cgraphx 1.4.3 → 2.0.0

package/dist/core/db/index.js

@@ -0,0 +1,260 @@
+"use strict";
+/**
+ * Database Base Layer
+ *
+ * SQLite connection management over the built-in `node:sqlite`. This is the
+ * shared, SCHEMA-AGNOSTIC base layer: `open()` creates (or opens) `cgraphx.db`
+ * and applies connection-level PRAGMAs, but applies NO schema and runs NO
+ * migrations. Subsystems that need tables (markdown, timeline) own their own
+ * `ensureSchema` and apply it on top of a connection from `open()`.
+ *
+ * What was removed vs. the cgraphx 1.x lineage:
+ *   - the graph `schema.sql` application (this layer serves non-graph subsystems)
+ *   - `runMigrations` / `getCurrentVersion` / `CURRENT_SCHEMA_VERSION`
+ *   - the `initialize()` factory (open() now creates-or-opens) and
+ *     `getSchemaVersion()` (no shared `schema_versions` table at this layer)
+ */
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.DATABASE_FILENAME = exports.DatabaseConnection = void 0;
+exports.getDatabasePath = getDatabasePath;
+const sqlite_adapter_1 = require("./sqlite-adapter");
+const fs = __importStar(require("fs"));
+const path = __importStar(require("path"));
+const directory_1 = require("../directory");
+/**
+ * Apply connection-level PRAGMAs.
+ *
+ * `busy_timeout` is set FIRST, before any pragma that might touch the database
+ * file (notably `journal_mode`). If another process holds a write lock at open
+ * time, the later pragmas — and the connection's first query — then wait out
+ * the lock instead of throwing "database is locked" immediately.
+ *
+ * The 5s window rides out a normal write; with WAL, reads never block on a
+ * writer, so this timeout only governs cross-process write contention.
+ */
+function configureConnection(db) {
+    db.pragma('busy_timeout = 5000'); // MUST be first — see above
+    db.pragma('foreign_keys = ON');
+    db.pragma('journal_mode = WAL'); // node:sqlite supports WAL on every platform
+    db.pragma('synchronous = NORMAL'); // safe with WAL mode
+    db.pragma('cache_size = -64000'); // 64 MB page cache
+    db.pragma('temp_store = MEMORY'); // temp tables in memory
+    db.pragma('mmap_size = 268435456'); // 256 MB memory-mapped I/O
+}
+/**
+ * Database connection wrapper with lifecycle management. Schema-agnostic — no
+ * table is assumed to exist. Use `open()` to get a connection, then have the
+ * caller apply its own schema if it needs tables.
+ */
+class DatabaseConnection {
+    db;
+    dbPath;
+    backend;
+    /**
+     * `dev:ino` of the DB file at the moment we opened it (or null when the
+     * platform/filesystem reports no usable inode). Lets us notice when the file
+     * we hold open has been unlinked and REPLACED by a new file at the same path
+     * — `.cgraphx/` deleted and re-`init`ed under a long-lived process — at which
+     * point our fd reads a now-dead inode forever. See `isReplacedOnDisk`.
+     */
+    openedInode;
+    constructor(db, dbPath, backend) {
+        this.db = db;
+        this.dbPath = dbPath;
+        this.backend = backend;
+        this.openedInode = statInode(dbPath);
+    }
+    /**
+     * Open a database at `dbPath`, creating it (and its parent directory) if
+     * missing. Applies connection PRAGMAs. Applies NO schema and runs NO
+     * migrations — callers that need tables apply their own `ensureSchema`.
+     */
+    static open(dbPath) {
+        // Ensure parent directory exists so a first-run db can be created.
+        const dir = path.dirname(dbPath);
+        if (!fs.existsSync(dir)) {
+            fs.mkdirSync(dir, { recursive: true });
+        }
+        const { db, backend } = (0, sqlite_adapter_1.createDatabase)(dbPath);
+        configureConnection(db);
+        return new DatabaseConnection(db, dbPath, backend);
+    }
+    /**
+     * Get the underlying database instance
+     */
+    getDb() {
+        return this.db;
+    }
+    /**
+     * Get the SQLite backend serving this connection. Per-instance so
+     * cross-project queries report the right backend even when multiple project
+     * DBs are open in the same process.
+     */
+    getBackend() {
+        return this.backend;
+    }
+    /**
+     * Get database file path
+     */
+    getPath() {
+        return this.dbPath;
+    }
+    /**
+     * The journal mode actually in effect (e.g. 'wal', 'delete').
+     *
