for(request, Some(platform_requirement_filter.clone()))?;
         drop(rule_set_generator);
         self.check_for_root_require_problems(request, platform_requirement_filter.as_ref())?;
         self.decisions = Decisions::new(self.pool.clone());
@@ -667,22 +665,12 @@ impl Solver {
             seen.insert(literal.abs(), true);
         }
 
-        // TODO(phase-b): Decisions does not expose an `iter()` matching PHP's foreach.
-        // Walk the decision queue directly through offsets to avoid borrowing issues
-        // (we still need to call back into `&self` while iterating).
-        let mut offset = 0_usize;
-        while offset < self.decisions.count() {
-            let decision_literal = self.decisions.at_offset(offset).0;
-
-            offset += 1;
-
+        for (decision_literal, why) in self.decisions.iter() {
             // skip literals that are not in this rule
             if !seen.contains_key(&decision_literal.abs()) {
                 continue;
             }
 
-            let why = self.decisions.at_offset(offset - 1).1.clone();
-
             problem.add_rule(why.clone());
             self.analyze_unsolvable_rule(&mut problem, why.clone(), &mut rule_seen);
 
diff --git a/crates/shirabe/src/downloader/file_downloader.rs b/crates/shirabe/src/downloader/file_downloader.rs
index 54b0882..e5112cc 100644
--- a/crates/shirabe/src/downloader/file_downloader.rs
+++ b/crates/shirabe/src/downloader/file_downloader.rs
@@ -551,12 +551,7 @@ impl DownloaderInterface for FileDownloader {
         for bin in package.get_binaries() {
             let bin_path = format!("{}/{}", path, bin);
             if file_exists(&bin_path) && !is_executable(&bin_path) {
-                // TODO(phase-b): Silencer::call_named for native PHP function
-                let _ = Silencer::call(|| {
-                    let _ = bin_path;
-                    let _ = umask();
-                    Ok(())
-                });
+                let _ = Silencer::call(|| Ok(shirabe_php_shim::chmod(&bin_path, 0o777 & !umask())));
             }
         }
 
diff --git a/crates/shirabe/src/downloader/git_downloader.rs b/crates/shirabe/src/downloader/git_downloader.rs
index 7dace1b..47dd959 100644
--- a/crates/shirabe/src/downloader/git_downloader.rs
+++ b/crates/shirabe/src/downloader/git_downloader.rs
@@ -1240,7 +1240,6 @@ impl VcsDownloader for GitDownloader {
             io_interface::NORMAL,
         );
         let slice_end = 10_usize.min(changes.len());
-        // TODO(phase-b): PHP passes the list directly to writeError; joined here so write_error3 takes &str
         self.inner
             .io
             .write_error3(&changes[..slice_end].join("\n"), true, io_interface::NORMAL);
@@ -1291,7 +1290,6 @@ impl VcsDownloader for GitDownloader {
                     .into());
                 }
                 Some("v") => {
-                    // TODO(phase-b): PHP passes list directly; joined here for &str arg
                     self.inner
                         .io
                         .write_error3(&changes.join("\n"), true, io_interface::NORMAL);
@@ -1307,7 +1305,6 @@ impl VcsDownloader for GitDownloader {
 
             if do_help {
                 // help:
-                // TODO(phase-b): PHP passes list directly; joined here for &str arg
                 self.inner.io.write_error3(
                     &[
                         format!(
diff --git a/crates/shirabe/src/event_dispatcher/event_dispatcher.rs b/crates/shirabe/src/event_dispatcher/event_dispatcher.rs
index a9da6e8..729979d 100644
--- a/crates/shirabe/src/event_dispatcher/event_dispatcher.rs
+++ b/crates/shirabe/src/event_dispatcher/event_dispatcher.rs
@@ -1067,8 +1067,6 @@ impl EventDispatcher {
         let package = composer.get_package();
         let scripts = package.get_scripts();
 
