mir_analyzer/

project.rs

/// Project-level orchestration: file discovery, pass 1, pass 2.
use std::path::{Path, PathBuf};
use std::sync::Arc;

use rayon::prelude::*;

use std::collections::{HashMap, HashSet};

use crate::cache::{hash_content, AnalysisCache};
use mir_codebase::Codebase;
use mir_issues::Issue;
use mir_types::Union;

use crate::collector::DefinitionCollector;

// ---------------------------------------------------------------------------
// ProjectAnalyzer
// ---------------------------------------------------------------------------

pub struct ProjectAnalyzer {
    pub codebase: Arc<Codebase>,
    /// Optional cache — when `Some`, Pass 2 results are read/written per file.
    pub cache: Option<AnalysisCache>,
    /// Called once after each file completes Pass 2 (used for progress reporting).
    pub on_file_done: Option<Arc<dyn Fn() + Send + Sync>>,
    /// PSR-4 autoloader mapping from composer.json, if available.
    pub psr4: Option<Arc<crate::composer::Psr4Map>>,
    /// Whether stubs have already been loaded (to avoid double-loading).
    stubs_loaded: std::sync::atomic::AtomicBool,
    /// When true, run dead code detection at the end of analysis.
    pub find_dead_code: bool,
}

impl ProjectAnalyzer {
    pub fn new() -> Self {
        Self {
            codebase: Arc::new(Codebase::new()),
            cache: None,
            on_file_done: None,
            psr4: None,
            stubs_loaded: std::sync::atomic::AtomicBool::new(false),
            find_dead_code: false,
        }
    }

    /// Create a `ProjectAnalyzer` with a disk-backed cache stored under `cache_dir`.
    pub fn with_cache(cache_dir: &Path) -> Self {
        Self {
            codebase: Arc::new(Codebase::new()),
            cache: Some(AnalysisCache::open(cache_dir)),
            on_file_done: None,
            psr4: None,
            stubs_loaded: std::sync::atomic::AtomicBool::new(false),
            find_dead_code: false,
        }
    }

    /// Create a `ProjectAnalyzer` from a project root containing `composer.json`.
    /// Returns the analyzer (with `psr4` set) and the `Psr4Map` so callers can
    /// call `map.project_files()` / `map.vendor_files()`.
    pub fn from_composer(
        root: &Path,
    ) -> Result<(Self, crate::composer::Psr4Map), crate::composer::ComposerError> {
        let map = crate::composer::Psr4Map::from_composer(root)?;
        let psr4 = Arc::new(map.clone());
        let analyzer = Self {
            codebase: Arc::new(Codebase::new()),
            cache: None,
            on_file_done: None,
            psr4: Some(psr4),
            stubs_loaded: std::sync::atomic::AtomicBool::new(false),
            find_dead_code: false,
        };
        Ok((analyzer, map))
    }

    /// Expose codebase for external use (e.g., pre-loading stubs from CLI).
    pub fn codebase(&self) -> &Arc<Codebase> {
        &self.codebase
    }

    /// Load PHP built-in stubs. Called automatically by `analyze` if not done yet.
    pub fn load_stubs(&self) {
        if !self
            .stubs_loaded
            .swap(true, std::sync::atomic::Ordering::SeqCst)
        {
            crate::stubs::load_stubs(&self.codebase);
        }
    }

    /// Run the full analysis pipeline on a set of file paths.
    pub fn analyze(&self, paths: &[PathBuf]) -> AnalysisResult {
        let mut all_issues = Vec::new();
        let mut parse_errors = Vec::new();

        // ---- Load PHP built-in stubs (before Pass 1 so user code can override)
        self.load_stubs();

        // ---- Pre-Pass-2 invalidation: evict dependents of changed files ------
        // Uses the reverse dep graph persisted from the previous run.
        if let Some(cache) = &self.cache {
            let changed: Vec<String> = paths
                .iter()
                .filter_map(|p| {
                    let path_str = p.to_string_lossy().into_owned();
                    let content = std::fs::read_to_string(p).ok()?;
                    let h = hash_content(&content);
                    if cache.get(&path_str, &h).is_none() {
                        Some(path_str)
                    } else {
                        None
                    }
                })
                .collect();
            if !changed.is_empty() {
                cache.evict_with_dependents(&changed);
            }
        }

        // ---- Pass 1: read files in parallel ----------------------------------
        let file_data: Vec<(Arc<str>, String)> = paths
            .par_iter()
            .filter_map(|path| match std::fs::read_to_string(path) {
                Ok(src) => Some((Arc::from(path.to_string_lossy().as_ref()), src)),
                Err(e) => {
                    eprintln!("Cannot read {}: {}", path.display(), e);
                    None
                }
            })
            .collect();

        // ---- Pre-index pass: walk the AST to build FQCN index, file imports, and namespaces ---
        file_data.par_iter().for_each(|(file, src)| {
            use php_ast::ast::StmtKind;
            let arena = bumpalo::Bump::new();
            let result = php_rs_parser::parse(&arena, src);

            let mut current_namespace: Option<String> = None;
            let mut imports: std::collections::HashMap<String, String> =
                std::collections::HashMap::new();
            let mut file_ns_set = false;

            // Index a flat list of stmts under a given namespace prefix.
            let index_stmts =
                |stmts: &[php_ast::ast::Stmt<'_, '_>],
                 ns: Option<&str>,
                 imports: &mut std::collections::HashMap<String, String>| {
                    for stmt in stmts.iter() {
                        match &stmt.kind {
                            StmtKind::Use(use_decl) => {
                                for item in use_decl.uses.iter() {
                                    let full_name = crate::parser::name_to_string(&item.name);
                                    let alias = item.alias.unwrap_or_else(|| {
                                        full_name.rsplit('\\').next().unwrap_or(&full_name)
                                    });
                                    imports.insert(alias.to_string(), full_name);
                                }
                            }
                            StmtKind::Class(decl) => {
                                if let Some(n) = decl.name {
                                    let fqcn = match ns {
                                        Some(ns) => format!("{}\\{}", ns, n),
                                        None => n.to_string(),
                                    };
                                    self.codebase.known_symbols.insert(Arc::from(fqcn.as_str()));
                                }
                            }
                            StmtKind::Interface(decl) => {
                                let fqcn = match ns {
                                    Some(ns) => format!("{}\\{}", ns, decl.name),
                                    None => decl.name.to_string(),
                                };
                                self.codebase.known_symbols.insert(Arc::from(fqcn.as_str()));
                            }
                            StmtKind::Trait(decl) => {
                                let fqcn = match ns {
                                    Some(ns) => format!("{}\\{}", ns, decl.name),
                                    None => decl.name.to_string(),
                                };
                                self.codebase.known_symbols.insert(Arc::from(fqcn.as_str()));
                            }
                            StmtKind::Enum(decl) => {
                                let fqcn = match ns {
                                    Some(ns) => format!("{}\\{}", ns, decl.name),
                                    None => decl.name.to_string(),
                                };
                                self.codebase.known_symbols.insert(Arc::from(fqcn.as_str()));
                            }
                            StmtKind::Function(decl) => {
                                let fqn = match ns {
                                    Some(ns) => format!("{}\\{}", ns, decl.name),
                                    None => decl.name.to_string(),
                                };
                                self.codebase.known_symbols.insert(Arc::from(fqn.as_str()));
                            }
                            _ => {}
                        }
                    }
                };

