@mka-rainmaker/ama 0.1.0

package/dist/store/sqlite.js

@@ -0,0 +1,298 @@
+import { createRequire } from "node:module";
+// A static `import "node:sqlite"` emits its ExperimentalWarning during ESM *linking* — before
+// any module body runs, too early to filter. So this side-effect import installs the filter
+// first, and node:sqlite is loaded at runtime (below) with the filter already in place. (ama-hee)
+import "../runtime/quiet-sqlite-warning.js";
+/** node:sqlite's `DatabaseSync`, loaded at runtime (not statically) so the quiet filter imported
+ *  above is installed before its module-load ExperimentalWarning fires. (ama-hee) */
+const { DatabaseSync } = createRequire(import.meta.url)("node:sqlite");
+/**
+ * SQLite-backed graph store using Node's built-in {@link DatabaseSync} — no
+ * native dependency. Two tables (nodes, edges) mirror the in-memory store; the
+ * implicit `rowid` preserves insertion order so query results match the
+ * in-memory backend exactly (verified by the shared store contract).
+ *
+ * Pass a file path to persist across processes, or omit it for an in-memory db.
+ */
+export class SqliteStore {
+    db;
+    constructor(location = ":memory:") {
+        this.db = new DatabaseSync(location);
+        // WAL lets readers run concurrently with a writer (no-op for :memory:).
+        // synchronous=NORMAL is the safe, fast pairing with WAL; busy_timeout
+        // lets concurrent connections wait out a lock instead of failing.
+        this.db.exec(`
+      PRAGMA journal_mode = WAL;
+      PRAGMA synchronous = NORMAL;
+      PRAGMA busy_timeout = 5000;
+    `);
+        this.db.exec(`
+      CREATE TABLE IF NOT EXISTS nodes (
+        id             TEXT PRIMARY KEY,
+        kind           TEXT NOT NULL,
+        name           TEXT NOT NULL,
+        file           TEXT NOT NULL,
+        qualified_name TEXT NOT NULL,
+        start_line     INTEGER,
+        end_line       INTEGER,
+        tier           TEXT NOT NULL
+      );
+      CREATE INDEX IF NOT EXISTS nodes_name ON nodes(name);
+      CREATE TABLE IF NOT EXISTS edges (
+        from_id    TEXT NOT NULL,
+        to_id      TEXT NOT NULL,
+        kind       TEXT NOT NULL,
+        provenance TEXT,
+        at_line    INTEGER,
+        at_column  INTEGER,
+        at_sites   TEXT
+      );
+      CREATE INDEX IF NOT EXISTS edges_from ON edges(from_id);
+      CREATE INDEX IF NOT EXISTS edges_to ON edges(to_id);
+      -- (from, to, kind) identifies an edge; the unique index lets INSERT OR
+      -- IGNORE collapse the same fact emitted twice into a single row.
+      CREATE UNIQUE INDEX IF NOT EXISTS edges_unique ON edges(from_id, to_id, kind);
+      CREATE VIRTUAL TABLE IF NOT EXISTS nodes_fts USING fts5(name, id UNINDEXED);
+      CREATE TABLE IF NOT EXISTS files (
+        path     TEXT PRIMARY KEY,
+        size     INTEGER NOT NULL,
+        mtime_ms REAL NOT NULL,
+        hash     TEXT NOT NULL
+      );
+      CREATE TABLE IF NOT EXISTS meta (
+        key   TEXT PRIMARY KEY,
+        value TEXT NOT NULL
+      );
+    `);
+        // Additive migrations for DBs created before a column existed — each `ADD
+        // COLUMN` throws if present, so guard each independently (ama-m8k.1, ama-hft.9).
+        for (const ddl of [
+            "ALTER TABLE edges ADD COLUMN provenance TEXT",
+            "ALTER TABLE edges ADD COLUMN at_line INTEGER",
+            "ALTER TABLE edges ADD COLUMN at_column INTEGER",
+            "ALTER TABLE edges ADD COLUMN at_sites TEXT",
+        ]) {
+            try {
+                this.db.exec(ddl);
+            }
+            catch {
+                // Column already present — nothing to do.
+            }
+        }
+    }
+    addNode(node) {
+        this.db
+            .prepare(`INSERT OR REPLACE INTO nodes
+           (id, kind, name, file, qualified_name, start_line, end_line, tier)
+         VALUES (?, ?, ?, ?, ?, ?, ?, ?)`)
+            .run(node.id, node.kind, node.name, node.file, node.qualifiedName, node.range?.startLine ?? null, node.range?.endLine ?? null, node.tier);
+        // Keep the FTS row idempotent too: re-adding an id (a re-indexed file) must
+        // not leave a stale duplicate behind, since fts5 has no INSERT OR REPLACE.
