Delete sql.js: remove db.ts, wasm, dependency, and all sql.js code paths

- Remove paperforge/plugin/src/services/db.ts (sql.js wrapper, initDatabase/searchMetadata/SearchResultItem)
- Remove paperforge/plugin/sql-wasm.wasm (644KB binary)
- Remove sql.js and @types/sql.js from package.json; npm install to update lockfile
- dashboard.ts: remove import of db.ts, remove _sqlJsInitialized/_sqlJsFailed state,
  remove the sql.js search path block entirely — all searches go straight to CLI spawn.
  Clean up stale comments.
- Bundle drops from 346KB to 167KB; 6 test files / 58 tests still pass

paperforge/plugin/package-lock.json

@@ -7,12 +7,8 @@
     "": {
       "name": "paperforge-plugin",
       "version": "1.0.0",
-      "dependencies": {
-        "sql.js": "^1.14.1"
-      },
       "devDependencies": {
         "@types/node": "^20.0.0",
-        "@types/sql.js": "^1.4.11",
         "builtin-modules": "^3.3.0",
         "esbuild": "^0.25.0",
         "husky": "^9.1.7",
@@ -1004,13 +1000,6 @@
         "@types/tern": "*"
       }
     },
-    "node_modules/@types/emscripten": {
-      "version": "1.41.5",
-      "resolved": "https://registry.npmjs.org/@types/emscripten/-/emscripten-1.41.5.tgz",
-      "integrity": "sha512-cMQm7pxu6BxtHyqJ7mQZ2kXWV5SLmugybFdHCBbJ5eHzOo6VhBckEgAT3//rP5FwPHNPeEiq4SmQ5ucBwsOo4Q==",
-      "dev": true,
-      "license": "MIT"
-    },
     "node_modules/@types/estree": {
       "version": "1.0.9",
       "resolved": "https://registry.npmjs.org/@types/estree/-/estree-1.0.9.tgz",
@@ -1029,17 +1018,6 @@
         "undici-types": "~6.21.0"
       }
     },
-    "node_modules/@types/sql.js": {
-      "version": "1.4.11",
-      "resolved": "https://registry.npmjs.org/@types/sql.js/-/sql.js-1.4.11.tgz",
-      "integrity": "sha512-QXIx38p2ZThJaK9vP5ZdqdlRe1FG9I8SmCZOS7FHfB/2qPAjZwkL7/vlfPg6N/oWHuuOaGg/P/IRwfP2W0kWVQ==",
-      "dev": true,
-      "license": "MIT",
-      "dependencies": {
-        "@types/emscripten": "*",
-        "@types/node": "*"
-      }
-    },
     "node_modules/@types/tern": {
       "version": "0.23.9",
       "resolved": "https://registry.npmjs.org/@types/tern/-/tern-0.23.9.tgz",
@@ -2439,12 +2417,6 @@
         "node": ">=0.10.0"
       }
     },
-    "node_modules/sql.js": {
-      "version": "1.14.1",
-      "resolved": "https://registry.npmjs.org/sql.js/-/sql.js-1.14.1.tgz",
-      "integrity": "sha512-gcj8zBWU5cFsi9WUP+4bFNXAyF1iRpA3LLyS/DP5xlrNzGmPIizUeBggKa8DbDwdqaKwUcTEnChtd2grWo/x/A==",
-      "license": "MIT"
-    },
     "node_modules/stackback": {
       "version": "0.0.2",
       "resolved": "https://registry.npmjs.org/stackback/-/stackback-0.0.2.tgz",

paperforge/plugin/package.json

@@ -13,7 +13,6 @@
   },
   "devDependencies": {
     "@types/node": "^20.0.0",
-    "@types/sql.js": "^1.4.11",
     "builtin-modules": "^3.3.0",
     "esbuild": "^0.25.0",
     "husky": "^9.1.7",
@@ -24,8 +23,5 @@
     "prettier": "^3.8.4",
     "typescript": "^5.4.0",
     "vitest": "^2.1.0"
-  },
-  "dependencies": {
-    "sql.js": "^1.14.1"
   }
 }