            for stmt in result.program.stmts.iter() {
                match &stmt.kind {
                    StmtKind::Namespace(ns) => {
                        current_namespace =
                            ns.name.as_ref().map(|n| crate::parser::name_to_string(n));
                        if !file_ns_set {
                            if let Some(ref ns_str) = current_namespace {
                                self.codebase
                                    .file_namespaces
                                    .insert(file.clone(), ns_str.clone());
                                file_ns_set = true;
                            }
                        }
                        // Bracketed namespace: walk inner stmts for Use/Class/etc.
                        if let php_ast::ast::NamespaceBody::Braced(inner_stmts) = &ns.body {
                            index_stmts(inner_stmts, current_namespace.as_deref(), &mut imports);
                        }
                    }
                    _ => index_stmts(
                        std::slice::from_ref(stmt),
                        current_namespace.as_deref(),
                        &mut imports,
                    ),
                }
            }

            if !imports.is_empty() {
                self.codebase.file_imports.insert(file.clone(), imports);
            }
        });

        // ---- Pass 1: definition collection (sequential) -------------------------
        // DashMap handles concurrent writes, but sequential avoids contention.
        for (file, src) in &file_data {
            let arena = bumpalo::Bump::new();
            let result = php_rs_parser::parse(&arena, src);

            for err in &result.errors {
                let msg: String = err.to_string();
                parse_errors.push(Issue::new(
                    mir_issues::IssueKind::ParseError { message: msg },
                    mir_issues::Location {
                        file: file.clone(),
                        line: 1,
                        col_start: 0,
                        col_end: 0,
                    },
                ));
            }

            let collector =
                DefinitionCollector::new(&self.codebase, file.clone(), src, &result.source_map);
            let issues = collector.collect(&result.program);
            all_issues.extend(issues);
        }

        all_issues.extend(parse_errors);

        // ---- Finalize codebase (resolve inheritance, build dispatch tables) --
        self.codebase.finalize();

        // ---- Lazy-load unknown classes via PSR-4 (issue #50) ----------------
        if let Some(psr4) = &self.psr4 {
            self.lazy_load_missing_classes(psr4.clone(), &mut all_issues);
        }

        // ---- Build reverse dep graph and persist it for the next run ---------
        if let Some(cache) = &self.cache {
            let rev = build_reverse_deps(&self.codebase);
            cache.set_reverse_deps(rev);
        }

        // ---- Class-level checks (M11) ----------------------------------------
        let analyzed_file_set: std::collections::HashSet<std::sync::Arc<str>> =
            file_data.iter().map(|(f, _)| f.clone()).collect();
        let class_issues =
            crate::class::ClassAnalyzer::with_files(&self.codebase, analyzed_file_set, &file_data)
                .analyze_all();
        all_issues.extend(class_issues);

        // ---- Pass 2: analyze function/method bodies in parallel (M14) --------
        // Each file is analyzed independently; arena + parse happen inside the
        // rayon closure so there is no cross-thread borrow.
        // When a cache is present, files whose content hash matches a stored
        // entry skip re-analysis entirely (M17).
        let pass2_results: Vec<(Vec<Issue>, Vec<crate::symbol::ResolvedSymbol>)> = file_data
            .par_iter()
            .map(|(file, src)| {
                // Cache lookup
                let result = if let Some(cache) = &self.cache {
                    let h = hash_content(src);
                    if let Some((cached_issues, ref_locs)) = cache.get(file, &h) {
                        // Hit — replay reference locations so symbol_reference_locations
                        // is populated without re-running analyze_bodies.
                        self.codebase
                            .replay_reference_locations(file.clone(), &ref_locs);
                        (cached_issues, Vec::new())
                    } else {
                        // Miss — analyze and store
                        let arena = bumpalo::Bump::new();
                        let parsed = php_rs_parser::parse(&arena, src);
                        let (issues, symbols) = self.analyze_bodies(
                            &parsed.program,
                            file.clone(),
                            src,
                            &parsed.source_map,
                        );
                        let ref_locs = extract_reference_locations(&self.codebase, file);
                        cache.put(file, h, issues.clone(), ref_locs);
                        (issues, symbols)
                    }
                } else {
                    let arena = bumpalo::Bump::new();
                    let parsed = php_rs_parser::parse(&arena, src);
                    self.analyze_bodies(&parsed.program, file.clone(), src, &parsed.source_map)
                };
                if let Some(cb) = &self.on_file_done {
                    cb();
                }
                result
            })
            .collect();

        let mut all_symbols = Vec::new();
        for (issues, symbols) in pass2_results {
            all_issues.extend(issues);
            all_symbols.extend(symbols);
        }

        // Persist cache hits/misses to disk
        if let Some(cache) = &self.cache {
            cache.flush();
        }

        // ---- Dead-code detection (M18) --------------------------------------
        if self.find_dead_code {
            let dead_code_issues =
                crate::dead_code::DeadCodeAnalyzer::new(&self.codebase).analyze();
            all_issues.extend(dead_code_issues);
        }

        AnalysisResult {
            issues: all_issues,
            type_envs: std::collections::HashMap::new(),
            symbols: all_symbols,
        }
    }