+        this.db.prepare("DELETE FROM nodes_fts WHERE id = ?").run(node.id);
+        this.db.prepare("INSERT INTO nodes_fts (name, id) VALUES (?, ?)").run(node.name, node.id);
+    }
+    addEdge(edge) {
+        // OR IGNORE drops a duplicate (from, to, kind) via the edges_unique index.
+        this.db
+            .prepare(`INSERT OR IGNORE INTO edges (from_id, to_id, kind, provenance, at_line, at_column, at_sites)
+         VALUES (?, ?, ?, ?, ?, ?, ?)`)
+            .run(edge.from, edge.to, edge.kind, edge.provenance ?? null, edge.at?.line ?? null, edge.at?.column ?? null, edge.sites ? JSON.stringify(edge.sites) : null);
+    }
+    getNode(id) {
+        const row = this.db.prepare("SELECT * FROM nodes WHERE id = ?").get(id);
+        return row ? rowToNode(row) : undefined;
+    }
+    nodesByName(name) {
+        return this.db
+            .prepare("SELECT * FROM nodes WHERE name = ? ORDER BY rowid")
+            .all(name)
+            .map((r) => rowToNode(r));
+    }
+    searchByName(query, limit = 50) {
+        // FTS5 query syntax is permissive; restrict to identifier chars and run a
+        // prefix match. Names are single tokens, so this matches by leading prefix.
+        const term = query.replace(/[^A-Za-z0-9_]/g, " ").trim();
+        if (!term)
+            return [];
+        const seen = new Set();
+        const out = [];
+        const collect = (rows) => {
+            for (const row of rows) {
+                if (seen.has(row.id))
+                    continue;
+                seen.add(row.id);
+                const node = this.getNode(row.id);
+                if (node)
+                    out.push(node);
+            }
+        };
+        // FTS5 prefix match on the (single-token) name — fast and ranked.
+        collect(this.db
+            .prepare("SELECT id FROM nodes_fts WHERE nodes_fts MATCH ? ORDER BY rank LIMIT ?")
+            .all(`${term}*`, limit));
+        // Substring match on the qualified name, so a dotted ref ("Cls.method") and
+        // a container name resolve too — the FTS index only holds the simple name.
+        if (out.length < limit) {
+            collect(this.db
+                .prepare("SELECT id FROM nodes WHERE lower(qualified_name) LIKE ? LIMIT ?")
+                .all(`%${query.toLowerCase()}%`, limit));
+        }
+        return out.slice(0, limit);
+    }
+    edgesFrom(id, kind) {
+        const rows = kind
+            ? this.db
+                .prepare("SELECT * FROM edges WHERE from_id = ? AND kind = ? ORDER BY rowid")
+                .all(id, kind)
+            : this.db.prepare("SELECT * FROM edges WHERE from_id = ? ORDER BY rowid").all(id);
+        return rows.map((r) => rowToEdge(r));
+    }
+    edgesTo(id, kind) {
+        const rows = kind
+            ? this.db
+                .prepare("SELECT * FROM edges WHERE to_id = ? AND kind = ? ORDER BY rowid")
+                .all(id, kind)
+            : this.db.prepare("SELECT * FROM edges WHERE to_id = ? ORDER BY rowid").all(id);
+        return rows.map((r) => rowToEdge(r));
+    }
+    *allNodes() {
+        for (const row of this.db.prepare("SELECT * FROM nodes ORDER BY rowid").all()) {
+            yield rowToNode(row);
+        }
+    }
+    allEdges() {
+        return this.db
+            .prepare("SELECT * FROM edges ORDER BY rowid")
+            .all()
+            .map((r) => rowToEdge(r));
+    }
+    replaceEdgesByProvenance(provenance, edges) {
+        if (provenance === undefined)
+            this.db.prepare("DELETE FROM edges WHERE provenance IS NULL").run();
+        else
+            this.db.prepare("DELETE FROM edges WHERE provenance = ?").run(provenance);
+        for (const e of edges)
+            this.addEdge(e);
+    }
+    get nodeCount() {
+        return count(this.db, "nodes");
+    }
+    get edgeCount() {
+        return count(this.db, "edges");
+    }
+    recordFile(meta) {
+        this.db
+            .prepare(`INSERT OR REPLACE INTO files (path, size, mtime_ms, hash)
+         VALUES (?, ?, ?, ?)`)
+            .run(meta.path, meta.size, meta.mtimeMs, meta.hash);
+    }
+    getFile(path) {
+        const row = this.db.prepare("SELECT * FROM files WHERE path = ?").get(path);
+        return row ? rowToFile(row) : undefined;
+    }
+    allFiles() {
+        return this.db