-        // TODO(phase-b): RootPackage::get_scripts() returns Vec<String> per event;
-        // mirror PHP's is_empty_value semantics on the Vec form.
         let event_scripts: Vec<String> = match scripts.get(event.get_name()) {
             Some(v) if !v.is_empty() => v.clone(),
             _ => return Vec::new(),
@@ -1271,12 +1269,10 @@ impl EventDispatcher {
             package.clone(),
             packages,
         )?;
-        // TODO(phase-b): parse_autoloads also expects the filtered dev packages list
-        // (PhpMixed in this port).
         let map = generator.parse_autoloads(
             package_map,
             package.clone(),
-            shirabe_php_shim::PhpMixed::Null,
+            shirabe_php_shim::PhpMixed::Bool(false),
         );
 
         if self.loader.is_some() {
diff --git a/crates/shirabe/src/factory.rs b/crates/shirabe/src/factory.rs
index 101e4cd..f1c66ce 100644
--- a/crates/shirabe/src/factory.rs
+++ b/crates/shirabe/src/factory.rs
@@ -6,11 +6,11 @@ use shirabe_external_packages::symfony::console::formatter::OutputFormatter;
 use shirabe_external_packages::symfony::console::formatter::OutputFormatterStyle;
 use shirabe_external_packages::symfony::console::output::ConsoleOutput;
 use shirabe_php_shim::{
-    InvalidArgumentException, PATHINFO_EXTENSION, PHP_EOL, Phar, PhpMixed, RuntimeException,
-    UnexpectedValueException, ZipArchive, array_keys, array_replace_recursive, class_exists,
-    dirname, extension_loaded, file_exists, file_get_contents, file_put_contents, implode,
-    in_array, is_array, is_dir, is_file, is_string, json_decode, pathinfo, realpath, str_replace,
-    strpos, strtr, substr, trim,
+    InvalidArgumentException, PATHINFO_EXTENSION, PHP_EOL, PHP_OS, Phar, PhpMixed,
+    RuntimeException, UnexpectedValueException, ZipArchive, array_keys, array_replace_recursive,
+    class_exists, dirname, extension_loaded, file_exists, file_get_contents, file_put_contents,
+    implode, in_array, is_array, is_dir, is_file, is_string, json_decode, mkdir, pathinfo,
+    realpath, str_replace, strpos, strtr, substr, trim,
 };
 
 use crate::autoload::AutoloadGenerator;
@@ -175,7 +175,7 @@ impl Factory {
         }
 
         let user_dir = Self::get_user_dir()?;
-        if Platform::php_os() == "Darwin" {
+        if PHP_OS == "Darwin" {
             // Migrate existing cache dir in old location if present
             if is_dir(&format!("{}/cache", home))
                 && !is_dir(&format!("{}/Library/Caches/composer", user_dir))
@@ -309,7 +309,7 @@ impl Factory {
                     if !is_dir(dir) {
                         let dir_owned = dir.clone();
                         let _ = Silencer::call(|| {
-                            Ok::<bool, anyhow::Error>(Platform::mkdir(&dir_owned, 0o777, true))
+                            Ok::<bool, anyhow::Error>(mkdir(&dir_owned, 0o777, true))
                         });
                     }
                     let path = format!("{}/.htaccess", dir);
diff --git a/crates/shirabe/src/installer.rs b/crates/shirabe/src/installer.rs
index 1578fc1..3c68b90 100644
--- a/crates/shirabe/src/installer.rs
+++ b/crates/shirabe/src/installer.rs
@@ -58,6 +58,7 @@ use crate::dependency_resolver::Request;
 use crate::dependency_resolver::SecurityAdvisoryPoolFilter;
 use crate::dependency_resolver::Solver;
 use crate::dependency_resolver::SolverProblemsException;
+use crate::dependency_resolver::UpdateAllowTransitiveDeps;
 use crate::dependency_resolver::operation::InstallOperation;
 use crate::dependency_resolver::operation::OperationInterface;
 use crate::dependency_resolver::operation::UninstallOperation;
@@ -143,7 +144,7 @@ pub struct Installer {
     allowed_types: Option<Vec<String>>,
     pub(crate) update_mirrors: bool,
     pub(crate) update_allow_list: Option<Vec<String>>,
-    pub(crate) update_allow_transitive_dependencies: i64,
+    pub(crate) update_allow_transitive_dependencies: UpdateAllowTransitiveDeps,
     pub(crate) suggested_packages_reporter:
         std::rc::Rc<std::cell::RefCell<SuggestedPackagesReporter>>,
     pub(crate) platform_requirement_filter: std::rc::Rc<dyn PlatformRequirementFilterInterface>,
@@ -217,7 +218,7 @@ impl Installer {
             allowed_types: None,
             update_mirrors: false,
             update_allow_list: None,
-            update_allow_transitive_dependencies: Request::UPDATE_ONLY_LISTED,
+            update_allow_transitive_dependencies: UpdateAllowTransitiveDeps::UpdateOnlyListed,
             suggested_packages_reporter,
             platform_requirement_filter,
             additional_fixed_repository: None,
@@ -653,8 +654,10 @@ impl Installer {
 