    /// Lazily load class definitions for referenced-but-unknown FQCNs via PSR-4.
    ///
    /// After Pass 1 and `codebase.finalize()`, some classes referenced as parents
    /// or interfaces may not be in the codebase (they weren't in the initial file
    /// list). This method iterates up to `max_depth` times, each time resolving
    /// unknown parent/interface FQCNs via the PSR-4 map, running Pass 1 on those
    /// files, and re-finalizing the codebase. The loop stops when no new files
    /// are discovered.
    fn lazy_load_missing_classes(
        &self,
        psr4: Arc<crate::composer::Psr4Map>,
        all_issues: &mut Vec<Issue>,
    ) {
        use std::collections::HashSet;

        let max_depth = 10; // prevent infinite chains
        let mut loaded: HashSet<String> = HashSet::new();

        for _ in 0..max_depth {
            // Collect all referenced FQCNs that aren't in the codebase
            let mut to_load: Vec<(String, PathBuf)> = Vec::new();

            for entry in self.codebase.classes.iter() {
                let cls = entry.value();

                // Check parent class
                if let Some(parent) = &cls.parent {
                    let fqcn = parent.as_ref();
                    if !self.codebase.classes.contains_key(fqcn) && !loaded.contains(fqcn) {
                        if let Some(path) = psr4.resolve(fqcn) {
                            to_load.push((fqcn.to_string(), path));
                        }
                    }
                }

                // Check interfaces
                for iface in &cls.interfaces {
                    let fqcn = iface.as_ref();
                    if !self.codebase.classes.contains_key(fqcn)
                        && !self.codebase.interfaces.contains_key(fqcn)
                        && !loaded.contains(fqcn)
                    {
                        if let Some(path) = psr4.resolve(fqcn) {
                            to_load.push((fqcn.to_string(), path));
                        }
                    }
                }
            }

            if to_load.is_empty() {
                break;
            }

            // Load each discovered file (Pass 1 only)
            for (fqcn, path) in to_load {
                loaded.insert(fqcn);
                if let Ok(src) = std::fs::read_to_string(&path) {
                    let file: Arc<str> = Arc::from(path.to_string_lossy().as_ref());
                    let arena = bumpalo::Bump::new();
                    let result = php_rs_parser::parse(&arena, &src);
                    let collector = crate::collector::DefinitionCollector::new(
                        &self.codebase,
                        file,
                        &src,
                        &result.source_map,
                    );
                    let issues = collector.collect(&result.program);
                    all_issues.extend(issues);
                }
            }

            // Re-finalize to include newly loaded classes in the inheritance graph.
            // Must reset the flag first so finalize() isn't a no-op.
            self.codebase.invalidate_finalization();
            self.codebase.finalize();
        }
    }

    /// Re-analyze a single file within the existing codebase.
    ///
    /// This is the incremental analysis API for LSP:
    /// 1. Removes old definitions from this file
    /// 2. Re-runs Pass 1 (definition collection) on the new content
    /// 3. Re-finalizes the codebase (rebuilds inheritance)
    /// 4. Re-runs Pass 2 (body analysis) on this file
    /// 5. Returns the analysis result for this file only
    pub fn re_analyze_file(&self, file_path: &str, new_content: &str) -> AnalysisResult {
        // 1. Remove old definitions from this file
        self.codebase.remove_file_definitions(file_path);

        // 2. Parse new content and run Pass 1
        let file: Arc<str> = Arc::from(file_path);
        let arena = bumpalo::Bump::new();
        let parsed = php_rs_parser::parse(&arena, new_content);

        let mut all_issues = Vec::new();

        // Collect parse errors
        for err in &parsed.errors {
            all_issues.push(Issue::new(
                mir_issues::IssueKind::ParseError {
                    message: err.to_string(),
                },
                mir_issues::Location {
                    file: file.clone(),
                    line: 1,
                    col_start: 0,
                    col_end: 0,
                },
            ));
        }

        let collector = DefinitionCollector::new(
            &self.codebase,
            file.clone(),
            new_content,
            &parsed.source_map,
        );
        all_issues.extend(collector.collect(&parsed.program));

        // 3. Re-finalize (invalidation already done by remove_file_definitions)
        self.codebase.finalize();

        // 4. Run Pass 2 on this file
        let (body_issues, symbols) = self.analyze_bodies(
            &parsed.program,
            file.clone(),
            new_content,
            &parsed.source_map,
        );
        all_issues.extend(body_issues);

        // 5. Update cache if present
        if let Some(cache) = &self.cache {
            let h = hash_content(new_content);
            cache.evict_with_dependents(&[file_path.to_string()]);
            let ref_locs = extract_reference_locations(&self.codebase, &file);
            cache.put(file_path, h, all_issues.clone(), ref_locs);
        }

        AnalysisResult {
            issues: all_issues,
            type_envs: HashMap::new(),
            symbols,
        }
    }

    /// Analyze a PHP source string without a real file path.
    /// Useful for tests and LSP single-file mode.
    pub fn analyze_source(source: &str) -> AnalysisResult {
        use crate::collector::DefinitionCollector;
        let analyzer = ProjectAnalyzer::new();
        analyzer.load_stubs();
        let file: Arc<str> = Arc::from("<source>");
        let arena = bumpalo::Bump::new();
        let result = php_rs_parser::parse(&arena, source);
        let mut all_issues = Vec::new();
        let collector =
            DefinitionCollector::new(&analyzer.codebase, file.clone(), source, &result.source_map);
        all_issues.extend(collector.collect(&result.program));
        analyzer.codebase.finalize();
        let mut type_envs = std::collections::HashMap::new();
        let mut all_symbols = Vec::new();
        all_issues.extend(analyzer.analyze_bodies_typed(
            &result.program,
            file.clone(),
            source,
            &result.source_map,
            &mut type_envs,
            &mut all_symbols,
        ));
        AnalysisResult {
            issues: all_issues,
            type_envs,
            symbols: all_symbols,
        }
    }