paperforge/plugin/src/services/db.ts

@@ -1,119 +0,0 @@
-import * as fs from "fs";
-import * as path from "path";
-import initSqlJs from "sql.js";
-import type {
-  Database as SqlJsDatabase,
-  Statement as SqlJsStatement,
-  SqlValue,
-} from "sql.js";
-
-// ── Types ──
-
-export interface SearchResultItem {
-  zotero_key: string;
-  title: string;
-  first_author: string;
-  year: string;
-  journal: string;
-  domain: string;
-  abstract: string;
-  rank: number;
-}
-
-// ── Module-level state (lazy init) ──
-
-let _db: SqlJsDatabase | null = null;
-let _queryStmt: SqlJsStatement | null = null;
-
-// ── FTS5 query transform ──
-// FTS5 requires explicit operators between terms: "rotator cuff" → "rotator AND cuff"
-// Quoted phrases like '"rotator cuff"' are passed through verbatim.
-
-function transformFtsQuery(input: string): string {
-  input = input.trim();
-  if (!input) return "";
-
-  // Already a quoted phrase — pass through as-is
-  if (input.startsWith('"') && input.endsWith('"')) {
-    return input;
-  }
-
-  const terms = input.split(/\s+/).filter(Boolean);
-  if (terms.length === 0) return "";
-  return terms.join(" AND ");
-}
-
-// ── Database init (lazy) ──
-
-function sqlValueToString(v: SqlValue): string {
-  if (v === null || v === undefined) return "";
-  if (typeof v === "string") return v;
-  if (v instanceof Uint8Array) return new TextDecoder().decode(v);
-  return String(v);
-}
-
-function sqlValueToNumber(v: SqlValue): number {
-  if (v === null || v === undefined) return 0;
-  if (typeof v === "number") return v;
-  return Number(v);
-}
-
-export async function initDatabase(vaultPath: string): Promise<void> {
-  const dbPath = path.join(
-    vaultPath,
-    "System",
-    "PaperForge",
-    "indexes",
-    "paperforge.db"
-  );
-
-  if (!fs.existsSync(dbPath)) {
-    throw new Error(`PaperForge database not found at ${dbPath}`);
-  }
-
-  const SQL = await initSqlJs({
-    locateFile: (file: string) => path.join(__dirname, file),
-  });
-
-  const buffer = fs.readFileSync(dbPath);
-  _db = new SQL.Database(new Uint8Array(buffer));
-
-  _queryStmt = _db.prepare(
-    `SELECT zotero_key, title, first_author, year, journal, domain, abstract, rank
-     FROM paper_fts
-     WHERE paper_fts MATCH ?
-     ORDER BY rank
-     LIMIT ?`
-  );
-}
-
-// ── Search ──
-
-export function searchMetadata(
-  query: string,
-  limit: number = 20
-): SearchResultItem[] | null {
-  if (!_db || !_queryStmt) return null;
-
-  const transformed = transformFtsQuery(query);
-  if (!transformed) return [];
-
-  _queryStmt.bind([transformed, limit]);
-
-  const results: SearchResultItem[] = [];
-  while (_queryStmt.step()) {
-    const row = _queryStmt.getAsObject();
-    results.push({
-      zotero_key: sqlValueToString(row.zotero_key),
-      title: sqlValueToString(row.title),
-      first_author: sqlValueToString(row.first_author),
-      year: sqlValueToString(row.year),
-      journal: sqlValueToString(row.journal),
-      domain: sqlValueToString(row.domain),
-      abstract: sqlValueToString(row.abstract),
-      rank: sqlValueToNumber(row.rank),
-    });
-  }
-  _queryStmt.reset();
-  return results;
-}

paperforge/plugin/src/views/dashboard.ts

@@ -51,11 +51,6 @@ import {
   restoreVersion,
   compareVersions,
 } from "../services/version-history";
-import {
-  initDatabase,
-  searchMetadata,
-  type SearchResultItem,
-} from "../services/db";
 
 // ── Interface for plugin ref used by static open ──
 
@@ -101,8 +96,6 @@ export class PaperForgeStatusView extends ItemView {
   _searchInput: HTMLInputElement | null = null;
   _searchResultsEl: HTMLElement | null = null;
   _searchTimer: ReturnType<typeof setTimeout> | undefined = undefined;
-  _sqlJsInitialized: boolean = false;
-  _sqlJsFailed: boolean = false;
 
   constructor(leaf: WorkspaceLeaf) {
     super(leaf);
@@ -2396,7 +2389,7 @@ export class PaperForgeStatusView extends ItemView {
       cls: "paperforge-search-results",
     });
 
-    // Detect @ mode prefix + debounced metadata search via sql.js
+    // Detect @ mode prefix + debounced metadata search
     this._searchInput.addEventListener("input", () => {
       const val = this._searchInput?.value || "";
       if (val.startsWith("@") && !val.startsWith("@ ")) {
@@ -2411,7 +2404,7 @@ export class PaperForgeStatusView extends ItemView {
       // Debounced metadata search for non-@ queries
       if (!val.startsWith("@") && val.trim()) {
         this._searchTimer = setTimeout(() => {
-          this.executeSearch({ source: "sqljs" });
+          this.executeSearch();
         }, 200);
       }
     });
@@ -2424,12 +2417,12 @@ export class PaperForgeStatusView extends ItemView {
           clearTimeout(this._searchTimer);
           this._searchTimer = undefined;
         }
-        this.executeSearch({ source: "cli" });
+        this.executeSearch();
       }
     });
   }
 
