code-auditor-mcp 3.10.0 → 4.0.1

package/dist/codeIndexDB.d.ts

@@ -139,7 +139,7 @@ export declare class CodeIndexDB {
         updated: number;
         removed: number;
     } | null>;
-    bulkCleanup(): Promise<{
+    bulkCleanup(projectRoot?: string): Promise<{
         scannedCount: number;
         removedCount: number;
         removedFiles: string[];

package/dist/codeIndexDB.d.ts.map

@@ -1 +1 @@
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package/dist/codeIndexDB.js

@@ -30,6 +30,12 @@ function computeContentHash(body, signature) {
     const normalized = (body ?? '').replace(/\s+/g, ' ').trim() + '|' + (signature ?? '').trim();
     return createHash('sha256').update(normalized).digest('hex');
 }
+// ── Path containment ─────────────────────────────────────────────────────
+/** True when `filePath` is `root` itself or a descendant of `root` (not outside it). */
+function isPathUnderRoot(root, filePath) {
+    const rel = path.relative(root, filePath);
+    return rel === '' || (!rel.startsWith('..') && !path.isAbsolute(rel));
+}
 class SqliteCollectionAdapter {
     db;
     tableName;
@@ -245,7 +251,7 @@ export class CodeIndexDB {
     taskRepository = null;
     stmts = new Map();
     // ── Schema version ──────────────────────────────────────────────────
-    static SCHEMA_VERSION = 12;
+    static SCHEMA_VERSION = 16;
     constructor(dbPath = ':memory:') {
         this.dbPath = dbPath === ':memory:' ? dbPath : path.resolve(dbPath);
     }
@@ -736,6 +742,94 @@ export class CodeIndexDB {
             });
             backfill();
         }
+        // Migration 12 → 13: import_specifiers (Spec 60 — import classification at
+        // emission). One row per static import specifier occurrence, classified
+        // package / unresolved-alias / internal-resolved / internal-broken /
+        // unresolved-virtual (Spec 60.1 widened the three-class scheme to five;
+        // `classification` is free TEXT, no constraint, so no further migration).
+        // Nothing consumes it yet (Spec 61 persists edges; Spec 62 derives coverage).
+        // Flat — resolved_path inline, no lookup table, no join.
+        if (currentVersion < 13) {
+            this.db.exec(`
+        CREATE TABLE IF NOT EXISTS import_specifiers (
+          file_path       TEXT NOT NULL,
+          specifier       TEXT NOT NULL,
+          classification  TEXT NOT NULL,
+          resolved_path   TEXT,
+          line            INTEGER,
+          PRIMARY KEY (file_path, specifier, line)
+        );
+        CREATE INDEX IF NOT EXISTS idx_import_specifiers_class ON import_specifiers(classification);
+        CREATE INDEX IF NOT EXISTS idx_import_specifiers_resolved ON import_specifiers(resolved_path);
+      `);
+        }
+        // Migration 13 → 14: schema_usage identity becomes a coordinate (Spec 61
+        // Amendment A). function_name stops holding source text and becomes the
+        // nullable display name (null for anonymous handlers); identity is the
+        // inline (file_path, function_start_line, function_start_column) coordinate.
+        // function_name drops its NOT NULL so anonymous handlers store NULL, distinct
+        // from 'top-level' (function_start_line IS NULL). Old rows keep their
+        // (now-legacy) names but are regenerated on the next per-file sync.