+            .prepare("SELECT * FROM files ORDER BY rowid")
+            .all()
+            .map((r) => rowToFile(r));
+    }
+    removeFile(path) {
+        // Order matters: the edge/fts deletes reference the file's nodes, so they
+        // must run before the nodes themselves are gone. Edges arriving from other
+        // files (to_id in this file) are deliberately left in place.
+        const owned = "(SELECT id FROM nodes WHERE file = ?)";
+        this.db.prepare(`DELETE FROM edges WHERE from_id IN ${owned}`).run(path);
+        this.db.prepare(`DELETE FROM nodes_fts WHERE id IN ${owned}`).run(path);
+        this.db.prepare("DELETE FROM nodes WHERE file = ?").run(path);
+        this.db.prepare("DELETE FROM files WHERE path = ?").run(path);
+    }
+    reconcileFile(path, nodes, edges) {
+        const newIds = new Set(nodes.map((n) => n.id));
+        const oldIds = this.db.prepare("SELECT id FROM nodes WHERE file = ?").all(path).map((r) => r.id);
+        // 1. Drop symbols that disappeared (and the edges leaving them).
+        const delEdgesFrom = this.db.prepare("DELETE FROM edges WHERE from_id = ?");
+        const delFts = this.db.prepare("DELETE FROM nodes_fts WHERE id = ?");
+        const delNode = this.db.prepare("DELETE FROM nodes WHERE id = ?");
+        for (const id of oldIds) {
+            if (newIds.has(id))
+                continue;
+            delEdgesFrom.run(id);
+            delFts.run(id);
+            delNode.run(id);
+        }
+        // 2. Upsert the file's current nodes (addNode is idempotent).
+        for (const n of nodes)
+            this.addNode(n);
+        // 3. Reconcile the edges the file owns to exactly `edges`: delete the ones
+        //    no longer emitted, then add the rest (INSERT OR IGNORE dedupes).
+        const fresh = new Set(edges.map(edgeKey));
+        const owned = this.db
+            .prepare("SELECT from_id, to_id, kind FROM edges WHERE from_id IN (SELECT id FROM nodes WHERE file = ?)")
+            .all(path);
+        const delEdge = this.db.prepare("DELETE FROM edges WHERE from_id = ? AND to_id = ? AND kind = ?");
+        for (const e of owned) {
+            if (!fresh.has(edgeKey(rowToEdge(e))))
+                delEdge.run(e.from_id, e.to_id, e.kind);
+        }
+        for (const e of edges)
+            this.addEdge(e);
+    }
+    setMeta(key, value) {
+        this.db.prepare("INSERT OR REPLACE INTO meta (key, value) VALUES (?, ?)").run(key, value);
+    }
+    getMeta(key) {
+        const row = this.db.prepare("SELECT value FROM meta WHERE key = ?").get(key);
+        return row ? row.value : undefined;
+    }
+    clear() {
+        // Wipe data but keep the schema, so a re-index into a persistent file starts
+        // clean without dropping/recreating tables.
+        this.db.exec("DELETE FROM edges; DELETE FROM nodes_fts; DELETE FROM nodes; DELETE FROM files; DELETE FROM meta;");
+    }
+    /** Close the underlying database. Required for file-backed stores. */
+    close() {
+        this.db.close();
+    }
+}
+function rowToNode(r) {
+    const node = {
+        id: r.id,
+        kind: r.kind,
+        name: r.name,
+        file: r.file,
+        qualifiedName: r.qualified_name,
+        tier: r.tier,
+    };
+    if (r.start_line !== null && r.end_line !== null) {
+        node.range = { startLine: r.start_line, endLine: r.end_line };
+    }
+    return node;
+}
+function rowToEdge(r) {
+    const edge = { from: r.from_id, to: r.to_id, kind: r.kind };
+    if (r.provenance)
+        edge.provenance = r.provenance;
+    if (r.at_line !== null && r.at_column !== null) {
+        edge.at = { line: r.at_line, column: r.at_column };
+    }
+    if (r.at_sites)
+        edge.sites = JSON.parse(r.at_sites);
+    return edge;
+}
+/** Canonical identity of an edge: its (from, to, kind) triple, as printable JSON. */
+function edgeKey(e) {
+    return JSON.stringify([e.from, e.to, e.kind]);
+}
+function rowToFile(r) {
+    return {
+        path: r.path,
+        size: Number(r.size),
+        mtimeMs: Number(r.mtime_ms),
+        hash: r.hash,
+    };
+}
+function count(db, table) {
+    const row = db.prepare(`SELECT count(*) AS c FROM ${table}`).get();
+    return Number(row.c);
+}
+//# sourceMappingURL=sqlite.js.map

