seshat-scanner 0.3.1

//! Scan orchestration — full and incremental project scan pipeline.
//!
//! Coordinates file discovery, parsing, module structure analysis,
//! manifest analysis, documentation ingestion, and persistence of all
//! results to the database.
//!
//! On re-scan, unchanged files (same content hash) are skipped. Changed
//! files are re-parsed and their IR updated. New files are parsed and
//! inserted. Deleted files have their IR removed from the database.
//! Module structure (nodes + edges) is rebuilt from the full set of
//! parsed files on every scan.

use std::collections::{HashMap, HashSet};
use std::path::{Path, PathBuf};

use globset::{Glob, GlobSetBuilder};
use ignore::WalkBuilder;
use seshat_core::{BranchId, Edge, EdgeId, NodeId, ProjectFile, ScanConfig};
use seshat_storage::{
    BranchRepository, Database, EdgeRepository, FileIRRepository, NodeRepository,
    RepoMetadataRepository, SqliteBranchRepository, SqliteEdgeRepository, SqliteFileIRRepository,
    SqliteNodeRepository, SqliteRepoMetadataRepository,
};

use crate::discovery::discover_files;
use crate::documentation::parse_documentation;
use crate::error::ScanError;
use crate::git_dates::collect_git_file_dates;
use crate::manifest::{ManifestAnalysis, ManifestType, analyze_manifests};
use crate::module_structure::build_module_graph;
use crate::parser::{content_hash, parse_file};

/// Progress events emitted by [`scan_project`].
///
/// The callback receives these events at key pipeline stages, allowing
/// the CLI to drive progress indicators (spinner, progress bar, etc.).
#[derive(Debug, Clone)]
pub enum ScanProgress {
    /// File discovery phase: `count` files found so far.
    Discovering { count: usize },
    /// Discovery complete. `total` files will be scanned.
    DiscoveryDone { total: usize },
    /// Git history collection phase is starting.
    CollectingGitHistory,
    /// Git history collection complete.
    GitHistoryDone,
    /// A file has been processed (parsed or skipped). `done` of `total`.
    Scanning { done: usize, total: usize },
    /// Scanning (parse) phase complete.
    ScanningDone,
    /// Persisting IR and building module graph (steps 4-7).
    BuildingModuleGraph,
    /// Module graph build complete.
    ModuleGraphDone,
    /// Analyzing manifests and documentation (steps 8-9).
    AnalyzingProjectFiles,
    /// Manifest/docs analysis complete.
    ProjectFilesDone,

    // -- Submodule progress events (emitted by the scan orchestrator in US-004+) --
    /// A submodule was detected in `.gitmodules`.
    /// `path` is the relative mount path (e.g. `"vendor/lib"`).
    SubmoduleDetected { path: String },
    /// A submodule scan is starting.
    /// `path` is the relative mount path, `name` is the short directory name.
    ScanningSubmodule { path: String, name: String },
    /// A submodule scan completed successfully.
    /// `path` is the relative mount path.
    ScanningSubmoduleDone { path: String },
    /// A submodule is up-to-date (commit hash unchanged since last scan).
    /// `path` is the relative mount path, `hash` is the current commit hash.
    SubmoduleUpToDate { path: String, hash: String },
    /// A submodule was skipped (not initialized, excluded, etc.).
    /// `path` is the relative mount path, `reason` explains why.
    SubmoduleSkipped { path: String, reason: String },
}

/// No-op progress callback — used when caller does not need progress.
fn noop_progress(_: &ScanProgress) {}

/// Summary of a completed scan operation.
#[derive(Debug, Clone)]
pub struct ScanResult {
    /// Number of source files discovered.
    pub files_discovered: usize,
    /// Number of source files parsed (may differ from discovered if some were skipped).
    pub files_parsed: usize,
    /// Number of knowledge nodes persisted.
    pub nodes_persisted: usize,
    /// Number of edges persisted.
    pub edges_persisted: usize,
    /// Number of manifest files analyzed.
    pub manifests_analyzed: usize,
    /// Number of documentation files ingested.
    pub docs_ingested: usize,
    /// Manifest analysis results (dependency declarations + usage stats).
    pub manifest_analyses: Vec<ManifestAnalysis>,
    /// Incremental scan statistics (present on re-scans).
    pub incremental: Option<IncrementalStats>,
    /// Git file dates collected during the scan (file path → last commit timestamp).
    /// Exposed so that callers (e.g., CLI) can use them for trend computation
    /// without re-running `collect_git_file_dates()`.
    pub file_dates: HashMap<PathBuf, i64>,
    /// Submodule paths excluded from root discovery (always excluded — they get
    /// their own separate DBs). Empty when the project has no `.gitmodules`.
    pub excluded_submodules: Vec<String>,
    /// Source content for **every** discovered file (full and incremental scans).
    ///
    /// On a **full scan** all files are read and stored here.
    /// On an **incremental re-scan** all files are still read (we must read
    /// every file to compute its content hash for change detection anyway), so
    /// the source is never discarded — it is always kept in this map.
    ///
    /// Used by convention detectors to extract real source snippets for
    /// evidence. Every file in `all_files` will have an entry here, so
    /// `detect_with_source` is always called (never the IR-only `detect`
    /// fallback) and snippets are always populated.
    ///
    /// Memory note: the map holds the full repo source in memory during the
    /// detection phase, then is dropped. For typical repos this is negligible.
    pub source_map: HashMap<PathBuf, String>,

    /// Paths of files that are **new or changed** in this scan.
    ///
    /// On a **full scan** this equals all discovered files (every file is new).
    /// On an **incremental re-scan** this contains only the files whose content
    /// hash changed or that are newly added.
    ///
    /// Used by embedding generation to skip re-embedding unchanged files
    /// (their embeddings are already current in the `code_embeddings` table).
    /// Convention detectors use the full `source_map` instead.
    pub changed_paths: HashSet<PathBuf>,
}