+        if (currentVersion < 14) {
+            const suCols = this.db
+                .prepare(`PRAGMA table_info('schema_usage')`)
+                .all();
+            if (!suCols.some((c) => c.name === 'function_start_line')) {
+                this.db.exec(`
+          ALTER TABLE schema_usage RENAME TO schema_usage_old;
+          CREATE TABLE schema_usage (
+            id            INTEGER PRIMARY KEY AUTOINCREMENT,
+            schema_id     TEXT,
+            table_name    TEXT NOT NULL,
+            file_path     TEXT NOT NULL,
+            function_name TEXT,
+            function_start_line   INTEGER,
+            function_start_column INTEGER,
+            usage_type    TEXT NOT NULL,
+            line          INTEGER,
+            "column"      INTEGER,
+            raw_query     TEXT,
+            parameters    TEXT,
+            origin        TEXT,
+            recorded_at   TEXT DEFAULT (datetime('now'))
+          );
+          INSERT INTO schema_usage (id, schema_id, table_name, file_path, function_name, usage_type, line, "column", raw_query, parameters, recorded_at)
+            SELECT id, schema_id, table_name, file_path, function_name, usage_type, line, "column", raw_query, parameters, recorded_at FROM schema_usage_old;
+          DROP TABLE schema_usage_old;
+          CREATE INDEX IF NOT EXISTS idx_schema_usage_table ON schema_usage(table_name);
+          CREATE INDEX IF NOT EXISTS idx_schema_usage_file ON schema_usage(file_path);
+          CREATE INDEX IF NOT EXISTS idx_schema_usage_function ON schema_usage(function_name);
+          CREATE INDEX IF NOT EXISTS idx_schema_usage_usage_type ON schema_usage(usage_type);
+        `);
+            }
+        }
+        // Migration 14 → 15: tool's own git sha on the run (the second axis next to
+        // tool_version). `git_sha` already records the *audited project* commit; this
+        // records the *code-auditor* commit so a count change is attributable to a
+        // tool commit, not just a version. NULL when running from a published
+        // install (no .git) — best-effort, and tool_version stays always-present.
+        if (currentVersion < 15) {
+            const runCols = this.db
+                .prepare(`PRAGMA table_info('findings_ledger_runs')`)
+                .all();
+            if (!runCols.some((c) => c.name === 'tool_git_sha')) {
+                this.db.exec(`ALTER TABLE findings_ledger_runs ADD COLUMN tool_git_sha TEXT`);
+            }
+        }
+        // Migration 15 → 16: schema_usage gains an `origin` column. Rows produced by
+        // the knex-style fluent-builder read extractor carry `origin = 'query-builder'`;
+        // every other extractor (raw SQL, tagged template, .sql, ORM) leaves it NULL.
+        // The cross-domain lifecycle rules use it to exempt tables whose usage is
+        // entirely query-builder — scratch/test tables built and consumed through the
+        // fluent builder are not one-sided lifecycle defects.
+        if (currentVersion < 16) {
+            const suCols = this.db
+                .prepare(`PRAGMA table_info('schema_usage')`)
+                .all();
+            if (!suCols.some((c) => c.name === 'origin')) {
+                this.db.exec(`ALTER TABLE schema_usage ADD COLUMN origin TEXT`);
+            }
+        }
     }
     // ── SQLite schema ───────────────────────────────────────────────────
     createSchema() {
@@ -895,12 +989,15 @@ export class CodeIndexDB {
         schema_id     TEXT,
         table_name    TEXT NOT NULL,
         file_path     TEXT NOT NULL,
-        function_name TEXT NOT NULL,
+        function_name TEXT,
+        function_start_line   INTEGER,
+        function_start_column INTEGER,
         usage_type    TEXT NOT NULL,
         line          INTEGER,
         "column"      INTEGER,
         raw_query     TEXT,
         parameters    TEXT,
+        origin        TEXT,
         recorded_at   TEXT DEFAULT (datetime('now'))
       );
       CREATE INDEX IF NOT EXISTS idx_schema_usage_table ON schema_usage(table_name);
@@ -957,6 +1054,7 @@ export class CodeIndexDB {
         git_sha      TEXT,
         git_dirty    INTEGER NOT NULL DEFAULT 0,
         tool_version TEXT NOT NULL,
+        tool_git_sha TEXT,
         command      TEXT NOT NULL,
         surface      TEXT NOT NULL,
         scope        TEXT NOT NULL,
@@ -1426,10 +1524,13 @@ export class CodeIndexDB {
             dependency_depth: func.metadata?.dependencyDepth ?? 0,
             purpose: func.purpose ?? '',
             context: func.context ?? '',
-            body: func.body ?? func.metadata?.body ?? null,
-            content_hash: enhanced.content_hash ?? computeContentHash(func.body ?? func.metadata?.body, enhanced.signature),
+            body: func.body ?? null,
+            content_hash: enhanced.content_hash ?? computeContentHash(func.body, enhanced.signature),
             last_modified: lastModified ?? new Date().toISOString(),
-            metadata_json: func.metadata ? JSON.stringify(func.metadata) : '{}',
+            // body lives only in the dedicated `body` column, never in metadata_json
+            // (previously triple-stored). JSON.stringify omits the undefined value, so
+            // this strips any stray `body` key at the write boundary.