package/dist/store/sqlite.js.map

@@ -0,0 +1 @@
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package/dist/store/types.d.ts

@@ -0,0 +1,76 @@
+import type { EdgeKind, GraphEdge, GraphNode } from "../graph/index.js";
+/** Per-file fingerprint used to detect staleness for incremental re-indexing. */
+export interface FileMeta {
+    /** Repo-relative path. */
+    path: string;
+    size: number;
+    mtimeMs: number;
+    /** Content hash — the exact-change signal when size/mtime are inconclusive. */
+    hash: string;
+}
+/**
+ * Storage contract shared by every backend (in-memory today, SQLite next).
+ * The query and indexer layers depend only on this interface, so swapping the
+ * backing store never touches them.
+ */
+export interface Store {
+    addNode(node: GraphNode): void;
+    addEdge(edge: GraphEdge): void;
+    getNode(id: string): GraphNode | undefined;
+    /** Nodes whose simple (unqualified) name matches exactly. */
+    nodesByName(name: string): GraphNode[];
+    /**
+     * Symbols whose name matches `query` by prefix (case-insensitive). Backends
+     * may match more loosely (the in-memory store does substring), but every
+     * backend must at least return names the query is a prefix of.
+     */
+    searchByName(query: string, limit?: number): GraphNode[];
+    /** Edges leaving `id`, optionally filtered by kind. */
+    edgesFrom(id: string, kind?: EdgeKind): GraphEdge[];
+    /** Edges arriving at `id`, optionally filtered by kind. */
+    edgesTo(id: string, kind?: EdgeKind): GraphEdge[];
+    /** Every node — for stats and full scans. */
+    allNodes(): IterableIterator<GraphNode>;
+    /** Every edge — for whole-graph derivations (e.g. dispatch re-derivation). */
+    allEdges(): GraphEdge[];
+    /**
+     * Replace every edge with the given provenance by `edges` (drop the old, add the
+     * new). Used to re-derive a whole-graph edge class — dispatch fan-out / Overrides
+     * (provenance "dispatch") — after an incremental reindex, which a single-file
+     * analyze can't reproduce on its own. (ama-tr1)
+     */
+    replaceEdgesByProvenance(provenance: GraphEdge["provenance"], edges: GraphEdge[]): void;
+    readonly nodeCount: number;
+    readonly edgeCount: number;
+    /** Record (or replace) a file's fingerprint. */
+    recordFile(meta: FileMeta): void;
+    getFile(path: string): FileMeta | undefined;
+    allFiles(): FileMeta[];
+    /**
+     * Remove everything a file owns: its fingerprint, its nodes, and the edges
+     * that originate from those nodes. Edges owned by *other* files are left
+     * untouched — so an inbound edge may briefly dangle into a removed node until
+     * that other file is itself re-indexed. The reconcile primitive behind
+     * single-file re-indexing.
+     */
+    removeFile(path: string): void;
+    /**
+     * Apply a file's freshly-analyzed nodes and edges as a *minimal delta*: upsert
+     * its nodes, drop only the symbols that disappeared, and reconcile the edges
+     * it owns (those leaving its nodes) to exactly `edges`. Unchanged data and
+     * everything owned by other files is left in place, so an edit churns only
+     * what actually changed. Handles both creating and editing a file;
+     * {@link removeFile} handles deletion.
+     */
+    reconcileFile(path: string, nodes: GraphNode[], edges: GraphEdge[]): void;
+    /** Persist (or replace) an arbitrary string value, e.g. coverage metadata. */
+    setMeta(key: string, value: string): void;
+    getMeta(key: string): string | undefined;
+    /** Drop everything — nodes, edges, files, and metadata — for a clean rebuild
+     * of a store that may already hold a previous index (a persistent backend). */
+    clear(): void;
+    /** Release any underlying resources (a SQLite connection). A no-op for the
+     * in-memory store; call before discarding a store you replaced. */
+    close(): void;
+}
+//# sourceMappingURL=types.d.ts.map