/// Statistics for an incremental re-scan.
#[derive(Debug, Clone, Default)]
pub struct IncrementalStats {
    /// Files unchanged (same content hash) — skipped re-parsing.
    pub files_unchanged: usize,
    /// Files whose content changed — re-parsed and IR updated.
    pub files_changed: usize,
    /// New files not in previous scan — parsed and inserted.
    pub files_new: usize,
    /// Files deleted since last scan — IR removed from DB.
    pub files_deleted: usize,
}

/// Orchestrate a project scan with automatic incremental support.
///
/// Convenience wrapper that calls [`scan_project_with_progress`] with a
/// no-op callback.
pub fn scan_project(
    root: &Path,
    config: &ScanConfig,
    db: &Database,
    branch_id: BranchId,
) -> Result<ScanResult, ScanError> {
    scan_project_with_progress(root, config, db, noop_progress, branch_id)
}

/// Orchestrate a project scan with automatic incremental support and
/// progress reporting.
///
/// If the database already contains file IR records for the branch,
/// the scan runs incrementally:
/// - Unchanged files (same content hash) are skipped
/// - Changed files are re-parsed and their IR updated
/// - New files are parsed and inserted
/// - Deleted files have their IR removed
///
/// Module structure (nodes + edges) is always rebuilt from the full set
/// of currently-valid parsed files (combining unchanged from DB + newly
/// parsed).
///
/// # Arguments
///
/// * `root` - The project root directory to scan.
/// * `config` - Scan configuration (exclude patterns, file size limit).
/// * `db` - The database handle for persistence.
/// * `on_progress` - Callback invoked at key pipeline stages.
/// * `branch_id` - The git branch identifier to scope all scan data.
///
/// # Returns
///
/// A [`ScanResult`] summarizing what was persisted.
pub fn scan_project_with_progress(
    root: &Path,
    config: &ScanConfig,
    db: &Database,
    on_progress: impl Fn(&ScanProgress),
    branch_id: BranchId,
) -> Result<ScanResult, ScanError> {
    let conn = db.connection().clone();
    let file_ir_repo = SqliteFileIRRepository::new(conn.clone());
    let node_repo = SqliteNodeRepository::new(conn.clone());
    let edge_repo = SqliteEdgeRepository::new(conn.clone());
    let branch_repo = SqliteBranchRepository::new(conn);

    let branch = branch_id;

    // Register the branch in the `branches` table so freshness checks
    // and `list_branches` can find it. Idempotent — safe to call on every
    // scan. (US-003; US-009 layers `set_last_scanned_commit` on top.)
    branch_repo.ensure_branch_exists(&branch)?;

    // P18+P19: snapshot HEAD BEFORE discovery starts. The sentinel
    // write at the tail uses this captured value rather than re-reading
    // HEAD post-scan, so a commit that landed mid-scan cannot fool the
    // freshness check into thinking the new tree was already indexed.
    // Doing this inside the orchestrator means every scan path (CLI
    // scan, watcher rescan, fallback, review sync) gets the right
    // sentinel automatically — no per-caller wiring required.
    let head_at_scan_start: Option<String> = crate::git_utils::get_head_commit(root);

    // ------------------------------------------------------------------
    // Step 1: Discover source files
    // ------------------------------------------------------------------
    let discovery_result = discover_files(root, config)?;
    let discovered = discovery_result.files;
    let excluded_submodules = discovery_result.excluded_submodules;
    let files_discovered = discovered.len();
    on_progress(&ScanProgress::Discovering {
        count: files_discovered,
    });
    on_progress(&ScanProgress::DiscoveryDone {
        total: files_discovered,
    });
    tracing::info!(count = files_discovered, "Discovered source files");

    // ------------------------------------------------------------------
    // Step 1b: Collect git file dates
    // ------------------------------------------------------------------
    on_progress(&ScanProgress::CollectingGitHistory);
    let git_file_dates = collect_git_file_dates(root)?;
    on_progress(&ScanProgress::GitHistoryDone);
    if !git_file_dates.is_empty() {
        tracing::info!(
            files_with_dates = git_file_dates.len(),
            "Collected git file dates"
        );
    }

    // ------------------------------------------------------------------
    // Step 2: Check for existing data (incremental mode)
    // ------------------------------------------------------------------
    let stored_hashes = file_ir_repo.get_file_hashes_by_branch(&branch)?;
    let is_incremental = !stored_hashes.is_empty();

    // Build a set of discovered file paths (relative, as stored in DB)
    let discovered_paths: HashSet<String> = discovered
        .iter()
        .map(|df| df.path.to_string_lossy().to_string())
        .collect();

    // ------------------------------------------------------------------
    // Step 3: Read, hash, and selectively parse files
    // ------------------------------------------------------------------
    let mut parsed_files: Vec<ProjectFile> = Vec::with_capacity(files_discovered);
    // source_map holds source for ALL discovered files — unchanged and changed
    // alike.  Every file is read from disk anyway to compute its content hash,
    // so keeping the source costs no extra I/O.  Convention detectors need
    // source for every file to produce real snippets; discarding source for
    // unchanged files was the root cause of empty snippets in evidence.
    let mut source_map: HashMap<PathBuf, String> = HashMap::new();
    // changed_paths tracks only new/changed files so that embedding generation
    // can skip re-embedding unchanged files (their embeddings are current in DB).
    let mut changed_paths: HashSet<PathBuf> = HashSet::new();
    let mut incremental_stats = IncrementalStats::default();

    let mut scan_done: usize = 0;
    for df in &discovered {
        // df.path is RELATIVE to root (Bug #3 fix). Use it as the IR key
        // (so worktree-prefix differences don't fragment files_ir) and join
        // with root for any I/O.
        let file_path_str = df.path.to_string_lossy().to_string();
        let abs_path = root.join(&df.path);

        let source = match std::fs::read_to_string(&abs_path) {
            Ok(s) => s,
            Err(e) => {
                tracing::warn!(path = %abs_path.display(), error = %e, "Failed to read file, skipping");
                scan_done += 1;
                on_progress(&ScanProgress::Scanning {
                    done: scan_done,
                    total: files_discovered,
                });
                continue;
            }
        };