+     * SQLite silently keeps the prior mode if WAL can't be enabled — e.g. on
+     * filesystems without shared-memory support (some network/virtualized mounts,
+     * WSL2 /mnt). So the effective mode can differ from what
+     * `configureConnection` requested. Surfaced in `cgraphx status` so a
+     * "database is locked" report is triageable: 'wal' ⇒ readers never block on
+     * a writer; anything else ⇒ they can.
+     */
+    getJournalMode() {
+        const raw = this.db.pragma('journal_mode');
+        const row = Array.isArray(raw) ? raw[0] : raw;
+        const mode = row && typeof row === 'object'
+            ? row.journal_mode
+            : row;
+        return String(mode ?? '').toLowerCase();
+    }
+    /**
+     * Execute a function within a transaction
+     */
+    transaction(fn) {
+        return this.db.transaction(fn)();
+    }
+    /**
+     * Get database file size in bytes
+     */
+    getSize() {
+        const stats = fs.statSync(this.dbPath);
+        return stats.size;
+    }
+    /**
+     * Optimize database (vacuum and analyze)
+     */
+    optimize() {
+        this.db.exec('VACUUM');
+        this.db.exec('ANALYZE');
+    }
+    /**
+     * Lightweight, non-blocking maintenance to run after bulk writes. Two
+     * operations:
+     *
+     *   - `PRAGMA optimize` — incremental ANALYZE; SQLite only re-analyzes tables
+     *     whose row counts changed materially since the last ANALYZE.
+     *
+     *   - `PRAGMA wal_checkpoint(PASSIVE)` — fold pending WAL pages back into the
+     *     main database file so the WAL file doesn't grow unboundedly between
+     *     automatic checkpoints.
+     *
+     * Both operations are silently swallowed on failure — they're a best-effort
+     * optimization, never load-bearing for correctness.
+     */
+    runMaintenance() {
+        try {
+            this.db.exec('PRAGMA optimize');
+        }
+        catch {
+            // ignore
+        }
+        try {
+            this.db.exec('PRAGMA wal_checkpoint(PASSIVE)');
+        }
+        catch {
+            // ignore (e.g., not in WAL mode)
+        }
+    }
+    /**
+     * Close the database connection
+     */
+    close() {
+        this.db.close();
+    }
+    /**
+     * Check if the database connection is open
+     */
+    isOpen() {
+        return this.db.open;
+    }
+    /**
+     * True when the DB file at our path has been REPLACED on disk since we opened
+     * it — a different inode now lives at the same path, so the fd we still hold
+     * points at a now-unlinked inode that can never receive new writes. The
+     * trigger is removing and recreating `.cgraphx/` at the same path under a
+     * long-lived process (`rm -rf .cgraphx` + `cgraphx init`). Returns false when
+     * the inode is unchanged, when the file is momentarily absent (mid-recreate —
+     * nothing to reopen onto yet), or when the platform doesn't report a usable
+     * inode (Windows can't unlink an open file and its st_ino is unreliable, so
+     * this never fires there).
+     */
+    isReplacedOnDisk() {
+        if (this.openedInode === null)
+            return false;
+        const current = statInode(this.dbPath);
+        return current !== null && current !== this.openedInode;
+    }
+}
+exports.DatabaseConnection = DatabaseConnection;
+/**
+ * `dev:ino` for a path, or null if it can't be stat'd or the platform doesn't
+ * report a usable inode. Windows st_ino is unreliable across handle reopens, so
+ * we deliberately return null there — the deleted-but-open-inode hazard this
+ * guards is a POSIX file-semantics issue that doesn't arise on Windows (an open
+ * file can't be unlinked).
+ */
+function statInode(p) {
+    if (process.platform === 'win32')
+        return null;
+    try {
+        const s = fs.statSync(p);
+        return `${s.dev}:${s.ino}`;
+    }
+    catch {
+        return null;
+    }
+}
+/**
+ * Default database filename
+ */
+exports.DATABASE_FILENAME = 'cgraphx.db';
+/**
+ * Get the default database path for a project
+ */
+function getDatabasePath(projectRoot) {
+    return path.join((0, directory_1.getCodeGraphDir)(projectRoot), exports.DATABASE_FILENAME);
+}
+//# sourceMappingURL=index.js.map

package/dist/core/db/index.js.map

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package/dist/core/db/migrate.d.ts