    /// Pass 2: walk all function/method bodies in one file, return issues, and
    /// write inferred return types back to the codebase.
    fn analyze_bodies<'arena, 'src>(
        &self,
        program: &php_ast::ast::Program<'arena, 'src>,
        file: Arc<str>,
        source: &str,
        source_map: &php_rs_parser::source_map::SourceMap,
    ) -> (Vec<mir_issues::Issue>, Vec<crate::symbol::ResolvedSymbol>) {
        use php_ast::ast::StmtKind;

        let mut all_issues = Vec::new();
        let mut all_symbols = Vec::new();

        for stmt in program.stmts.iter() {
            match &stmt.kind {
                StmtKind::Function(decl) => {
                    self.analyze_fn_decl(
                        decl,
                        &file,
                        source,
                        source_map,
                        &mut all_issues,
                        &mut all_symbols,
                    );
                }
                StmtKind::Class(decl) => {
                    self.analyze_class_decl(
                        decl,
                        &file,
                        source,
                        source_map,
                        &mut all_issues,
                        &mut all_symbols,
                    );
                }
                StmtKind::Enum(decl) => {
                    self.analyze_enum_decl(decl, &file, source, source_map, &mut all_issues);
                }
                StmtKind::Namespace(ns) => {
                    if let php_ast::ast::NamespaceBody::Braced(stmts) = &ns.body {
                        for inner in stmts.iter() {
                            match &inner.kind {
                                StmtKind::Function(decl) => {
                                    self.analyze_fn_decl(
                                        decl,
                                        &file,
                                        source,
                                        source_map,
                                        &mut all_issues,
                                        &mut all_symbols,
                                    );
                                }
                                StmtKind::Class(decl) => {
                                    self.analyze_class_decl(
                                        decl,
                                        &file,
                                        source,
                                        source_map,
                                        &mut all_issues,
                                        &mut all_symbols,
                                    );
                                }
                                StmtKind::Enum(decl) => {
                                    self.analyze_enum_decl(
                                        decl,
                                        &file,
                                        source,
                                        source_map,
                                        &mut all_issues,
                                    );
                                }
                                _ => {}
                            }
                        }
                    }
                }
                _ => {}
            }
        }

        (all_issues, all_symbols)
    }

    /// Analyze a single function declaration body and collect issues + inferred return type.
    #[allow(clippy::too_many_arguments)]
    fn analyze_fn_decl<'arena, 'src>(
        &self,
        decl: &php_ast::ast::FunctionDecl<'arena, 'src>,
        file: &Arc<str>,
        source: &str,
        source_map: &php_rs_parser::source_map::SourceMap,
        all_issues: &mut Vec<mir_issues::Issue>,
        all_symbols: &mut Vec<crate::symbol::ResolvedSymbol>,
    ) {
        let fn_name = decl.name;
        let body = &decl.body;
        // Check parameter and return type hints for undefined classes.
        for param in decl.params.iter() {
            if let Some(hint) = &param.type_hint {
                check_type_hint_classes(hint, &self.codebase, file, source, source_map, all_issues);
            }
        }
        if let Some(hint) = &decl.return_type {
            check_type_hint_classes(hint, &self.codebase, file, source, source_map, all_issues);
        }
        use crate::context::Context;
        use crate::stmt::StatementsAnalyzer;
        use mir_issues::IssueBuffer;

        // Resolve function name using the file's namespace (handles namespaced functions)
        let resolved_fn = self.codebase.resolve_class_name(file.as_ref(), fn_name);
        let func_opt: Option<mir_codebase::storage::FunctionStorage> = self
            .codebase
            .functions
            .get(resolved_fn.as_str())
            .map(|r| r.clone())
            .or_else(|| self.codebase.functions.get(fn_name).map(|r| r.clone()))
            .or_else(|| {
                self.codebase
                    .functions
                    .iter()
                    .find(|e| e.short_name.as_ref() == fn_name)
                    .map(|e| e.value().clone())
            });

        let fqn = func_opt.as_ref().map(|f| f.fqn.clone());
        // Always use the codebase entry when its params match the AST (same count + names).
        // This covers the common case and preserves docblock-enriched types.
        // When names differ (two files define the same unnamespaced function), fall back to
        // the AST params so param variables are always in scope for this file's body.
        let (params, return_ty): (Vec<mir_codebase::FnParam>, _) = match &func_opt {
            Some(f)
                if f.params.len() == decl.params.len()
                    && f.params
                        .iter()
                        .zip(decl.params.iter())
                        .all(|(cp, ap)| cp.name.as_ref() == ap.name) =>
            {
                (f.params.clone(), f.return_type.clone())
            }
            _ => {
                let ast_params = decl
                    .params
                    .iter()
                    .map(|p| mir_codebase::FnParam {
                        name: Arc::from(p.name),
                        ty: None,
                        default: p.default.as_ref().map(|_| mir_types::Union::mixed()),
                        is_variadic: p.variadic,
                        is_byref: p.by_ref,
                        is_optional: p.default.is_some() || p.variadic,
                    })
                    .collect();
                (ast_params, None)
            }
        };

        let mut ctx = Context::for_function(&params, return_ty, None, None, None, false, true);
        let mut buf = IssueBuffer::new();
        let mut sa = StatementsAnalyzer::new(
            &self.codebase,
            file.clone(),
            source,
            source_map,
            &mut buf,
            all_symbols,
        );
        sa.analyze_stmts(body, &mut ctx);
        let inferred = merge_return_types(&sa.return_types);
        drop(sa);

        emit_unused_params(&params, &ctx, "", file, all_issues);
        emit_unused_variables(&ctx, file, all_issues);
        all_issues.extend(buf.into_issues());

        if let Some(fqn) = fqn {
            if let Some(mut func) = self.codebase.functions.get_mut(fqn.as_ref()) {
                func.inferred_return_type = Some(inferred);
            }
        }
    }

    /// Analyze all method bodies on a class declaration and collect issues + inferred return types.
    #[allow(clippy::too_many_arguments)]
    fn analyze_class_decl<'arena, 'src>(
        &self,
        decl: &php_ast::ast::ClassDecl<'arena, 'src>,
        file: &Arc<str>,
        source: &str,
        source_map: &php_rs_parser::source_map::SourceMap,
        all_issues: &mut Vec<mir_issues::Issue>,
        all_symbols: &mut Vec<crate::symbol::ResolvedSymbol>,
    ) {
        use crate::context::Context;
        use crate::stmt::StatementsAnalyzer;
        use mir_issues::IssueBuffer;

        let class_name = decl.name.unwrap_or("<anonymous>");
        // Resolve the FQCN using the file's namespace/imports — avoids ambiguity
        // when multiple classes share the same short name across namespaces.
        let resolved = self.codebase.resolve_class_name(file.as_ref(), class_name);
        let fqcn: &str = &resolved;
        let parent_fqcn = self
            .codebase
            .classes
            .get(fqcn)
            .and_then(|c| c.parent.clone());

        for member in decl.members.iter() {
            let php_ast::ast::ClassMemberKind::Method(method) = &member.kind else {
                continue;
            };