        if is_incremental {
            // Compute hash first to check if file changed
            let new_hash = content_hash(&source);

            if let Some(stored_hash) = stored_hashes.get(&file_path_str) {
                if *stored_hash == new_hash {
                    // Unchanged — skip re-parsing, load existing IR from DB.
                    // Keep source in source_map so detectors can still produce
                    // real snippets for this file's evidence entries.
                    incremental_stats.files_unchanged += 1;
                    tracing::debug!(path = %df.path.display(), "File unchanged, skipping re-parse");
                    source_map.insert(df.path.clone(), source);
                    scan_done += 1;
                    on_progress(&ScanProgress::Scanning {
                        done: scan_done,
                        total: files_discovered,
                    });
                    continue;
                }
                // Changed — re-parse
                incremental_stats.files_changed += 1;
                tracing::debug!(path = %df.path.display(), "File changed, re-parsing");
            } else {
                // New file
                incremental_stats.files_new += 1;
                tracing::debug!(path = %df.path.display(), "New file, parsing");
            }
        }

        // Pass the RELATIVE path to parse_file so ProjectFile.path (which
        // becomes files_ir.file_path on upsert) is worktree-independent.
        let mut project_file = parse_file(&df.path, &source, df.language);

        // Strip local project packages from the dependency list so they are
        // not mistaken for external dependencies by the detectors.
        // This is most relevant for Python monorepos where `from myawesomeapp.web
        // import X` looks identical to `from requests import X` syntactically.
        if !config.local_packages.is_empty() {
            project_file
                .dependencies_used
                .retain(|dep| !config.local_packages.contains(&dep.package));
        }

        parsed_files.push(project_file);
        changed_paths.insert(df.path.clone()); // new/changed — needs embedding update
        source_map.insert(df.path.clone(), source); // keep source alive for detectors
        scan_done += 1;
        on_progress(&ScanProgress::Scanning {
            done: scan_done,
            total: files_discovered,
        });
    }
    on_progress(&ScanProgress::ScanningDone);

    let files_parsed = parsed_files.len();
    tracing::info!(count = files_parsed, "Parsed source files");

    on_progress(&ScanProgress::BuildingModuleGraph);

    // ------------------------------------------------------------------
    // Step 4: Handle deleted files (present in DB but not on disk)
    //
    // Symbol-index rows are deleted alongside `files_ir` in one transaction so
    // the index stays consistent with the IR.  NotFound is swallowed
    // defensively — the symbol-index half is still attempted inside the same
    // tx, which also sweeps any orphan rows left by an earlier non-atomic
    // delete.
    // ------------------------------------------------------------------
    if is_incremental {
        for stored_path in stored_hashes.keys() {
            if !discovered_paths.contains(stored_path) {
                tracing::info!(path = %stored_path, "File deleted, removing IR from DB");
                let _ = file_ir_repo.delete_with_symbol_index(&branch, stored_path);
                incremental_stats.files_deleted += 1;
            }
        }
    }

    // ------------------------------------------------------------------
    // Step 5: Persist file IR + symbol-index (new and changed files)
    //
    // Each file goes through a single transaction so the IR and the
    // symbol_definitions / symbol_imports rows commit together — preventing
    // the index from drifting out of sync with files_ir on a partial write.
    // ------------------------------------------------------------------
    for pf in &parsed_files {
        // git_file_dates keys are relative paths (as returned by gix tree walk).
        // pf.path is absolute (from WalkBuilder), so we must strip the root
        // prefix before looking up the commit date.
        let rel = pf.path.strip_prefix(root).unwrap_or(&pf.path);
        let commit_date = git_file_dates.get(rel).copied();
        file_ir_repo.upsert_with_symbol_index(&branch, pf, commit_date)?;
    }
    tracing::info!(count = files_parsed, "Stored file IR records");

    // ------------------------------------------------------------------
    // Step 6: Gather all current parsed files for module graph
    //
    // For incremental scans, we need the full set: unchanged files
    // (loaded from DB) + newly parsed files.
    // ------------------------------------------------------------------
    let all_parsed_files = if is_incremental && incremental_stats.files_unchanged > 0 {
        // Load all IR from DB (which now has the updated set)
        file_ir_repo.get_by_branch(&branch)?
    } else {
        // Fresh scan or all files changed — use what we just parsed
        parsed_files.clone()
    };

    // ------------------------------------------------------------------
    // Step 7: Rebuild module structure graph
    //
    // On re-scan, delete old module nodes and edges first, then
    // re-insert. This is simpler and more correct than trying to diff
    // the module graph.
    // ------------------------------------------------------------------
    if is_incremental {
        let deleted_edges = edge_repo.delete_by_branch(&branch)?;
        // Use delete_facts_by_branch (not delete_by_branch) to preserve
        // user-confirmed conventions and observations written by `seshat review`.
        let deleted_nodes = node_repo.delete_facts_by_branch(&branch)?;
        tracing::debug!(
            nodes = deleted_nodes,
            edges = deleted_edges,
            "Cleared old module structure for rebuild"
        );
    }

    let module_graph = build_module_graph(root, &all_parsed_files, &branch);

    // Persist module nodes with placeholder → real ID remapping.
    let mut id_remap: HashMap<NodeId, NodeId> = HashMap::new();
    let mut nodes_persisted: usize = 0;

    for node in &module_graph.nodes {
        let inserted = node_repo.insert(node)?;
        id_remap.insert(node.id, inserted.id);
        nodes_persisted += 1;
    }

    // Persist module edges with remapped source/target IDs.
    let mut edges_persisted: usize = 0;

    for edge in &module_graph.edges {
        let remapped_edge = remap_edge(edge, &id_remap);
        edge_repo.insert(&remapped_edge)?;
        edges_persisted += 1;
    }

    tracing::info!(
        nodes = nodes_persisted,
        edges = edges_persisted,
        "Persisted module structure"
    );

    on_progress(&ScanProgress::ModuleGraphDone);
    on_progress(&ScanProgress::AnalyzingProjectFiles);