-  async executeSearch(options: { source?: "auto" | "cli" | "sqljs" } = {}) {
+  async executeSearch() {
     if (!this._searchInput || !this._searchResultsEl) return;
     const raw = this._searchInput.value.trim();
     if (!raw) return;
@@ -2440,7 +2433,7 @@ export class PaperForgeStatusView extends ItemView {
 
     const mode = isDeep ? "retrieve" : "search";
 
-    // Resolve vault path (used by both sql.js and CLI paths)
+    // Resolve vault path for CLI search
     const adapter = this.app.vault.adapter;
     let vaultPath = "";
     if (adapter && typeof adapter === "object" && "basePath" in adapter) {
@@ -2449,34 +2442,7 @@ export class PaperForgeStatusView extends ItemView {
     }
 
     this._searchResultsEl.empty();
-
-    // ── sql.js metadata search path (non-@ queries only) ──
-    if (
-      mode === "search" &&
-      (options.source === "auto" || options.source === "sqljs")
-    ) {
-      if (vaultPath) {
-        try {
-          if (!this._sqlJsInitialized && !this._sqlJsFailed) {
-            await initDatabase(vaultPath);
-            this._sqlJsInitialized = true;
-          }
-          if (this._sqlJsInitialized) {
-            const results = searchMetadata(query, 20);
-            if (results !== null) {
-              this.renderSearchResults(results, false);
-              return;
-            }
-          }
-        } catch (e) {
-          console.error("PaperForge sql.js search failed:", e);
-          this._sqlJsFailed = true;
-        }
-      }
-      // sql.js unavailable — fall through to CLI
-    }
-
-    // ── CLI search path (deep search or sql.js fallback) ──
+    // ── CLI search path (deep search only) ──
     this._searchResultsEl.createEl("div", {
       cls: "paperforge-search-loading",
       text: "Searching...",
@@ -2515,10 +2481,10 @@ export class PaperForgeStatusView extends ItemView {
         undefined,
         undefined
       );
-
+    const deepFlag = mode === "retrieve" ? ["--deep"] : [];
     const child = spawn(
       pythonExe,
-      [...pyExtra, "-m", "paperforge", mode, query, "--json"],
+      [...pyExtra, "-m", "paperforge", mode, query, ...deepFlag, "--json"],
       { cwd: vaultPath, timeout: 30000 }
     );
 
@@ -2561,11 +2527,9 @@ export class PaperForgeStatusView extends ItemView {
           const d = (parsed as Record<string, unknown>).data;
           if (d && typeof d === "object") {
             const dd = d as Record<string, unknown>;
-            // search output: data.matches
+            // Unified PFResult v1: data.matches
             if ("matches" in dd && Array.isArray(dd.matches)) {
               results = dd.matches as unknown[];
-            } else if ("results" in dd && Array.isArray(dd.results)) {
-              results = dd.results as unknown[];
             }
           }
         }
@@ -2674,21 +2638,10 @@ export class PaperForgeStatusView extends ItemView {
         cls: "paperforge-search-result-meta",
       });
 
-      if (typeof rec["authors"] === "string") {
+      if (typeof rec["first_author"] === "string" && rec["first_author"]) {
         meta.createEl("span", {
           cls: "paperforge-search-result-author",
-          text: rec["authors"],
-        });
-      } else if (Array.isArray(rec["authors"])) {
-        meta.createEl("span", {
-          cls: "paperforge-search-result-author",
-          text: (rec["authors"] as string[]).slice(0, 3).join("; "),
-        });
-      }
-      if (typeof rec["year"] === "number" || typeof rec["year"] === "string") {
-        meta.createEl("span", {
-          cls: "paperforge-search-result-year",
-          text: String(rec["year"]),
+          text: rec["first_author"],
         });
       }
       if (typeof rec["journal"] === "string" && rec["journal"]) {
@@ -2727,10 +2680,10 @@ export class PaperForgeStatusView extends ItemView {
       // @ mode: matched text
       if (
         isDeep &&
-        typeof rec["matched_text"] === "string" &&
-        rec["matched_text"]
+        typeof rec["text"] === "string" &&
+        rec["text"]
       ) {
-        const mt = rec["matched_text"] as string;
+        const mt = rec["text"] as string;
         card.createEl("div", {
           cls: "paperforge-search-result-source",
           text: mt.length > 300 ? mt.slice(0, 300) + "..." : mt,