            // Check parameter and return type hints for undefined classes (even abstract methods).
            for param in method.params.iter() {
                if let Some(hint) = &param.type_hint {
                    check_type_hint_classes(
                        hint,
                        &self.codebase,
                        file,
                        source,
                        source_map,
                        all_issues,
                    );
                }
            }
            if let Some(hint) = &method.return_type {
                check_type_hint_classes(hint, &self.codebase, file, source, source_map, all_issues);
            }

            let Some(body) = &method.body else { continue };

            let method_storage = self.codebase.get_method(fqcn, method.name);
            let (params, return_ty) = method_storage
                .as_ref()
                .map(|m| (m.params.clone(), m.return_type.clone()))
                .unwrap_or_default();

            let is_ctor = method.name == "__construct";
            let mut ctx = Context::for_method(
                &params,
                return_ty,
                Some(Arc::from(fqcn)),
                parent_fqcn.clone(),
                Some(Arc::from(fqcn)),
                false,
                is_ctor,
                method.is_static,
            );

            let mut buf = IssueBuffer::new();
            let mut sa = StatementsAnalyzer::new(
                &self.codebase,
                file.clone(),
                source,
                source_map,
                &mut buf,
                all_symbols,
            );
            sa.analyze_stmts(body, &mut ctx);
            let inferred = merge_return_types(&sa.return_types);
            drop(sa);

            emit_unused_params(&params, &ctx, method.name, file, all_issues);
            emit_unused_variables(&ctx, file, all_issues);
            all_issues.extend(buf.into_issues());

            if let Some(mut cls) = self.codebase.classes.get_mut(fqcn) {
                if let Some(m) = cls.own_methods.get_mut(method.name) {
                    m.inferred_return_type = Some(inferred);
                }
            }
        }
    }

    /// Like `analyze_bodies` but also populates `type_envs` with per-scope type environments.
    #[allow(clippy::too_many_arguments)]
    fn analyze_bodies_typed<'arena, 'src>(
        &self,
        program: &php_ast::ast::Program<'arena, 'src>,
        file: Arc<str>,
        source: &str,
        source_map: &php_rs_parser::source_map::SourceMap,
        type_envs: &mut std::collections::HashMap<
            crate::type_env::ScopeId,
            crate::type_env::TypeEnv,
        >,
        all_symbols: &mut Vec<crate::symbol::ResolvedSymbol>,
    ) -> Vec<mir_issues::Issue> {
        use php_ast::ast::StmtKind;
        let mut all_issues = Vec::new();
        for stmt in program.stmts.iter() {
            match &stmt.kind {
                StmtKind::Function(decl) => {
                    self.analyze_fn_decl_typed(
                        decl,
                        &file,
                        source,
                        source_map,
                        &mut all_issues,
                        type_envs,
                        all_symbols,
                    );
                }
                StmtKind::Class(decl) => {
                    self.analyze_class_decl_typed(
                        decl,
                        &file,
                        source,
                        source_map,
                        &mut all_issues,
                        type_envs,
                        all_symbols,
                    );
                }
                StmtKind::Enum(decl) => {
                    self.analyze_enum_decl(decl, &file, source, source_map, &mut all_issues);
                }
                StmtKind::Namespace(ns) => {
                    if let php_ast::ast::NamespaceBody::Braced(stmts) = &ns.body {
                        for inner in stmts.iter() {
                            match &inner.kind {
                                StmtKind::Function(decl) => {
                                    self.analyze_fn_decl_typed(
                                        decl,
                                        &file,
                                        source,
                                        source_map,
                                        &mut all_issues,
                                        type_envs,
                                        all_symbols,
                                    );
                                }
                                StmtKind::Class(decl) => {
                                    self.analyze_class_decl_typed(
                                        decl,
                                        &file,
                                        source,
                                        source_map,
                                        &mut all_issues,
                                        type_envs,
                                        all_symbols,
                                    );
                                }
                                StmtKind::Enum(decl) => {
                                    self.analyze_enum_decl(
                                        decl,
                                        &file,
                                        source,
                                        source_map,
                                        &mut all_issues,
                                    );
                                }
                                _ => {}
                            }
                        }
                    }
                }
                _ => {}
            }
        }
        all_issues
    }

    /// Like `analyze_fn_decl` but also captures a `TypeEnv` for the function scope.
    #[allow(clippy::too_many_arguments)]
    fn analyze_fn_decl_typed<'arena, 'src>(
        &self,
        decl: &php_ast::ast::FunctionDecl<'arena, 'src>,
        file: &Arc<str>,
        source: &str,
        source_map: &php_rs_parser::source_map::SourceMap,
        all_issues: &mut Vec<mir_issues::Issue>,
        type_envs: &mut std::collections::HashMap<
            crate::type_env::ScopeId,
            crate::type_env::TypeEnv,
        >,
        all_symbols: &mut Vec<crate::symbol::ResolvedSymbol>,
    ) {
        use crate::context::Context;
        use crate::stmt::StatementsAnalyzer;
        use mir_issues::IssueBuffer;

        let fn_name = decl.name;
        let body = &decl.body;

        for param in decl.params.iter() {
            if let Some(hint) = &param.type_hint {
                check_type_hint_classes(hint, &self.codebase, file, source, source_map, all_issues);
            }
        }
        if let Some(hint) = &decl.return_type {
            check_type_hint_classes(hint, &self.codebase, file, source, source_map, all_issues);
        }

        let resolved_fn = self.codebase.resolve_class_name(file.as_ref(), fn_name);
        let func_opt: Option<mir_codebase::storage::FunctionStorage> = self
            .codebase
            .functions
            .get(resolved_fn.as_str())
            .map(|r| r.clone())
            .or_else(|| self.codebase.functions.get(fn_name).map(|r| r.clone()))
            .or_else(|| {
                self.codebase
                    .functions
                    .iter()
                    .find(|e| e.short_name.as_ref() == fn_name)
                    .map(|e| e.value().clone())
            });