    // ------------------------------------------------------------------
    // Step 8: Discover and analyze dependency manifests
    // ------------------------------------------------------------------
    let manifests = discover_manifests(root)?;
    let manifests_analyzed = manifests.len();

    let manifest_analyses = if !manifests.is_empty() {
        let analysis = analyze_manifests(&manifests, &all_parsed_files)?;
        tracing::info!(count = analysis.len(), "Analyzed dependency manifests");
        analysis
    } else {
        Vec::new()
    };

    // ------------------------------------------------------------------
    // Step 8b: Persist auto-detected internal names to repo_metadata
    //
    // Collect all internal_names from manifest analyses, union with
    // config.local_packages (normalising hyphens to underscores), and write
    // as a JSON array under the "workspace_crates" key so the graph layer
    // can read them at query time.
    //
    // Only writes when names are non-empty — an empty list on re-scan would
    // erase previously valid names from a prior scan.
    // ------------------------------------------------------------------
    {
        let mut internal_names: Vec<String> = manifest_analyses
            .iter()
            .flat_map(|a| a.internal_names.iter().cloned())
            .filter(|n| !n.trim().is_empty())
            .collect();

        // Union with config.local_packages — normalise hyphens to underscores
        // so they match the normalised crate/package names from manifests.
        // Dedup with a set, preserving order of auto-detected names first.
        let mut seen: HashSet<String> = internal_names.iter().cloned().collect();
        for pkg in &config.local_packages {
            let normalised = pkg.trim().replace('-', "_");
            if !normalised.is_empty() && seen.insert(normalised.clone()) {
                internal_names.push(normalised);
            }
        }

        if internal_names.is_empty() {
            tracing::debug!("No internal names to persist — skipping workspace_crates write");
        } else {
            let json = serde_json::to_string(&internal_names).unwrap_or_else(|e| {
                tracing::warn!(error = %e, "Failed to serialise workspace_crates, storing []");
                "[]".to_owned()
            });

            let meta_repo = SqliteRepoMetadataRepository::new(db.connection().clone());
            if let Err(e) = meta_repo.set("workspace_crates", &json) {
                tracing::warn!(error = %e, "Failed to persist workspace_crates to repo_metadata");
            } else {
                tracing::info!(
                    count = internal_names.len(),
                    "Persisted workspace_crates to repo_metadata"
                );
            }
        }
    }

    // ------------------------------------------------------------------
    // Step 9: Discover and parse documentation files
    // ------------------------------------------------------------------
    let doc_files = discover_documentation(root, config)?;
    let docs_ingested = doc_files.len();

    for (doc_path, doc_content) in &doc_files {
        match parse_documentation(doc_path, doc_content, &branch) {
            Ok(doc_result) => {
                for node in &doc_result.nodes {
                    node_repo.insert(node)?;
                    nodes_persisted += 1;
                }
            }
            Err(e) => {
                tracing::warn!(
                    path = %doc_path.display(),
                    error = %e,
                    "Failed to parse documentation, skipping"
                );
            }
        }
    }

    tracing::info!(
        count = docs_ingested,
        nodes = nodes_persisted,
        "Ingested documentation"
    );

    on_progress(&ScanProgress::ProjectFilesDone);

    // P19: record the freshness sentinel at the END of the scan, using
    // the HEAD captured BEFORE discovery (P18). Storage errors here are
    // logged but not fatal — the scan itself succeeded and shouldn't
    // regress because the sentinel write hit a transient SQLite error.
    if let Some(head) = head_at_scan_start.as_deref()
        && let Err(e) = branch_repo.set_last_scanned_commit(&branch, head)
    {
        tracing::warn!(
            error = %e,
            branch = %branch.0,
            "scan_project: failed to record last_scanned_commit; \
             freshness gate may re-trigger sync next startup"
        );
    }

    Ok(ScanResult {
        files_discovered,
        files_parsed,
        nodes_persisted,
        edges_persisted,
        manifests_analyzed,
        docs_ingested,
        manifest_analyses,
        incremental: if is_incremental {
            Some(incremental_stats)
        } else {
            None
        },
        file_dates: git_file_dates,
        excluded_submodules,
        source_map,
        changed_paths,
    })
}

/// Remap an edge's source and target IDs using the placeholder → real ID mapping.
///
/// If an ID is not found in the mapping (shouldn't happen in normal flow),
/// the original ID is preserved.
fn remap_edge(edge: &Edge, id_remap: &HashMap<NodeId, NodeId>) -> Edge {
    Edge {
        id: EdgeId(0), // DB will assign real ID
        source_id: id_remap
            .get(&edge.source_id)
            .copied()
            .unwrap_or(edge.source_id),
        target_id: id_remap
            .get(&edge.target_id)
            .copied()
            .unwrap_or(edge.target_id),
        edge_type: edge.edge_type,
        branch_id: edge.branch_id.clone(),
        weight: edge.weight,
        metadata: edge.metadata.clone(),
    }
}

/// Discover dependency manifest files in the project root directory.
///
/// Looks for known manifest filenames (`Cargo.toml`, `package.json`,
/// `pyproject.toml`) in the root directory only (not recursively).
fn discover_manifests(root: &Path) -> Result<Vec<(PathBuf, String, ManifestType)>, ScanError> {
    let mut manifests = Vec::new();

    for filename in ManifestType::all_filenames() {
        let path = root.join(filename);
        if path.is_file() {
            let content = std::fs::read_to_string(&path).map_err(|e| ScanError::ManifestError {
                path: path.clone(),
                reason: format!("Failed to read manifest: {e}"),
            })?;

            if let Some(manifest_type) = ManifestType::from_filename(filename) {
                manifests.push((path, content, manifest_type));
            }
        }
    }