@@ -0,0 +1,29 @@
+/**
+ * One-time data migrations for the shared `.cgraphx/cgraphx.db`.
+ *
+ * 2.0 removed the code-graph layer that gave cgraphx its 1.x name. Projects
+ * initialized under 1.x still carry the graph tables — now orphaned, and often
+ * large: `nodes` / `edges` / `files` / `unresolved_refs`, the `nodes_fts` FTS5
+ * index (and its shadow tables), plus the graph layer's `project_metadata` and
+ * bare `schema_versions`. `dropLegacyGraphTables` removes exactly those,
+ * preserving the 2.0 `markdown_*` / `timeline_*` data (2.0 versioning uses the
+ * prefixed `markdown_schema_versions` / `timeline_schema_versions`, never the
+ * bare `schema_versions`).
+ */
+export interface LegacyGraphCleanup {
+    /** Graph tables that actually existed and were dropped. */
+    dropped: string[];
+}
+/**
+ * Drop the orphaned 1.x code-graph tables from a project's `.cgraphx/cgraphx.db`.
+ *
+ * Idempotent and cheap — a no-op once the tables are gone, and a no-op for
+ * projects 2.0 created (they never had them). Only the known graph table names
+ * are ever dropped (never a blanket "drop everything non-2.0"), so current and
+ * future `markdown_*` / `timeline_*` / subsystem tables are safe.
+ *
+ * @returns The graph tables that were present and dropped (empty when none,
+ *          or when the project has no `.cgraphx/cgraphx.db` yet).
+ */
+export declare function dropLegacyGraphTables(projectRoot: string): LegacyGraphCleanup;
+//# sourceMappingURL=migrate.d.ts.map

package/dist/core/db/migrate.d.ts.map

@@ -0,0 +1 @@
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package/dist/core/db/migrate.js

@@ -0,0 +1,100 @@
+"use strict";
+/**
+ * One-time data migrations for the shared `.cgraphx/cgraphx.db`.
+ *
+ * 2.0 removed the code-graph layer that gave cgraphx its 1.x name. Projects
+ * initialized under 1.x still carry the graph tables — now orphaned, and often
+ * large: `nodes` / `edges` / `files` / `unresolved_refs`, the `nodes_fts` FTS5
+ * index (and its shadow tables), plus the graph layer's `project_metadata` and
+ * bare `schema_versions`. `dropLegacyGraphTables` removes exactly those,
+ * preserving the 2.0 `markdown_*` / `timeline_*` data (2.0 versioning uses the
+ * prefixed `markdown_schema_versions` / `timeline_schema_versions`, never the
+ * bare `schema_versions`).
+ */
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.dropLegacyGraphTables = dropLegacyGraphTables;
+const fs = __importStar(require("fs"));
+const index_1 = require("./index");
+/**
+ * The 1.x code-graph tables, orphaned by the 2.0 rebuild (from the removed
+ * `src/db/schema.sql`). `nodes_fts` is an FTS5 virtual table — listed FIRST so
+ * it's dropped before its content table (`nodes`); DROP TABLE on it cascades to
+ * its shadow tables (nodes_fts_data / _idx / _content / _docsize / _config).
+ */
+const LEGACY_GRAPH_TABLES = [
+    'nodes_fts',
+    'nodes',
+    'edges',
+    'files',
+    'unresolved_refs',
+    'project_metadata',
+    'schema_versions',
+];
+/**
+ * Drop the orphaned 1.x code-graph tables from a project's `.cgraphx/cgraphx.db`.
+ *
+ * Idempotent and cheap — a no-op once the tables are gone, and a no-op for
+ * projects 2.0 created (they never had them). Only the known graph table names
+ * are ever dropped (never a blanket "drop everything non-2.0"), so current and
+ * future `markdown_*` / `timeline_*` / subsystem tables are safe.
+ *
+ * @returns The graph tables that were present and dropped (empty when none,
+ *          or when the project has no `.cgraphx/cgraphx.db` yet).
+ */
+function dropLegacyGraphTables(projectRoot) {
+    const dbPath = (0, index_1.getDatabasePath)(projectRoot);
+    if (!fs.existsSync(dbPath))
+        return { dropped: [] };
+    const conn = index_1.DatabaseConnection.open(dbPath);
+    try {
+        const db = conn.getDb();
+        const dropped = [];
+        for (const table of LEGACY_GRAPH_TABLES) {
+            // `table` comes from the fixed LEGACY_GRAPH_TABLES const — safe to inline
+            // (no user input, no injection surface).
+            const row = db.prepare(`SELECT name FROM sqlite_master WHERE type = 'table' AND name = '${table}'`).get();
+            if (row) {
+                db.prepare(`DROP TABLE "${table}"`).run();
+                dropped.push(table);
+            }
+        }
+        return { dropped };
+    }
+    finally {
+        conn.close();
+    }
+}
+//# sourceMappingURL=migrate.js.map

