@tiagojct/subsub 0.10.0 → 0.11.0

package/README.md

@@ -17,7 +17,7 @@ A Zotero librarian and research assistant that runs on your computer, in your br
 
 * **Code-Enforced Safety Gate**: The model **cannot** modify your library without your explicit approval. Every change is calculated first as a dry-run preview (+added in green, -removed in red) and executed only when you confirm.
 * **Full Journal & Reversible Edits**: Every library modification is recorded with a unique journal ID and can be reverted anytime using `/undo`.
-* **One assistant, one switch**: Sub-Sub reads items, searches PubMed, Europe PMC and OpenAlex, finds gaps, checks citations in manuscripts and writes Markdown notes in your Sub-Sub folder (it can sit inside an Obsidian vault). With **library changes** on (the default), it also tags, imports by DOI, PMID or ISBN, repairs metadata, finds duplicates, attaches open-access PDFs and checks retractions, in the same conversation. Turn library changes off (`/library off`, or the switch in the browser view) to read only.
+* **Two modes**: The **Researcher** (the default) reads items, searches PubMed, Europe PMC and OpenAlex, finds gaps, checks citations in manuscripts and writes Markdown notes in your Sub-Sub folder (it can sit inside an Obsidian vault). It also does everything the Librarian does, so you can research a topic and import and tag what you find in the same conversation. The **Librarian** manages the library only: it tags, imports by DOI, PMID or ISBN, repairs metadata, finds duplicates, attaches open-access PDFs and checks retractions. It has no search tools; use it with a fast, cheap model for tagging sessions. Each mode can have its own model. In both modes, every library change needs your approval.
 * **Local & Private**: Listens strictly on `127.0.0.1` protected by an authenticated single-origin session cookie. Your library contents remain on your computer.
 * **Modern Web Interface & Terminal UI**: Use Sub-Sub in your browser with desktop shortcuts (`~/Applications/Sub-Sub.app`, Start menu, or `.desktop`), or launch it right in your terminal with adaptive color themes.
 
@@ -104,7 +104,7 @@ Starting Sub-Sub with `subsub web` (or `subsub serve`) launches the browser appl
 