    Ok(manifests)
}

/// Discover documentation files in the project.
///
/// Uses the same [`WalkBuilder`] infrastructure as source-file discovery so
/// that `.gitignore`, hidden files, and `config.exclude_paths` are all
/// respected consistently across every discovery flow.
///
/// Only `.md` (always), `.json` (JSON Schema only), `.yaml`/`.yml`
/// (OpenAPI only) files are returned.
fn discover_documentation(
    root: &Path,
    config: &ScanConfig,
) -> Result<Vec<(PathBuf, String)>, ScanError> {
    let doc_extensions = ["md", "json", "yaml", "yml"];

    // Build a GlobSet from exclude_paths so we can efficiently check each
    // relative path against the user-configured exclusions.
    let exclude_globset = {
        let mut builder = GlobSetBuilder::new();
        for pattern in &config.exclude_paths {
            let glob = Glob::new(pattern).map_err(|e| ScanError::DiscoveryError {
                path: root.to_path_buf(),
                reason: format!("Invalid exclude_paths pattern '{pattern}': {e}"),
            })?;
            builder.add(glob);
        }
        builder.build().map_err(|e| ScanError::DiscoveryError {
            path: root.to_path_buf(),
            reason: format!("Failed to build exclude globset: {e}"),
        })?
    };

    let mut doc_files = Vec::new();

    let walker = WalkBuilder::new(root)
        .hidden(true) // skip hidden files/dirs (respects .gitignore convention)
        .git_ignore(true) // respect .gitignore
        .git_global(true) // respect global gitignore
        .git_exclude(true) // respect .git/info/exclude
        .build();

    for entry_result in walker {
        let entry = match entry_result {
            Ok(e) => e,
            Err(err) => {
                tracing::warn!("Doc walk error: {err}");
                continue;
            }
        };

        // Only process regular files.
        let Some(file_type) = entry.file_type() else {
            continue;
        };
        if !file_type.is_file() {
            continue;
        }

        let path = entry.path();

        // Check extension first (cheap filter).
        let ext = match path.extension().and_then(|e| e.to_str()) {
            Some(e) => e,
            None => continue,
        };
        if !doc_extensions.contains(&ext) {
            continue;
        }

        // Compute relative path and check against exclude_paths.
        let relative = path.strip_prefix(root).unwrap_or(path).to_path_buf();
        if !exclude_globset.is_empty() && exclude_globset.is_match(&relative) {
            tracing::debug!(
                path = %relative.display(),
                "Skipping doc file (matched exclude_paths)"
            );
            continue;
        }

        // Read content and validate format.
        let content = match std::fs::read_to_string(path) {
            Ok(c) => c,
            Err(e) => {
                tracing::warn!(path = %path.display(), error = %e, "Cannot read doc file");
                continue;
            }
        };

        // For JSON and YAML, only ingest if they match a supported doc format.
        if (ext == "json" || ext == "yaml" || ext == "yml")
            && !is_documentation_content(ext, &content)
        {
            continue;
        }

        doc_files.push((relative, content));
    }

    Ok(doc_files)
}

/// Check if file content matches a known documentation format.
///
/// JSON files must look like a JSON Schema (have `$schema`, `properties`, or
/// `type` + `title`). YAML files must have `openapi` or `swagger` top-level key.
fn is_documentation_content(ext: &str, content: &str) -> bool {
    match ext {
        "json" => {
            // Check for JSON Schema indicators
            let Ok(value) = serde_json::from_str::<serde_json::Value>(content) else {
                return false;
            };
            let obj = match value.as_object() {
                Some(o) => o,
                None => return false,
            };
            obj.contains_key("$schema")
                || obj.contains_key("properties")
                || (obj.contains_key("type") && obj.contains_key("title"))
        }
        "yaml" | "yml" => {
            // Check for OpenAPI/Swagger indicators
            let Ok(value) = serde_yml::from_str::<serde_yml::Value>(content) else {
                return false;
            };
            let mapping = match value.as_mapping() {
                Some(m) => m,
                None => return false,
            };
            let has_openapi = mapping.contains_key(serde_yml::Value::String("openapi".to_string()));
            let has_swagger = mapping.contains_key(serde_yml::Value::String("swagger".to_string()));
            has_openapi || has_swagger
        }
        _ => false,
    }
}

#[cfg(test)]
mod tests {
    use super::*;
    use seshat_core::ScanConfig;
    use seshat_storage::Database;
    use std::fs;
    use tempfile::tempdir;

    /// Helper: create a minimal project in a temp directory for testing.
    fn create_test_project() -> tempfile::TempDir {
        let dir = tempdir().expect("create tempdir");
        let root = dir.path();

        // Create .git directory so WalkBuilder activates .gitignore parsing
        fs::create_dir_all(root.join(".git")).unwrap();

        // Create source files
        let src = root.join("src");
        fs::create_dir_all(&src).unwrap();

        fs::write(
            src.join("main.rs"),
            r#"
use std::io;
use crate::config::Config;

pub fn main() {
    println!("hello");
}

fn helper() -> bool {
    true
}
"#,
        )
        .unwrap();

        fs::write(
            src.join("config.rs"),
            r#"
pub struct Config {
    pub name: String,
    pub debug: bool,
}

impl Config {
    pub fn new() -> Self {
        Config {
            name: String::new(),
            debug: false,
        }
    }
}
"#,
        )
        .unwrap();

        // Create a subdirectory with another file
        let utils = src.join("utils");
        fs::create_dir_all(&utils).unwrap();

        fs::write(
            utils.join("format.rs"),
            r#"
use crate::config::Config;

pub fn format_name(config: &Config) -> String {
    config.name.clone()
}
"#,
        )
        .unwrap();

        // Create a markdown doc
        fs::write(
            root.join("README.md"),
            r#"# Test Project