         // pass the allow list into the request, so the pool builder can apply it
         if let Some(ref allow_list) = self.update_allow_list {
-            // TODO(phase-b): convert i64 self.update_allow_transitive_dependencies into the enum
-            let _ = allow_list;
+            request.set_update_allow_list(
+                allow_list.clone(),
+                self.update_allow_transitive_dependencies,
+            );
         }
 
         let pool = std::rc::Rc::new(std::cell::RefCell::new(repository_set.create_pool(
@@ -1324,7 +1327,7 @@ impl Installer {
                 .borrow_mut()
                 .get_minimum_stability()
                 .unwrap_or_else(|_| String::new());
-            // TODO(phase-b): locker.get_stability_flags returns IndexMap<String, String>; convert to i64
+            // locker stores stability flags as stringified ints; recover the int form here.
             stability_flags = self
                 .locker
                 .borrow_mut()
@@ -1378,9 +1381,15 @@ impl Installer {
                 [VersionParser::parse_stability(&self.package.get_version()).as_str()],
         );
 
-        // TODO(phase-b): convert root_aliases (Vec<IndexMap<String, String>>) into Vec<RootAliasInput>
-        let root_aliases_input: Vec<crate::repository::RootAliasInput> = vec![];
-        let _ = root_aliases;
+        let root_aliases_input: Vec<crate::repository::RootAliasInput> = root_aliases
+            .into_iter()
+            .map(|alias| crate::repository::RootAliasInput {
+                package: alias.get("package").cloned().unwrap_or_default(),
+                version: alias.get("version").cloned().unwrap_or_default(),
+                alias: alias.get("alias").cloned().unwrap_or_default(),
+                alias_normalized: alias.get("alias_normalized").cloned().unwrap_or_default(),
+            })
+            .collect();
         let temporary_constraints: IndexMap<String, AnyConstraint> = IndexMap::new();
         let mut repository_set = RepositorySet::new(
             &minimum_stability,
@@ -1522,20 +1531,11 @@ impl Installer {
     ) -> anyhow::Result<()> {
         // if we're updating mirrors we want to keep exactly the same versions installed which are in the lock file, but we want current remote metadata
         if self.update_mirrors {
-            let excluded_packages: IndexMap<String, i64> = if !include_dev_requires {
-                // TODO(phase-b): locker.get_dev_package_names returns Result<Vec<String>>
-                let names = self
-                    .locker
-                    .borrow_mut()
-                    .get_dev_package_names()
-                    .unwrap_or_default();
-                names
-                    .into_iter()
-                    .enumerate()
-                    .map(|(i, name)| (name, i as i64))
-                    .collect()
+            let excluded_packages: indexmap::IndexSet<String> = if !include_dev_requires {
+                let names = self.locker.borrow_mut().get_dev_package_names()?;
+                names.into_iter().collect()
             } else {
-                IndexMap::new()
+                indexmap::IndexSet::new()
             };
 