        let fqn = func_opt.as_ref().map(|f| f.fqn.clone());
        let (params, return_ty): (Vec<mir_codebase::FnParam>, _) = match &func_opt {
            Some(f)
                if f.params.len() == decl.params.len()
                    && f.params
                        .iter()
                        .zip(decl.params.iter())
                        .all(|(cp, ap)| cp.name.as_ref() == ap.name) =>
            {
                (f.params.clone(), f.return_type.clone())
            }
            _ => {
                let ast_params = decl
                    .params
                    .iter()
                    .map(|p| mir_codebase::FnParam {
                        name: Arc::from(p.name),
                        ty: None,
                        default: p.default.as_ref().map(|_| mir_types::Union::mixed()),
                        is_variadic: p.variadic,
                        is_byref: p.by_ref,
                        is_optional: p.default.is_some() || p.variadic,
                    })
                    .collect();
                (ast_params, None)
            }
        };

        let mut ctx = Context::for_function(&params, return_ty, None, None, None, false, true);
        let mut buf = IssueBuffer::new();
        let mut sa = StatementsAnalyzer::new(
            &self.codebase,
            file.clone(),
            source,
            source_map,
            &mut buf,
            all_symbols,
        );
        sa.analyze_stmts(body, &mut ctx);
        let inferred = merge_return_types(&sa.return_types);
        drop(sa);

        // Capture TypeEnv for this scope
        let scope_name = fqn.clone().unwrap_or_else(|| Arc::from(fn_name));
        type_envs.insert(
            crate::type_env::ScopeId::Function {
                file: file.clone(),
                name: scope_name,
            },
            crate::type_env::TypeEnv::new(ctx.vars.clone()),
        );

        emit_unused_params(&params, &ctx, "", file, all_issues);
        emit_unused_variables(&ctx, file, all_issues);
        all_issues.extend(buf.into_issues());

        if let Some(fqn) = fqn {
            if let Some(mut func) = self.codebase.functions.get_mut(fqn.as_ref()) {
                func.inferred_return_type = Some(inferred);
            }
        }
    }

    /// Like `analyze_class_decl` but also captures a `TypeEnv` per method scope.
    #[allow(clippy::too_many_arguments)]
    fn analyze_class_decl_typed<'arena, 'src>(
        &self,
        decl: &php_ast::ast::ClassDecl<'arena, 'src>,
        file: &Arc<str>,
        source: &str,
        source_map: &php_rs_parser::source_map::SourceMap,
        all_issues: &mut Vec<mir_issues::Issue>,
        type_envs: &mut std::collections::HashMap<
            crate::type_env::ScopeId,
            crate::type_env::TypeEnv,
        >,
        all_symbols: &mut Vec<crate::symbol::ResolvedSymbol>,
    ) {
        use crate::context::Context;
        use crate::stmt::StatementsAnalyzer;
        use mir_issues::IssueBuffer;

        let class_name = decl.name.unwrap_or("<anonymous>");
        let resolved = self.codebase.resolve_class_name(file.as_ref(), class_name);
        let fqcn: &str = &resolved;
        let parent_fqcn = self
            .codebase
            .classes
            .get(fqcn)
            .and_then(|c| c.parent.clone());

        for member in decl.members.iter() {
            let php_ast::ast::ClassMemberKind::Method(method) = &member.kind else {
                continue;
            };

            for param in method.params.iter() {
                if let Some(hint) = &param.type_hint {
                    check_type_hint_classes(
                        hint,
                        &self.codebase,
                        file,
                        source,
                        source_map,
                        all_issues,
                    );
                }
            }
            if let Some(hint) = &method.return_type {
                check_type_hint_classes(hint, &self.codebase, file, source, source_map, all_issues);
            }

            let Some(body) = &method.body else { continue };

            let method_storage = self.codebase.get_method(fqcn, method.name);
            let (params, return_ty) = method_storage
                .as_ref()
                .map(|m| (m.params.clone(), m.return_type.clone()))
                .unwrap_or_default();

            let is_ctor = method.name == "__construct";
            let mut ctx = Context::for_method(
                &params,
                return_ty,
                Some(Arc::from(fqcn)),
                parent_fqcn.clone(),
                Some(Arc::from(fqcn)),
                false,
                is_ctor,
                method.is_static,
            );

            let mut buf = IssueBuffer::new();
            let mut sa = StatementsAnalyzer::new(
                &self.codebase,
                file.clone(),
                source,
                source_map,
                &mut buf,
                all_symbols,
            );
            sa.analyze_stmts(body, &mut ctx);
            let inferred = merge_return_types(&sa.return_types);
            drop(sa);

            // Capture TypeEnv for this method scope
            type_envs.insert(
                crate::type_env::ScopeId::Method {
                    class: Arc::from(fqcn),
                    method: Arc::from(method.name),
                },
                crate::type_env::TypeEnv::new(ctx.vars.clone()),
            );

            emit_unused_params(&params, &ctx, method.name, file, all_issues);
            emit_unused_variables(&ctx, file, all_issues);
            all_issues.extend(buf.into_issues());

            if let Some(mut cls) = self.codebase.classes.get_mut(fqcn) {
                if let Some(m) = cls.own_methods.get_mut(method.name) {
                    m.inferred_return_type = Some(inferred);
                }
            }
        }
    }

    /// Discover all `.php` files under a directory, recursively.
    pub fn discover_files(root: &Path) -> Vec<PathBuf> {
        if root.is_file() {
            return vec![root.to_path_buf()];
        }
        let mut files = Vec::new();
        collect_php_files(root, &mut files);
        files
    }

    /// Pass 1 only: collect type definitions from `paths` into the codebase without
    /// analyzing method bodies or emitting issues. Used to load vendor types.
    pub fn collect_types_only(&self, paths: &[PathBuf]) {
        let file_data: Vec<(Arc<str>, String)> = paths
            .par_iter()
            .filter_map(|path| {
                std::fs::read_to_string(path)
                    .ok()
                    .map(|src| (Arc::from(path.to_string_lossy().as_ref()), src))
            })
            .collect();

        for (file, src) in &file_data {
            let arena = bumpalo::Bump::new();
            let result = php_rs_parser::parse(&arena, src);
            let collector =
                DefinitionCollector::new(&self.codebase, file.clone(), src, &result.source_map);
            // Ignore any issues emitted during vendor collection
            let _ = collector.collect(&result.program);
        }
    }