package/dist/store/types.d.ts.map

@@ -0,0 +1 @@
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package/dist/store/types.js

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+export {};
+//# sourceMappingURL=types.js.map

package/dist/store/types.js.map

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+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../src/store/types.ts"],"names":[],"mappings":""}

package/package.json

@@ -0,0 +1,59 @@
+{
+  "name": "@mka-rainmaker/ama",
+  "version": "0.1.0",
+  "description": "Local-first code-intelligence MCP server with deep, language-specific semantic parsing.",
+  "type": "module",
+  "license": "MIT",
+  "engines": {
+    "node": ">=24"
+  },
+  "bin": {
+    "ama": "dist/cli/index.js"
+  },
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/mka-rainmaker/ama.git"
+  },
+  "homepage": "https://github.com/mka-rainmaker/ama#readme",
+  "bugs": "https://github.com/mka-rainmaker/ama/issues",
+  "keywords": [
+    "mcp",
+    "model-context-protocol",
+    "code-intelligence",
+    "code-graph",
+    "static-analysis",
+    "typescript",
+    "ai-agents",
+    "developer-tools"
+  ],
+  "files": ["dist", "README.md", "LICENSE"],
+  "publishConfig": {
+    "access": "public"
+  },
+  "scripts": {
+    "build": "tsc",
+    "typecheck": "tsc --noEmit",
+    "test": "vitest run",
+    "test:watch": "vitest",
+    "serve": "node dist/mcp/server.js",
+    "serve:http": "node dist/mcp/http.js",
+    "serve:dev": "AMA_LOG_TOOLS=1 AMA_DB=.ama/index.db AMA_ROOT=. tsx watch src/mcp/http.ts",
+    "cli": "tsx src/cli/index.ts",
+    "format": "biome format --write .",
+    "lint": "biome check .",
+    "prepublishOnly": "npm run build && npm test"
+  },
+  "dependencies": {
+    "@modelcontextprotocol/sdk": "^1.13.0",
+    "tree-sitter-wasms": "^0.1.13",
+    "typescript": "^5.8.0",
+    "web-tree-sitter": "^0.20.8",
+    "zod": "^3.24.0"
+  },
+  "devDependencies": {
+    "@biomejs/biome": "^1.9.0",
+    "@types/node": "^24.0.0",
+    "tsx": "^4.19.0",
+    "vitest": "^3.0.0"
+  }
+}