package/dist/core/db/migrate.js.map

@@ -0,0 +1 @@
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package/dist/core/db/sqlite-adapter.d.ts

@@ -0,0 +1,51 @@
+/**
+ * SQLite Adapter
+ *
+ * Thin wrapper over Node's built-in `node:sqlite` (`DatabaseSync`), exposed
+ * through a small better-sqlite3-shaped interface so the rest of the codebase
+ * is storage-agnostic.
+ *
+ * cgraphx runs on Node >= 22.5, so `node:sqlite` (real SQLite, with WAL + FTS5)
+ * is always available — there is no native build step and no wasm fallback.
+ */
+export interface SqliteStatement {
+    run(...params: any[]): {
+        changes: number;
+        lastInsertRowid: number | bigint;
+    };
+    get(...params: any[]): any;
+    all(...params: any[]): any[];
+    /**
+     * Lazily yield result rows one at a time instead of materializing the whole
+     * set with `all()`. Use for unbounded scans so memory stays O(1) in the row
+     * count rather than O(rows).
+     */
+    iterate(...params: any[]): IterableIterator<any>;
+}
+export interface SqliteDatabase {
+    prepare(sql: string): SqliteStatement;
+    exec(sql: string): void;
+    pragma(str: string, options?: {
+        simple?: boolean;
+    }): any;
+    transaction<T>(fn: (...args: any[]) => T): (...args: any[]) => T;
+    close(): void;
+    readonly open: boolean;
+}
+/**
+ * The active SQLite backend. Only one now (`node:sqlite`); kept as a named type
+ * so `cgraphx status` and the per-instance reporting have a stable shape.
+ */
+export type SqliteBackend = 'node-sqlite';
+/**
+ * Create a database connection backed by `node:sqlite`.
+ *
+ * Returns the active backend alongside the db so each `DatabaseConnection` can
+ * report it per-instance — multiple project DBs can be open in one process, so
+ * a process-global would race.
+ */
+export declare function createDatabase(dbPath: string): {
+    db: SqliteDatabase;
+    backend: SqliteBackend;
+};
+//# sourceMappingURL=sqlite-adapter.d.ts.map

package/dist/core/db/sqlite-adapter.d.ts.map

@@ -0,0 +1 @@
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package/dist/core/db/sqlite-adapter.js