    /// Check type hints in enum methods for undefined classes.
    #[allow(clippy::too_many_arguments)]
    fn analyze_enum_decl<'arena, 'src>(
        &self,
        decl: &php_ast::ast::EnumDecl<'arena, 'src>,
        file: &Arc<str>,
        source: &str,
        source_map: &php_rs_parser::source_map::SourceMap,
        all_issues: &mut Vec<mir_issues::Issue>,
    ) {
        use php_ast::ast::EnumMemberKind;
        for member in decl.members.iter() {
            let EnumMemberKind::Method(method) = &member.kind else {
                continue;
            };
            for param in method.params.iter() {
                if let Some(hint) = &param.type_hint {
                    check_type_hint_classes(
                        hint,
                        &self.codebase,
                        file,
                        source,
                        source_map,
                        all_issues,
                    );
                }
            }
            if let Some(hint) = &method.return_type {
                check_type_hint_classes(hint, &self.codebase, file, source, source_map, all_issues);
            }
        }
    }
}

impl Default for ProjectAnalyzer {
    fn default() -> Self {
        Self::new()
    }
}

// ---------------------------------------------------------------------------
// UTF-16 offset conversion utility
// ---------------------------------------------------------------------------

/// Convert a byte offset to a UTF-16 column on a given line.
/// Returns (line, col_utf16) where col is 0-based UTF-16 code unit count.
fn offset_to_line_col_utf16(
    source: &str,
    offset: u32,
    source_map: &php_rs_parser::source_map::SourceMap,
) -> (u32, u16) {
    let lc = source_map.offset_to_line_col(offset);
    let line = lc.line + 1;

    // Find the start of the line containing this offset
    let byte_offset = offset as usize;
    let line_start_byte = if byte_offset == 0 {
        0
    } else {
        // Find the position after the last newline before this offset
        source[..byte_offset]
            .rfind('\n')
            .map(|p| p + 1)
            .unwrap_or(0)
    };

    // Count UTF-16 code units from line start to the offset
    let col_utf16 = source[line_start_byte..byte_offset]
        .chars()
        .map(|c| c.len_utf16() as u16)
        .sum();

    (line, col_utf16)
}

// ---------------------------------------------------------------------------
// Type-hint class existence checker
// ---------------------------------------------------------------------------

/// Walk a `TypeHint` AST node and emit `UndefinedClass` for any named class
/// that does not exist in the codebase.  Skips PHP built-in type keywords.
fn check_type_hint_classes<'arena, 'src>(
    hint: &php_ast::ast::TypeHint<'arena, 'src>,
    codebase: &Codebase,
    file: &Arc<str>,
    source: &str,
    source_map: &php_rs_parser::source_map::SourceMap,
    issues: &mut Vec<mir_issues::Issue>,
) {
    use php_ast::ast::TypeHintKind;
    match &hint.kind {
        TypeHintKind::Named(name) => {
            let name_str = crate::parser::name_to_string(name);
            // Skip built-in pseudo-types that are not real classes.
            if is_pseudo_type(&name_str) {
                return;
            }
            let resolved = codebase.resolve_class_name(file.as_ref(), &name_str);
            if !codebase.type_exists(&resolved) {
                let (line, col_start) =
                    offset_to_line_col_utf16(source, hint.span.start, source_map);
                let col_end = if hint.span.start < hint.span.end {
                    let (_end_line, end_col) =
                        offset_to_line_col_utf16(source, hint.span.end, source_map);
                    end_col
                } else {
                    col_start
                };
                issues.push(
                    mir_issues::Issue::new(
                        mir_issues::IssueKind::UndefinedClass { name: resolved },
                        mir_issues::Location {
                            file: file.clone(),
                            line,
                            col_start,
                            col_end: col_end.max(col_start + 1),
                        },
                    )
                    .with_snippet(crate::parser::span_text(source, hint.span).unwrap_or_default()),
                );
            }
        }
        TypeHintKind::Nullable(inner) => {
            check_type_hint_classes(inner, codebase, file, source, source_map, issues);
        }
        TypeHintKind::Union(parts) | TypeHintKind::Intersection(parts) => {
            for part in parts.iter() {
                check_type_hint_classes(part, codebase, file, source, source_map, issues);
            }
        }
        TypeHintKind::Keyword(_, _) => {} // built-in keyword, always valid
    }
}

/// Returns true for names that are PHP pseudo-types / special identifiers, not
/// real classes.
fn is_pseudo_type(name: &str) -> bool {
    matches!(
        name.to_lowercase().as_str(),
        "self"
            | "static"
            | "parent"
            | "null"
            | "true"
            | "false"
            | "never"
            | "void"
            | "mixed"
            | "object"
            | "callable"
            | "iterable"
    )
}

/// Magic methods whose parameters are passed by the PHP runtime, not user call sites.
const MAGIC_METHODS_WITH_RUNTIME_PARAMS: &[&str] = &[
    "__get",
    "__set",
    "__call",
    "__callStatic",
    "__isset",
    "__unset",
];

/// Emit `UnusedParam` issues for params that were never read in `ctx`.
/// Skips magic methods whose parameters are passed by the PHP runtime.
fn emit_unused_params(
    params: &[mir_codebase::FnParam],
    ctx: &crate::context::Context,
    method_name: &str,
    file: &Arc<str>,
    issues: &mut Vec<mir_issues::Issue>,
) {
    if MAGIC_METHODS_WITH_RUNTIME_PARAMS.contains(&method_name) {
        return;
    }
    for p in params {
        let name = p.name.as_ref().trim_start_matches('$');
        if !ctx.read_vars.contains(name) {
            issues.push(
                mir_issues::Issue::new(
                    mir_issues::IssueKind::UnusedParam {
                        name: name.to_string(),
                    },
                    mir_issues::Location {
                        file: file.clone(),
                        line: 1,
                        col_start: 0,
                        col_end: 0,
                    },
                )
                .with_snippet(format!("${}", name)),
            );
        }
    }
}

fn emit_unused_variables(
    ctx: &crate::context::Context,
    file: &Arc<str>,
    issues: &mut Vec<mir_issues::Issue>,
) {
    // Superglobals are always "used" — skip them
    const SUPERGLOBALS: &[&str] = &[
        "_SERVER", "_GET", "_POST", "_REQUEST", "_SESSION", "_COOKIE", "_FILES", "_ENV", "GLOBALS",
    ];
    for name in &ctx.assigned_vars {
        if ctx.param_names.contains(name) {
            continue;
        }
        if SUPERGLOBALS.contains(&name.as_str()) {
            continue;
        }
        // $this is implicitly used whenever the method accesses properties or
        // calls other methods — never report it as unused.
        if name == "this" {
            continue;
        }
        if name.starts_with('_') {
            continue;
        }
        if !ctx.read_vars.contains(name) {
            issues.push(mir_issues::Issue::new(
                mir_issues::IssueKind::UnusedVariable { name: name.clone() },
                mir_issues::Location {
                    file: file.clone(),
                    line: 1,
                    col_start: 0,
                    col_end: 0,
                },
            ));
        }
    }
}