## Overview
A simple test project.

## Features
- Feature one
- Feature two
"#,
        )
        .unwrap();

        dir
    }

    #[test]
    fn scan_project_discovers_and_parses_files() {
        let dir = create_test_project();
        let root = dir.path();
        let db = Database::open(":memory:").expect("open DB");
        let config = ScanConfig::default();

        let result =
            scan_project(root, &config, &db, BranchId::from("main")).expect("scan should succeed");

        assert_eq!(result.files_discovered, 3, "should discover 3 .rs files");
        assert_eq!(result.files_parsed, 3, "should parse all 3 files");
    }

    #[test]
    fn scan_project_stores_ir_in_database() {
        let dir = create_test_project();
        let root = dir.path();
        let db = Database::open(":memory:").expect("open DB");
        let config = ScanConfig::default();

        scan_project(root, &config, &db, BranchId::from("main")).expect("scan should succeed");

        // Verify IR records exist in database
        let conn = db.connection().clone();
        let file_ir_repo = SqliteFileIRRepository::new(conn);
        let branch_id = BranchId::from("main");

        let all_files = file_ir_repo.get_by_branch(&branch_id).expect("get files");
        assert_eq!(all_files.len(), 3, "should have 3 file IR records");
    }

    #[test]
    fn scan_project_stores_content_hash() {
        let dir = create_test_project();
        let root = dir.path();
        let db = Database::open(":memory:").expect("open DB");
        let config = ScanConfig::default();

        scan_project(root, &config, &db, BranchId::from("main")).expect("scan should succeed");

        // Verify content hashes are stored
        let conn = db.connection().clone();
        let file_ir_repo = SqliteFileIRRepository::new(conn);
        let branch_id = BranchId::from("main");

        let all_files = file_ir_repo.get_by_branch(&branch_id).expect("get files");
        for pf in &all_files {
            assert!(
                !pf.content_hash.is_empty(),
                "content hash should be non-empty for {}",
                pf.path.display()
            );
        }
    }

    #[test]
    fn scan_project_persists_module_nodes() {
        let dir = create_test_project();
        let root = dir.path();
        let db = Database::open(":memory:").expect("open DB");
        let config = ScanConfig::default();

        let result =
            scan_project(root, &config, &db, BranchId::from("main")).expect("scan should succeed");

        // We have files in src/ and src/utils/, so should have at least 2 module nodes
        assert!(
            result.nodes_persisted >= 2,
            "should persist at least 2 module nodes, got {}",
            result.nodes_persisted
        );

        // Verify nodes exist in DB
        let conn = db.connection().clone();
        let node_repo = SqliteNodeRepository::new(conn);
        let branch_id = BranchId::from("main");

        let nodes = node_repo.find_by_branch(&branch_id).expect("find nodes");
        assert!(
            nodes.len() >= 2,
            "should have at least 2 nodes in DB, got {}",
            nodes.len()
        );
    }

    #[test]
    fn scan_project_persists_edges() {
        let dir = create_test_project();
        let root = dir.path();
        let db = Database::open(":memory:").expect("open DB");
        let config = ScanConfig::default();

        let result =
            scan_project(root, &config, &db, BranchId::from("main")).expect("scan should succeed");

        // Should have PartOf edges at least (src/utils PartOf src)
        assert!(
            result.edges_persisted >= 1,
            "should persist at least 1 edge, got {}",
            result.edges_persisted
        );

        // Verify edges exist in DB
        let conn = db.connection().clone();
        let edge_repo = SqliteEdgeRepository::new(conn);

        let part_of_edges = edge_repo
            .find_by_type(seshat_core::EdgeType::PartOf)
            .expect("find PartOf edges");
        assert!(
            !part_of_edges.is_empty(),
            "should have at least 1 PartOf edge"
        );
    }

    #[test]
    fn scan_project_ingests_documentation() {
        let dir = create_test_project();
        let root = dir.path();
        let db = Database::open(":memory:").expect("open DB");
        let config = ScanConfig::default();

        let result =
            scan_project(root, &config, &db, BranchId::from("main")).expect("scan should succeed");

        assert!(
            result.docs_ingested >= 1,
            "should ingest at least 1 documentation file (README.md), got {}",
            result.docs_ingested
        );
    }

    #[test]
    fn scan_project_empty_directory() {
        let dir = tempdir().expect("create tempdir");
        let root = dir.path();

        // Create .git so WalkBuilder works
        fs::create_dir_all(root.join(".git")).unwrap();

        let db = Database::open(":memory:").expect("open DB");
        let config = ScanConfig::default();

        let result = scan_project(root, &config, &db, BranchId::from("main"))
            .expect("scan should succeed on empty project");

        assert_eq!(result.files_discovered, 0);
        assert_eq!(result.files_parsed, 0);
        assert_eq!(result.nodes_persisted, 0);
        assert_eq!(result.edges_persisted, 0);
    }

    #[test]
    fn scan_project_respects_config_exclude_paths() {
        let dir = create_test_project();
        let root = dir.path();

        // Exclude utils/ directory
        let config = ScanConfig {
            exclude_paths: vec!["**/utils/**".to_string()],
            ..ScanConfig::default()
        };

        let db = Database::open(":memory:").expect("open DB");

        let result =
            scan_project(root, &config, &db, BranchId::from("main")).expect("scan should succeed");

        // Should only discover main.rs and config.rs (not utils/format.rs)
        assert_eq!(
            result.files_discovered, 2,
            "should discover 2 files (utils excluded)"
        );
    }

    #[test]
    fn discover_manifests_finds_cargo_toml() {
        let dir = tempdir().expect("create tempdir");
        let root = dir.path();

        fs::write(
            root.join("Cargo.toml"),
            r#"[package]
name = "test"
version = "0.1.0"
edition = "2021"
"#,
        )
        .unwrap();

        let manifests = discover_manifests(root).expect("discover manifests");
        assert_eq!(manifests.len(), 1);
        assert_eq!(manifests[0].2, ManifestType::CargoToml);
    }