             for locked_package in locked_repository
@@ -1546,7 +1546,7 @@ impl Installer {
                 // exclude alias packages here as for root aliases, both alias and aliased are
                 // present in the lock repo and we only want to require the aliased version
                 if locked_package.as_alias().is_none()
-                    && !excluded_packages.contains_key(&locked_package.get_name())
+                    && !excluded_packages.contains(&locked_package.get_name())
                 {
                     request.require_name(
                         &locked_package.get_name(),
@@ -1893,21 +1893,8 @@ impl Installer {
     /// dependencies which are not root requirement or all transitive dependencies including root requirements
     pub fn set_update_allow_transitive_dependencies(
         &mut self,
-        update_allow_transitive_dependencies: i64,
+        update_allow_transitive_dependencies: UpdateAllowTransitiveDeps,
     ) -> anyhow::Result<&mut Self> {
-        let valid = [
-            Request::UPDATE_ONLY_LISTED,
-            Request::UPDATE_LISTED_WITH_TRANSITIVE_DEPS_NO_ROOT_REQUIRE,
-            Request::UPDATE_LISTED_WITH_TRANSITIVE_DEPS,
-        ];
-        if !valid.contains(&update_allow_transitive_dependencies) {
-            return Err(RuntimeException {
-                message: "Invalid value for updateAllowTransitiveDependencies supplied".to_string(),
-                code: 0,
-            }
-            .into());
-        }
-
         self.update_allow_transitive_dependencies = update_allow_transitive_dependencies;
 
         Ok(self)
diff --git a/crates/shirabe/src/installer/installation_manager.rs b/crates/shirabe/src/installer/installation_manager.rs
index 4a13e6b..4d5608d 100644
--- a/crates/shirabe/src/installer/installation_manager.rs
+++ b/crates/shirabe/src/installer/installation_manager.rs
@@ -486,7 +486,7 @@ impl InstallationManager {
             };
 
             if run_scripts && self.event_dispatcher.is_some() {
-                // TODO(phase-b): dispatch_package_event takes Box<dyn RepositoryInterface>/Vec<Box<...>>
+                // TODO(phase-c): dispatch_package_event takes Box<dyn RepositoryInterface>/Vec<Box<...>>
                 // but we hold &mut dyn here. Needs structural rework (likely shared Rc on repo and ops).
                 let _ = (
                     event_name,
diff --git a/crates/shirabe/src/io/buffer_io.rs b/crates/shirabe/src/io/buffer_io.rs
index 079b470..92f5714 100644
--- a/crates/shirabe/src/io/buffer_io.rs
+++ b/crates/shirabe/src/io/buffer_io.rs
@@ -59,8 +59,8 @@ impl BufferIO {
     }
 
     pub fn get_output(&self) -> String {
-        // TODO(phase-b): OutputInterface::get_stream returns PhpResource, while
-        // fseek/stream_get_contents take PhpMixed. Conversion is not yet defined.
+        // TODO(phase-c): OutputInterface::get_stream returns PhpResource, while
+        // fseek/stream_get_contents take PhpMixed. The PhpResource stream model is not yet defined.
         let stream: PhpMixed =
             todo!("PhpResource -> PhpMixed conversion for OutputInterface::get_stream");
         fseek(stream.clone(), 0);
@@ -93,7 +93,8 @@ impl BufferIO {
             &output,
         );
 
-        // TODO(phase-b): Preg::replace_callback returns Result<String>, unwrap for now
+        // TODO(phase-c): Preg::replace_callback returns Result<String>; PHP getOutput returns the
+        // string directly, so this is gated on the get_stream PhpResource model above.
         output.unwrap_or_default()
     }
 
diff --git a/crates/shirabe/src/package/version/version_guesser.rs b/crates/shirabe/src/package/version/version_guesser.rs
index 1afe910..3b61eac 100644
--- a/crates/shirabe/src/package/version/version_guesser.rs
+++ b/crates/shirabe/src/package/version/version_guesser.rs
@@ -436,8 +436,6 @@ impl VersionGuesser {
                 ],
                 path,
             )?;
-            // PHP: $result['commit'] = '';
-            // TODO(phase-b): VersionData::commit modeled as Option<String>; using Some(String::new())
             let commit = Some(String::new());
             let feature_version = Some(version.clone());
             let feature_pretty_version = Some(version);
diff --git a/crates/shirabe/src/repository/array_repository.rs b/crates/shirabe/src/repository/array_repository.rs
index df25235..1bee17b 100644
--- a/crates/shirabe/src/repository/array_repository.rs
+++ b/crates/shirabe/src/repository/array_repository.rs
@@ -144,6 +144,11 @@ impl ArrayRepository {
     pub(crate) fn initialize(&self) {
         *self.packages.borrow_mut() = Some(vec![]);
     }
+
+    /// Resets the packages cache so the next access re-runs `initialize`.
+    pub(crate) fn reset_packages(&self) {
+        *self.packages.borrow_mut() = None;
+    }
 }
 