/// Merge a list of return types into a single `Union`.
/// Returns `void` if the list is empty.
pub fn merge_return_types(return_types: &[Union]) -> Union {
    if return_types.is_empty() {
        return Union::single(mir_types::Atomic::TVoid);
    }
    return_types
        .iter()
        .fold(Union::empty(), |acc, t| Union::merge(&acc, t))
}

pub(crate) fn collect_php_files(dir: &Path, out: &mut Vec<PathBuf>) {
    if let Ok(entries) = std::fs::read_dir(dir) {
        for entry in entries.flatten() {
            // Skip symlinks — they can form cycles (e.g. .pnpm-store)
            if entry.file_type().map(|ft| ft.is_symlink()).unwrap_or(false) {
                continue;
            }
            let path = entry.path();
            if path.is_dir() {
                let name = path.file_name().and_then(|n| n.to_str()).unwrap_or("");
                if matches!(
                    name,
                    "vendor" | ".git" | "node_modules" | ".cache" | ".pnpm-store"
                ) {
                    continue;
                }
                collect_php_files(&path, out);
            } else if path.extension().and_then(|e| e.to_str()) == Some("php") {
                out.push(path);
            }
        }
    }
}

// ---------------------------------------------------------------------------
// AnalysisResult
// ---------------------------------------------------------------------------

// ---------------------------------------------------------------------------
// build_reverse_deps
// ---------------------------------------------------------------------------

/// Build a reverse dependency graph from the codebase after Pass 1.
///
/// Returns a map: `defining_file → {files that depend on it}`.
///
/// Dependency edges captured (all derivable from Pass 1 data):
/// - `use` imports  (`file_imports`)
/// - `extends` / `implements` / trait `use` from `ClassStorage`
fn build_reverse_deps(codebase: &Codebase) -> HashMap<String, HashSet<String>> {
    let mut reverse: HashMap<String, HashSet<String>> = HashMap::new();

    // Helper: record edge "defining_file → dependent_file"
    let mut add_edge = |symbol: &str, dependent_file: &str| {
        if let Some(defining_file) = codebase.symbol_to_file.get(symbol) {
            let def = defining_file.as_ref().to_string();
            if def != dependent_file {
                reverse
                    .entry(def)
                    .or_default()
                    .insert(dependent_file.to_string());
            }
        }
    };

    // use-import edges
    for entry in codebase.file_imports.iter() {
        let file = entry.key().as_ref().to_string();
        for fqcn in entry.value().values() {
            add_edge(fqcn, &file);
        }
    }

    // extends / implements / trait edges from ClassStorage
    for entry in codebase.classes.iter() {
        let defining = {
            let fqcn = entry.key().as_ref();
            codebase
                .symbol_to_file
                .get(fqcn)
                .map(|f| f.as_ref().to_string())
        };
        let Some(file) = defining else { continue };

        let cls = entry.value();
        if let Some(ref parent) = cls.parent {
            add_edge(parent.as_ref(), &file);
        }
        for iface in &cls.interfaces {
            add_edge(iface.as_ref(), &file);
        }
        for tr in &cls.traits {
            add_edge(tr.as_ref(), &file);
        }
    }

    reverse
}

// ---------------------------------------------------------------------------

/// Extract the reference locations recorded for `file` from the codebase into
/// a flat `Vec<(symbol_key, start, end)>` suitable for caching.
fn extract_reference_locations(codebase: &Codebase, file: &Arc<str>) -> Vec<(String, u32, u32)> {
    let Some(symbol_keys) = codebase.file_symbol_references.get(file.as_ref()) else {
        return Vec::new();
    };
    let mut out = Vec::new();
    for key in symbol_keys.iter() {
        let Some(by_file) = codebase.symbol_reference_locations.get(key.as_ref()) else {
            continue;
        };
        let Some(spans) = by_file.get(file.as_ref()) else {
            continue;
        };
        for &(s, e) in spans.iter() {
            out.push((key.to_string(), s, e));
        }
    }
    out
}

// ---------------------------------------------------------------------------

pub struct AnalysisResult {
    pub issues: Vec<Issue>,
    pub type_envs: std::collections::HashMap<crate::type_env::ScopeId, crate::type_env::TypeEnv>,
    /// Per-expression resolved symbols from Pass 2.
    pub symbols: Vec<crate::symbol::ResolvedSymbol>,
}

impl AnalysisResult {
    pub fn error_count(&self) -> usize {
        self.issues
            .iter()
            .filter(|i| i.severity == mir_issues::Severity::Error)
            .count()
    }

    pub fn warning_count(&self) -> usize {
        self.issues
            .iter()
            .filter(|i| i.severity == mir_issues::Severity::Warning)
            .count()
    }

    /// Group issues by source file.
    ///
    /// Returns a map from absolute file path to the slice of issues that belong
    /// to that file. Useful for LSP `textDocument/publishDiagnostics`, which
    /// pushes diagnostics per document.
    pub fn issues_by_file(&self) -> HashMap<std::sync::Arc<str>, Vec<&Issue>> {
        let mut map: HashMap<std::sync::Arc<str>, Vec<&Issue>> = HashMap::new();
        for issue in &self.issues {
            map.entry(issue.location.file.clone())
                .or_default()
                .push(issue);
        }
        map
    }

    /// Return the innermost resolved symbol whose span contains `byte_offset`
    /// in `file`, or `None` if no symbol was recorded at that position.
    ///
    /// When multiple symbols overlap (e.g. a method call whose span contains a
    /// property access span), the one with the smallest span is returned so the
    /// caller gets the most specific symbol at the cursor.
    ///
    /// Typical use: LSP `textDocument/references` and `textDocument/hover`.
    pub fn symbol_at(
        &self,
        file: &str,
        byte_offset: u32,
    ) -> Option<&crate::symbol::ResolvedSymbol> {
        self.symbols
            .iter()
            .filter(|s| {
                s.file.as_ref() == file && s.span.start <= byte_offset && byte_offset < s.span.end
            })
            .min_by_key(|s| s.span.end - s.span.start)
    }
}