+            metadata_json: func.metadata ? JSON.stringify({ ...func.metadata, body: undefined }) : '{}',
         };
     }
     // ── Function CRUD ───────────────────────────────────────────────────
@@ -1968,19 +2069,48 @@ export class CodeIndexDB {
             throw new Error(`Failed to sync file: ${error instanceof Error ? error.message : 'Unknown error'}`);
         }
     }
-    async bulkCleanup() {
+    async bulkCleanup(projectRoot) {
         this.ensureInitialized();
         const files = this.db.prepare('SELECT DISTINCT file_path FROM functions').all();
         const removedFiles = [];
         const errors = [];
         let removedCount = 0;
         let scannedCount = 0;
-        for (const { file_path: fp } of files) {
-            scannedCount++;
+        // Reconcile against the DISCOVERY set when a project root is given. A
+        // gitignored file (corpus-expansion/, .wrangler/dist, …) is no longer source
+        // even though it still exists on disk, so `fs.access` alone would keep its
+        // stale DRY rows forever. The root is passed explicitly (never inferred from
+        // the singleton, which a long-lived MCP process could have left stale); the
+        // root-less `index cleanup` CLI / MCP cleanup tools fall back to an on-disk
+        // existence check so they still drop rows for genuinely deleted files.
+        let discovered = null;
+        if (projectRoot) {
             try {
-                await fs.access(fp);
+                discovered = new Set(await discoverFiles(projectRoot));
             }
             catch {
+                // Discovery failure → fall back to the existence check rather than
+                // deleting everything we can't enumerate.
+                discovered = null;
+            }
+        }
+        for (const { file_path: fp } of files) {
+            scannedCount++;
+            let stale = false;
+            if (discovered) {
+                // Only reconcile paths under this root: the store is project-scoped, but
+                // a shared store can hold sibling-root paths we must not delete here.
+                stale = isPathUnderRoot(projectRoot, fp) && !discovered.has(fp);
+            }
+            else {
+                try {
+                    await fs.access(fp);
+                }
+                catch {
+                    stale = true;
+                }
+            }
+            if (stale) {
                 const result = this.db.prepare('DELETE FROM functions WHERE file_path = ?').run(fp);
                 removedCount += result.changes;
                 removedFiles.push(fp);
@@ -2030,14 +2160,28 @@ export class CodeIndexDB {
                 });
             }
         }
-        // Clean up stale entries for files that no longer exist on disk
+        // Clean up stale entries: a file is stale when it is no longer in the
+        // discovery set (deleted OR gitignored since the last sync). Comparing
+        // against discovery — not `fs.access` — makes a gitignored-but-present file
+        // an orphan too, matching what discoverFiles prunes at scan time. Without a
+        // project root (files came from the index itself), fall back to the on-disk
+        // existence check.