 impl RepositoryInterface for ArrayRepository {
diff --git a/crates/shirabe/src/repository/filesystem_repository.rs b/crates/shirabe/src/repository/filesystem_repository.rs
index 4a18dc9..411fa13 100644
--- a/crates/shirabe/src/repository/filesystem_repository.rs
+++ b/crates/shirabe/src/repository/filesystem_repository.rs
@@ -186,8 +186,7 @@ impl FilesystemRepository {
     }
 
     pub fn reload(&mut self) -> Result<()> {
-        // TODO(phase-b): clear inner packages cache (PHP: $this->packages = null)
-        self.inner.reload();
+        self.inner.reset_packages();
         self.initialize()
     }
 
diff --git a/crates/shirabe/src/repository/repository_factory.rs b/crates/shirabe/src/repository/repository_factory.rs
index 89334a1..993699f 100644
--- a/crates/shirabe/src/repository/repository_factory.rs
+++ b/crates/shirabe/src/repository/repository_factory.rs
@@ -321,10 +321,10 @@ impl RepositoryFactory {
         Ok(repo_map)
     }
 
-    pub fn generate_repository_name(
+    pub fn generate_repository_name<T>(
         index: &PhpMixed,
         repo: &IndexMap<String, PhpMixed>,
-        existing_repos: &IndexMap<String, RepositoryInterfaceHandle>,
+        existing_repos: &IndexMap<String, T>,
     ) -> String {
         let mut name = match index {
             PhpMixed::Int(_) => {
diff --git a/crates/shirabe/src/repository/repository_set.rs b/crates/shirabe/src/repository/repository_set.rs
index f632fbc..bf7b525 100644
--- a/crates/shirabe/src/repository/repository_set.rs
+++ b/crates/shirabe/src/repository/repository_set.rs
@@ -618,7 +618,6 @@ impl RepositorySet {
         }
 
         if !allowed_packages.is_empty() {
-            // TODO(phase-b): Request::restrict_packages signature
             request.restrict_packages(allowed_packages);
         }
 
diff --git a/crates/shirabe/src/repository/vcs/git_bitbucket_driver.rs b/crates/shirabe/src/repository/vcs/git_bitbucket_driver.rs
index 7eb253a..59e6b88 100644
--- a/crates/shirabe/src/repository/vcs/git_bitbucket_driver.rs
+++ b/crates/shirabe/src/repository/vcs/git_bitbucket_driver.rs
@@ -494,7 +494,9 @@ impl GitBitbucketDriver {
     /// @inheritDoc
     pub fn get_source(&self, identifier: &str) -> IndexMap<String, String> {
         if let Some(fallback) = self.fallback_driver.as_ref() {
-            // TODO(phase-b): trait returns Result; flatten for the inherent signature here
+            // TODO(phase-c): PHP getSource is infallible (: array), but the Rust trait made it
+            // Result, so the fallback's Result is flattened here. The faithful fix is making the
+            // VcsDriverInterface get_source/get_dist infallible across all implementations.
             return fallback.get_source(identifier).unwrap_or_default();
         }
 
@@ -511,7 +513,7 @@ impl GitBitbucketDriver {
     /// @inheritDoc
     pub fn get_dist(&self, identifier: &str) -> Option<IndexMap<String, String>> {
         if let Some(fallback) = self.fallback_driver.as_ref() {
-            // TODO(phase-b): trait returns Result; flatten for the inherent signature here
+            // TODO(phase-c): see get_source above — the trait's over-fallibility is flattened here.
             return fallback.get_dist(identifier).ok().flatten();
         }
 