    #[test]
    fn discover_manifests_finds_nothing_without_manifests() {
        let dir = tempdir().expect("create tempdir");
        let manifests = discover_manifests(dir.path()).expect("discover manifests");
        assert!(manifests.is_empty());
    }

    #[test]
    fn is_documentation_content_json_schema() {
        let content = r#"{"$schema": "http://json-schema.org/draft-07/schema#", "type": "object"}"#;
        assert!(is_documentation_content("json", content));

        let content = r#"{"name": "foo", "value": 42}"#;
        assert!(!is_documentation_content("json", content));
    }

    #[test]
    fn is_documentation_content_openapi() {
        let content = "openapi: '3.0.0'\ninfo:\n  title: Test\n  version: '1.0'\npaths: {}";
        assert!(is_documentation_content("yaml", content));

        let content = "name: test\nvalue: 42";
        assert!(!is_documentation_content("yaml", content));
    }

    #[test]
    fn remap_edge_applies_id_mapping() {
        let mut remap = HashMap::new();
        remap.insert(NodeId(1), NodeId(100));
        remap.insert(NodeId(2), NodeId(200));

        let edge = Edge {
            id: EdgeId(0),
            source_id: NodeId(1),
            target_id: NodeId(2),
            edge_type: seshat_core::EdgeType::DependsOn,
            branch_id: BranchId::from("main"),
            weight: 1.0,
            metadata: None,
        };

        let remapped = remap_edge(&edge, &remap);
        assert_eq!(remapped.source_id, NodeId(100));
        assert_eq!(remapped.target_id, NodeId(200));
    }

    #[test]
    fn scan_project_incremental_skips_unchanged() {
        let dir = create_test_project();
        let root = dir.path();
        let db = Database::open(":memory:").expect("open DB");
        let config = ScanConfig::default();

        // Initial scan
        let r1 = scan_project(root, &config, &db, BranchId::from("main")).expect("first scan");
        assert!(r1.incremental.is_none(), "first scan is not incremental");
        assert_eq!(r1.files_parsed, 3);

        // Re-scan without changes
        let r2 = scan_project(root, &config, &db, BranchId::from("main")).expect("second scan");
        assert!(r2.incremental.is_some(), "second scan is incremental");
        let stats = r2.incremental.unwrap();
        assert_eq!(stats.files_unchanged, 3);
        assert_eq!(stats.files_changed, 0);
        assert_eq!(stats.files_new, 0);
        assert_eq!(stats.files_deleted, 0);
        assert_eq!(r2.files_parsed, 0, "no files re-parsed");
    }

    #[test]
    fn scan_project_incremental_detects_modification() {
        let dir = create_test_project();
        let root = dir.path();
        let db = Database::open(":memory:").expect("open DB");
        let config = ScanConfig::default();

        // Initial scan
        scan_project(root, &config, &db, BranchId::from("main")).expect("first scan");

        // Modify a file
        fs::write(
            root.join("src/config.rs"),
            "pub struct Config { pub name: String, pub extra: bool }\n",
        )
        .unwrap();

        // Re-scan
        let r2 = scan_project(root, &config, &db, BranchId::from("main")).expect("second scan");
        let stats = r2.incremental.unwrap();
        assert_eq!(stats.files_changed, 1, "config.rs changed");
        assert_eq!(stats.files_unchanged, 2, "main.rs + format.rs unchanged");
        assert_eq!(r2.files_parsed, 1, "only changed file parsed");
    }

    #[test]
    fn scan_project_incremental_detects_addition() {
        let dir = create_test_project();
        let root = dir.path();
        let db = Database::open(":memory:").expect("open DB");
        let config = ScanConfig::default();

        scan_project(root, &config, &db, BranchId::from("main")).expect("first scan");

        // Add a new file
        fs::write(root.join("src/extra.rs"), "pub fn extra() {}").unwrap();

        let r2 = scan_project(root, &config, &db, BranchId::from("main")).expect("second scan");
        let stats = r2.incremental.unwrap();
        assert_eq!(stats.files_new, 1);
        assert_eq!(stats.files_unchanged, 3);
        assert_eq!(r2.files_discovered, 4);
    }

    #[test]
    fn scan_project_incremental_detects_deletion() {
        let dir = create_test_project();
        let root = dir.path();
        let db = Database::open(":memory:").expect("open DB");
        let config = ScanConfig::default();

        scan_project(root, &config, &db, BranchId::from("main")).expect("first scan");

        // Delete a file
        fs::remove_file(root.join("src/utils/format.rs")).unwrap();

        let r2 = scan_project(root, &config, &db, BranchId::from("main")).expect("second scan");
        let stats = r2.incremental.unwrap();
        assert_eq!(stats.files_deleted, 1);
        assert_eq!(stats.files_unchanged, 2);
        assert_eq!(r2.files_discovered, 2);

        // Verify DB no longer has the deleted file
        let conn = db.connection().clone();
        let file_ir_repo = SqliteFileIRRepository::new(conn);
        let branch = BranchId::from("main");
        let files = file_ir_repo.get_by_branch(&branch).unwrap();
        assert_eq!(files.len(), 2);
    }

    // ── source_map / changed_paths regression tests ───────────────────────────
    //
    // These tests pin the contract that prevents the "empty snippets" regression:
    // source_map must always contain ALL discovered files (so detectors can call
    // detect_with_source for every file), and changed_paths must contain only
    // the new/changed files (so embeddings are not regenerated unnecessarily).