+        const discoveredSet = projectRoot ? new Set(files) : null;
         const allIndexed = this.db.prepare('SELECT DISTINCT file_path FROM functions').all();
         for (const { file_path: fp } of allIndexed) {
-            try {
-                await fs.access(fp);
+            let stale = false;
+            if (discoveredSet) {
+                stale = isPathUnderRoot(projectRoot, fp) && !discoveredSet.has(fp);
             }
-            catch {
-                // File deleted — remove its functions
+            else {
+                try {
+                    await fs.access(fp);
+                }
+                catch {
+                    stale = true;
+                }
+            }
+            if (stale) {
                 const result = this.db.prepare('DELETE FROM functions WHERE file_path = ?').run(fp);
                 if (result.changes > 0) {
                     totalRemoved += result.changes;
@@ -2131,7 +2275,7 @@ export class CodeIndexDB {
                     const funcMeta = {
                         ...func,
                         complexity: func.complexity,
-                        content_hash: computeContentHash(func.body ?? func.metadata?.body, func.signature),
+                        content_hash: computeContentHash(func.body, func.signature),
                     };
                     const newHash = funcMeta.content_hash;
                     if (!existingRow) {
@@ -2678,12 +2822,12 @@ export class CodeIndexDB {
     }
     async recordSchemaUsage(usage, schemaId) {
         this.ensureInitialized();
-        const existing = this.db.prepare('SELECT id FROM schema_usage WHERE table_name = ? AND file_path = ? AND function_name = ? AND line = ?').get(usage.tableName, usage.filePath, usage.functionName, usage.line);
+        const existing = this.db.prepare('SELECT id FROM schema_usage WHERE table_name = ? AND file_path = ? AND function_start_line IS ? AND function_start_column IS ? AND line = ?').get(usage.tableName, usage.filePath, usage.functionStartLine ?? null, usage.functionStartColumn ?? null, usage.line);
         if (existing) {
-            this.db.prepare('UPDATE schema_usage SET schema_id = ?, usage_type = ?, "column" = ?, raw_query = ?, parameters = ?, recorded_at = ? WHERE id = ?').run(schemaId ?? 'default', usage.usageType, usage.column ?? null, usage.rawQuery ?? null, JSON.stringify(usage.parameters ?? []), new Date().toISOString(), existing.id);
+            this.db.prepare('UPDATE schema_usage SET schema_id = ?, function_name = ?, usage_type = ?, "column" = ?, raw_query = ?, parameters = ?, origin = ?, recorded_at = ? WHERE id = ?').run(schemaId ?? 'default', usage.functionName ?? null, usage.usageType, usage.column ?? null, usage.rawQuery ?? null, JSON.stringify(usage.parameters ?? []), usage.origin ?? null, new Date().toISOString(), existing.id);
         }
         else {
-            this.db.prepare('INSERT INTO schema_usage (schema_id, table_name, file_path, function_name, usage_type, line, "column", raw_query, parameters, recorded_at) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)').run(schemaId ?? 'default', usage.tableName, usage.filePath, usage.functionName, usage.usageType, usage.line ?? null, usage.column ?? null, usage.rawQuery ?? null, JSON.stringify(usage.parameters ?? []), new Date().toISOString());
+            this.db.prepare('INSERT INTO schema_usage (schema_id, table_name, file_path, function_name, function_start_line, function_start_column, usage_type, line, "column", raw_query, parameters, origin, recorded_at) VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)').run(schemaId ?? 'default', usage.tableName, usage.filePath, usage.functionName ?? null, usage.functionStartLine ?? null, usage.functionStartColumn ?? null, usage.usageType, usage.line ?? null, usage.column ?? null, usage.rawQuery ?? null, JSON.stringify(usage.parameters ?? []), usage.origin ?? null, new Date().toISOString());
         }
     }
     /**
@@ -2725,6 +2869,8 @@ export class CodeIndexDB {
             tableName: r.table_name,
             filePath: r.file_path,
             functionName: r.function_name,
+            functionStartLine: r.function_start_line,
+            functionStartColumn: r.function_start_column,
             usageType: r.usage_type,
             line: r.line,
             column: r.column,