@@ -886,14 +888,14 @@ impl GitBitbucketDriver {
         }
 
         if !extension_loaded("openssl") {
-            io.write_error(
+            io.write_error3(
                 &format!(
                     "Skipping Bitbucket git driver for {} because the OpenSSL PHP extension is missing.",
                     url
                 ),
+                true,
+                io_interface::VERBOSE,
             );
-            // PHP: writeError(..., true, io_interface::VERBOSE)
-            // TODO(phase-b): io_interface::VERBOSE verbosity argument
 
             return Ok(false);
         }
diff --git a/crates/shirabe/src/repository/vcs/svn_driver.rs b/crates/shirabe/src/repository/vcs/svn_driver.rs
index f4e2bba..911e982 100644
--- a/crates/shirabe/src/repository/vcs/svn_driver.rs
+++ b/crates/shirabe/src/repository/vcs/svn_driver.rs
@@ -33,8 +33,6 @@ pub struct SvnDriver {
     /// @var ?string
     pub(crate) root_identifier: Option<String>,
 
-    /// @var string|false
-    // TODO(phase-b): PHP uses 'false' as a sentinel; model as Option<String>
     pub(crate) trunk_path: Option<String>,
     /// @var string
     pub(crate) branches_path: String,
@@ -79,8 +77,10 @@ impl SvnDriver {
 
         SvnUtil::clean_env();
 
-        if let Some(PhpMixed::String(v)) = self.inner.repo_config.get("trunk-path").cloned() {
-            self.trunk_path = Some(v);
+        match self.inner.repo_config.get("trunk-path") {
+            Some(PhpMixed::Bool(false)) => self.trunk_path = None,
+            Some(PhpMixed::String(v)) => self.trunk_path = Some(v.clone()),
+            _ => {}
         }
         if let Some(PhpMixed::String(v)) = self.inner.repo_config.get("branches-path").cloned() {
             self.branches_path = v;
@@ -100,10 +100,11 @@ impl SvnDriver {
             self.package_path = format!("/{}", trim(&v, Some("/")));
         }
 
-        if let Some(trunk_path) = &self.trunk_path {
-            if let Some(pos) = strrpos(&self.inner.url, &format!("/{}", trunk_path)) {
-                self.base_url = substr(&self.inner.url, 0, Some(pos as i64));
-            }
+        if let Some(pos) = strrpos(
+            &self.inner.url,
+            &format!("/{}", self.trunk_path.as_deref().unwrap_or("")),
+        ) {
+            self.base_url = substr(&self.inner.url, 0, Some(pos as i64));
         }
 
         self.inner.cache = Some(Cache::new(
diff --git a/crates/shirabe/src/repository/vcs/vcs_driver.rs b/crates/shirabe/src/repository/vcs/vcs_driver.rs
index 1c05933..740d00e 100644
--- a/crates/shirabe/src/repository/vcs/vcs_driver.rs
+++ b/crates/shirabe/src/repository/vcs/vcs_driver.rs
@@ -234,7 +234,6 @@ pub trait VcsDriver: VcsDriverInterface {
 
             if self.should_cache(identifier) {
                 if let Some(ref composer_map) = composer {
-                    // TODO(phase-b): use a dedicated encode-with-options helper; reuse encode for now.
                     let composer_mixed = PhpMixed::Array(
                         composer_map
                             .iter()
diff --git a/crates/shirabe/src/repository/writable_array_repository.rs b/crates/shirabe/src/repository/writable_array_repository.rs
index bf9d094..0615ef6 100644
--- a/crates/shirabe/src/repository/writable_array_repository.rs
+++ b/crates/shirabe/src/repository/writable_array_repository.rs
@@ -48,6 +48,10 @@ impl WritableArrayRepository {
         self.dev_mode = None;
     }
 