    #[test]
    fn full_scan_source_map_contains_all_files() {
        let dir = create_test_project();
        let root = dir.path();
        let db = Database::open(":memory:").expect("open DB");
        let config = ScanConfig::default();

        let result =
            scan_project(root, &config, &db, BranchId::from("main")).expect("scan should succeed");

        // On a full scan every discovered file must be in source_map.
        assert_eq!(
            result.source_map.len(),
            result.files_discovered,
            "source_map must contain all {} discovered files on full scan, got {}",
            result.files_discovered,
            result.source_map.len()
        );
        // On a full scan all files are "new" → changed_paths == all files.
        assert_eq!(
            result.changed_paths.len(),
            result.files_discovered,
            "changed_paths must equal files_discovered on full scan"
        );
        // Every source must be non-empty (real file content).
        for (path, src) in &result.source_map {
            assert!(!src.is_empty(), "source for {:?} must not be empty", path);
        }
    }

    #[test]
    fn incremental_scan_source_map_contains_all_files() {
        // This is the regression test for the "empty snippets" bug:
        // on an incremental re-scan with no file changes, source_map must
        // still contain ALL files so that detect_with_source is called for
        // every file and snippets are populated.
        let dir = create_test_project();
        let root = dir.path();
        let db = Database::open(":memory:").expect("open DB");
        let config = ScanConfig::default();

        // Initial full scan.
        scan_project(root, &config, &db, BranchId::from("main")).expect("first scan");

        // Re-scan with NO file changes.
        let r2 = scan_project(root, &config, &db, BranchId::from("main")).expect("second scan");
        let stats = r2.incremental.as_ref().unwrap();

        assert_eq!(stats.files_unchanged, 3, "all 3 files should be unchanged");
        assert_eq!(r2.files_parsed, 0, "no files should be re-parsed");

        // KEY ASSERTION: source_map must still contain all files despite no re-parsing.
        assert_eq!(
            r2.source_map.len(),
            r2.files_discovered,
            "source_map must contain all {} files on incremental scan (no changes), got {} — \
             this would cause empty snippets in convention evidence",
            r2.files_discovered,
            r2.source_map.len()
        );

        // changed_paths must be empty — no files changed.
        assert!(
            r2.changed_paths.is_empty(),
            "changed_paths must be empty when no files changed, got {} paths",
            r2.changed_paths.len()
        );

        // Every source in the map must be non-empty.
        for (path, src) in &r2.source_map {
            assert!(
                !src.is_empty(),
                "source for {:?} must not be empty on incremental scan",
                path
            );
        }
    }

    #[test]
    fn scan_persists_workspace_crates_with_local_packages_union() {
        // Verify that after a scan, the repo_metadata["workspace_crates"] entry
        // contains auto-detected crate names (from Cargo.toml) UNIONED with
        // any config.local_packages entries, deduplicated.
        let dir = tempdir().expect("create tempdir");
        let root = dir.path();

        // Create a minimal .git directory so WalkBuilder works
        fs::create_dir_all(root.join(".git")).unwrap();

        // Write a Cargo.toml with a crate name
        fs::write(
            root.join("Cargo.toml"),
            r#"[package]
name = "auto-detected-crate"
version = "0.1.0"
edition = "2021"
"#,
        )
        .unwrap();

        // Write a dummy Rust source file so the scanner has something to parse
        let src = root.join("src");
        fs::create_dir_all(&src).unwrap();
        fs::write(src.join("lib.rs"), "pub fn hello() {}\n").unwrap();

        let config = ScanConfig {
            local_packages: vec![
                // User types hyphens; orchestrator normalises to underscores
                "extra-package".to_owned(),
                // Duplicate of auto-detected (hyphens normalised to underscores)
                "auto_detected_crate".to_owned(),
            ],
            ..ScanConfig::default()
        };

        let db = Database::open(":memory:").expect("open DB");
        scan_project(root, &config, &db, BranchId::from("main")).expect("scan should succeed");

        // Read workspace_crates back from repo_metadata
        let meta_repo = SqliteRepoMetadataRepository::new(db.connection().clone());
        let json = meta_repo
            .get("workspace_crates")
            .expect("repo_metadata query must succeed")
            .expect("workspace_crates key must be present after scan");

        let names: Vec<String> =
            serde_json::from_str(&json).expect("workspace_crates must be valid JSON array");

        // auto-detected crate name (normalised hyphens → underscores)
        assert!(
            names.contains(&"auto_detected_crate".to_owned()),
            "auto-detected crate must be present; got {:?}",
            names
        );
        // local_packages extra entry — normalised to underscores
        assert!(
            names.contains(&"extra_package".to_owned()),
            "extra_package (normalised) from local_packages must be present; got {:?}",
            names
        );
        // Must not have duplicates
        let unique: std::collections::HashSet<_> = names.iter().collect();
        assert_eq!(
            unique.len(),
            names.len(),
            "workspace_crates must not contain duplicates; got {:?}",
            names
        );
    }

    #[test]
    fn incremental_scan_changed_paths_contains_only_modified_files() {
        let dir = create_test_project();
        let root = dir.path();
        let db = Database::open(":memory:").expect("open DB");
        let config = ScanConfig::default();

        scan_project(root, &config, &db, BranchId::from("main")).expect("first scan");

        // Modify exactly one file.
        let changed_file_abs = root.join("src/config.rs");
        fs::write(&changed_file_abs, "pub struct Config { pub extra: bool }\n").unwrap();
        // After Bug #3, paths stored in source_map / changed_paths are
        // relative to the scan root.
        let changed_file = std::path::PathBuf::from("src/config.rs");

        let r2 = scan_project(root, &config, &db, BranchId::from("main")).expect("second scan");

        // source_map must still contain ALL files.
        assert_eq!(
            r2.source_map.len(),
            r2.files_discovered,
            "source_map must contain all files even on incremental scan"
        );

        // changed_paths must contain only the modified file.
        assert_eq!(
            r2.changed_paths.len(),
            1,
            "changed_paths must contain exactly 1 file (the modified one), got: {:?}",
            r2.changed_paths
        );
        assert!(
            r2.changed_paths.contains(&changed_file),
            "changed_paths must contain the modified file {:?}, got: {:?}",
            changed_file,
            r2.changed_paths
        );

        // Unchanged files must be in source_map but NOT in changed_paths.
        for path in r2.source_map.keys() {
            if path != &changed_file {
                assert!(
                    !r2.changed_paths.contains(path),
                    "unchanged file {:?} must not be in changed_paths",
                    path
                );
            }
        }
    }
}