@@ -0,0 +1,116 @@
+"use strict";
+/**
+ * SQLite Adapter
+ *
+ * Thin wrapper over Node's built-in `node:sqlite` (`DatabaseSync`), exposed
+ * through a small better-sqlite3-shaped interface so the rest of the codebase
+ * is storage-agnostic.
+ *
+ * cgraphx runs on Node >= 22.5, so `node:sqlite` (real SQLite, with WAL + FTS5)
+ * is always available — there is no native build step and no wasm fallback.
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.createDatabase = createDatabase;
+/**
+ * Wraps Node's built-in `node:sqlite` (`DatabaseSync`) to match the
+ * better-sqlite3 interface the rest of the code expects.
+ *
+ * node:sqlite is real SQLite compiled into Node, so it supports WAL, FTS5,
+ * mmap, and `@named` params natively — the only shims needed are the
+ * better-sqlite3 conveniences node:sqlite omits: a `.pragma()` helper, a
+ * `.transaction()` helper, and `open` (node:sqlite exposes `isOpen`).
+ */
+class NodeSqliteAdapter {
+    _db;
+    constructor(dbPath) {
+        // eslint-disable-next-line @typescript-eslint/no-require-imports
+        const { DatabaseSync } = require('node:sqlite');
+        this._db = new DatabaseSync(dbPath);
+    }
+    get open() {
+        return this._db.isOpen;
+    }
+    prepare(sql) {
+        // node:sqlite matches better-sqlite3's calling convention (variadic
+        // positional args, or a single object for @named params), so params forward
+        // through unchanged.
+        const stmt = this._db.prepare(sql);
+        return {
+            run(...params) {
+                const r = stmt.run(...params);
+                return {
+                    changes: Number(r?.changes ?? 0),
+                    lastInsertRowid: r?.lastInsertRowid ?? 0,
+                };
+            },
+            get(...params) {
+                return stmt.get(...params);
+            },
+            all(...params) {
+                return stmt.all(...params);
+            },
+            iterate(...params) {
+                return stmt.iterate(...params);
+            },
+        };
+    }
+    exec(sql) {
+        this._db.exec(sql);
+    }
+    pragma(str, options) {
+        const trimmed = str.trim();
+        // Write pragma ("key = value"): node:sqlite is real SQLite, so every pragma
+        // (WAL, mmap, synchronous, …) applies as-is.
+        if (trimmed.includes('=')) {
+            this._db.exec(`PRAGMA ${trimmed}`);
+            return;
+        }
+        // Read pragma. Default: the row object (e.g. { journal_mode: 'wal' }).
+        // `{ simple: true }` returns just the single column value, like better-sqlite3.
+        const row = this._db.prepare(`PRAGMA ${trimmed}`).get();
+        if (options?.simple) {
+            return row && typeof row === 'object' ? Object.values(row)[0] : row;
+        }
+        return row;
+    }
+    transaction(fn) {
+        return (...args) => {
+            this._db.exec('BEGIN');
+            try {
+                const result = fn(...args);
+                this._db.exec('COMMIT');
+                return result;
+            }
+            catch (error) {
+                this._db.exec('ROLLBACK');
+                throw error;
+            }
+        };
+    }
+    close() {
+        // node:sqlite's DatabaseSync.close() throws if already closed; make it
+        // idempotent to match better-sqlite3 (callers may close more than once).
+        if (this._db.isOpen)
+            this._db.close();
+    }
+}
+/**
+ * Create a database connection backed by `node:sqlite`.
+ *
+ * Returns the active backend alongside the db so each `DatabaseConnection` can
+ * report it per-instance — multiple project DBs can be open in one process, so
+ * a process-global would race.
+ */
+function createDatabase(dbPath) {
+    try {
+        return { db: new NodeSqliteAdapter(dbPath), backend: 'node-sqlite' };
+    }
+    catch (error) {
+        const msg = error instanceof Error ? error.message : String(error);
+        throw new Error('Failed to open SQLite via the built-in node:sqlite module.\n' +
+            'cgraphx requires node:sqlite (Node.js 22.5+). Install the self-contained\n' +
+            'cgraphx release (it bundles a compatible Node), or run on Node 22.5+.\n' +
+            `Underlying error: ${msg}`);
+    }
+}
+//# sourceMappingURL=sqlite-adapter.js.map

package/dist/core/db/sqlite-adapter.js.map

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package/dist/core/dbquery/cli.d.ts

@@ -0,0 +1,17 @@
+/**
+ * CLI wiring for the db-query subsystem.
+ *
+ * Exposes `registerDbCommands(program)` — called once from
+ * `src/cli/index.ts`. All db subcommands live under `cgraphx db <sub>`
+ * and are implemented in this file. Spec §5.2.
+ *
+ * Exit codes (spec §5.2):
+ *   0  success
+ *   2  config error (no profile / bad JSON / missing field)
+ *   3  safety rejection (write keyword / multi-statement)
+ *   4  connection failed / timeout / disabled
+ *   5  argument error (unknown mode, etc.)
+ */
+import type { Command } from 'commander';
+export declare function registerDbCommands(program: Command): void;
+//# sourceMappingURL=cli.d.ts.map

package/dist/core/dbquery/cli.d.ts.map

@@ -0,0 +1 @@
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