+    pub fn reset_packages(&self) {
+        self.inner.reset_packages();
+    }
+
     pub fn add_package(&mut self, package: crate::package::PackageInterfaceHandle) -> Result<()> {
         self.inner.add_package(package)
     }
diff --git a/crates/shirabe/src/util/http_downloader.rs b/crates/shirabe/src/util/http_downloader.rs
index 5d0eae6..434dedb 100644
--- a/crates/shirabe/src/util/http_downloader.rs
+++ b/crates/shirabe/src/util/http_downloader.rs
@@ -779,7 +779,8 @@ impl HttpDownloader {
             );
             http_map.insert("ignore_errors".to_string(), Box::new(PhpMixed::Bool(true)));
             ctx_options.insert("http".to_string(), PhpMixed::Array(http_map));
-            // TODO(phase-b): file_get_contents only takes a path; stream context arg dropped.
+            // TODO(phase-c): file_get_contents only takes a path; the stream context arg is dropped
+            // until the PHP stream-context layer is modeled.
             let _ = stream_context_create(&ctx_options, None);
             let test_connectivity = file_get_contents("https://8.8.8.8");
             Silencer::restore();
diff --git a/crates/shirabe/src/util/platform.rs b/crates/shirabe/src/util/platform.rs
index 3866a12..6a0c2d0 100644
--- a/crates/shirabe/src/util/platform.rs
+++ b/crates/shirabe/src/util/platform.rs
@@ -186,7 +186,6 @@ impl Platform {
                 return false;
             }
 
-            // TODO(phase-b): Silencer::call returns Result; PHP returns the value or false on error
             let file_contents = Silencer::call(|| Ok(file_get_contents("/proc/version")))
                 .ok()
                 .flatten()
@@ -294,7 +293,8 @@ impl Platform {
             Some(f) => f,
             None => {
                 if defined("STDOUT") {
-                    // TODO(phase-b): map STDOUT to the runtime stdout resource
+                    // TODO(phase-c): map the STDOUT constant to a runtime stdout resource; depends
+                    // on the unmodeled PHP stream/resource layer.
                     todo!("STDOUT constant")
                 } else {
                     let fd = fopen("php://stdout", "w");
@@ -330,7 +330,6 @@ impl Platform {
             return true;
         }
 
-        // TODO(phase-b): Silencer::call wraps the fstat call (`@fstat($fd)`)
         let stat = Silencer::call(|| Ok(fstat(fd)));
         let stat = match stat {
             Ok(s) => s,
@@ -427,25 +426,8 @@ impl Platform {
         "/dev/null".to_string()
     }
 
-    /// PHP: PHP_OS — returns the OS PHP was built on.
-    pub fn php_os() -> &'static str {
-        // TODO(phase-b): map to actual OS name (e.g. "Darwin", "Linux", "WINNT").
-        todo!()
-    }
-
     /// PHP: rename($from, $to) — wrap the std rename so callers can use Platform::rename.
     pub fn rename(from: &str, to: &str) -> bool {
         std::fs::rename(from, to).is_ok()
     }
-
-    /// PHP: mkdir($pathname, $mode, $recursive)
-    pub fn mkdir(pathname: &str, _mode: u32, recursive: bool) -> bool {
-        // TODO(phase-b): honor mode bits on Unix
-        let result = if recursive {
-            std::fs::create_dir_all(pathname)
-        } else {
-            std::fs::create_dir(pathname)
-        };
-        result.is_ok()
-    }
 }
diff --git a/crates/shirabe/src/util/remote_filesystem.rs b/crates/shirabe/src/util/remote_filesystem.rs
index bd4aaa8..dc6a2a4 100644
--- a/crates/shirabe/src/util/remote_filesystem.rs
+++ b/crates/shirabe/src/util/remote_filesystem.rs
@@ -720,7 +720,8 @@ impl RemoteFilesystem {
         }
 
         let mut caught_e: Option<anyhow::Error> = None;
-        // TODO(phase-b): wrap PHP's `file_get_contents` with stream context and error capture.
+        // TODO(phase-c): wrap PHP's `file_get_contents` with stream context and error capture;
+        // depends on the unmodeled PHP stream-context layer.
         let outer: Result<Option<String>, anyhow::Error> = Ok(None);
         match outer {
             Ok(v) => result = v,
@@ -743,7 +744,8 @@ impl RemoteFilesystem {
             *response_headers = http_get_last_response_headers().unwrap_or_default();
             http_clear_last_response_headers();
         } else {
-            // TODO(phase-b): read the magic `$http_response_header` PHP variable.
+            // TODO(phase-c): read the magic `$http_response_header` PHP variable; depends on the
+            // unmodeled PHP stream layer that populates it.
             *response_headers = Vec::new();
         }