 * **Approval Previews**: Shows server-computed dry-run diffs directly in the UI. Changes are applied only after clicking **Yes** or pressing <kbd>Y</kbd>.
 * **Keyboard-First Review**: In approval dialogs, press <kbd>Y</kbd> or <kbd>Cmd</kbd>/<kbd>Ctrl</kbd>+<kbd>Enter</kbd> to approve, or <kbd>N</kbd>/<kbd>Esc</kbd> to decline.
-* **Library changes switch**: In the header. Off, Sub-Sub reads, searches and writes notes only; the Library actions in the side panel are hidden.
+* **Mode buttons**: Researcher and Librarian, in the header. The side panel shows the actions of the mode: Research and Library in the Researcher, Library only in the Librarian. The model button saves the model for the current mode, or for both modes.
 * **Theme Switcher**: Header toggle between **Light**, **Dark**, and **System** themes.
 * **One-Click Copy**: Built-in copy buttons on all code snippets, BibTeX records, and assistant literature notes.
 * **Session Search & Markdown Export**: Filter conversation history in real time and download full discussions as Markdown notes.
@@ -118,8 +118,8 @@ Starting Sub-Sub with `subsub web` (or `subsub serve`) launches the browser appl
 ### Starting and commands
 
 ```sh
-subsub             # Start in the terminal
-subsub --read-only # Start with library changes off (this session only)
+subsub             # Start in the terminal (Researcher)
+subsub --librarian # Start in the Librarian
 subsub web         # Start browser view
 subsub -c          # Continue the previous session
 subsub -r          # Resume an older session
@@ -127,7 +127,8 @@ subsub -r          # Resume an older session
 
 Commands available within Sub-Sub:
 
-* `/library on|off`: Turn library changes on or off (saved). Without an argument, it toggles. `/librarian` and `/researcher`, the two modes before 0.10, still work: on and off.
+* `/researcher`: Change to the Researcher (research and library). Each mode can have its own model.
+* `/librarian`: Change to the Librarian (library only).
 * `/profile [name]`: View or change active profile (`reader`, `scholar`, `author`, `editor`).
 * `/subsub`: Display Zotero connection health and library statistics.
 * `/history`: List recent library changes with journal IDs.
@@ -137,11 +138,11 @@ Commands available within Sub-Sub:
 
 Type the command followed by arguments:
 
-* **Library** (need library changes on):
+* **Library (both modes)**:
   * `/tag-batch [size]`: Tag untagged items using your tag vocabulary.
   * `/clean-tags`: Find irregular tags and reconcile with your vocabulary.
   * `/import-queue [path]`: Import pending references from an inbox note.
-* **Research**:
+* **Research (Researcher)**:
   * `/lit <question>`: Literature review: the library first, then PubMed, Europe PMC and OpenAlex in one merged search; reads before it summarises; an evidence table, agreement, disagreement and open questions; references checked; one note in `Research/` (Scholar, Author, Editor).
   * `/compare <question or citekeys>`: Source matrix (claim, evidence type, caveats, confidence), agreements and disagreements (Scholar, Author, Editor).
   * `/review <path>`: Critical review of your own manuscript: FATAL, MAJOR and MINOR issues against the reporting guideline that applies (CONSORT, STROBE, PRISMA, STARD, TRIPOD), with quotations and a revision plan. Comments only (Author, Editor).
@@ -175,8 +176,8 @@ subsub review apply 13-31
 | `about` | string | Brief background context about your research domain | `null` |
 | `language` | string | Response language, or `"auto"` to match your input | `"English"` |
 | `vault` | string | Path to your Sub-Sub folder | `$ZOTERO_VAULT` |
-| `model` | string | The model, as provider/id; `""` to choose it in Sub-Sub | `"opencode-go/mimo-v2.6-pro"` |
-| `libraryChanges` | boolean | Library changes on (each change still needs your Yes) | `true` |
+| `models` | object | The model for each mode, as provider/id: `{"librarian": ..., "researcher": ...}`; `{}` to choose them in Sub-Sub. The 0.10 key `model` (one for both modes) still works; `libraryChanges` is ignored. | `{"librarian": "opencode-go/mimo-v2.6-flash", "researcher": "opencode-go/mimo-v2.6-pro"}` |
+| `defaultMode` | string | `"researcher"` or `"librarian"`: the mode Sub-Sub starts in | `"researcher"` |
 | `serverDir` | string | Local development path for `zotero-local-mcp` | PyPI package |
 | `look` | boolean| Show header banners and status lines in terminal | `true` |
 | `quotes` | boolean| Display quotes from *Moby-Dick* in terminal banner | `true` |
@@ -201,7 +202,7 @@ Sub-Sub finds open-access copies (Unpaywall, Europe PMC). For other papers, use
 2. Optional: set `"starbuckDir"` to a local copy of Starbuck. Without it, Sub-Sub runs the pinned Starbuck release with uv.
 3. Start Sub-Sub again and run `subsub doctor`. The line `Starbuck` must show `ok`.
 
-Sub-Sub gets four tools: `verify_check_manuscript`, `verify_check_references`, `verify_prepare_claims` and `verify_record_claims`. Starbuck writes its report to a `_starbuck` folder next to the manuscript. Inside the Sub-Sub folder or the working folder this needs no approval; elsewhere Sub-Sub asks first. Starbuck gets the contact email from the zotero-local-mcp env file. For the claim check, Sub-Sub's own model judges; Starbuck checks that every quoted passage is in the source.
+The Researcher gets four tools: `verify_check_manuscript`, `verify_check_references`, `verify_prepare_claims` and `verify_record_claims`. Starbuck writes its report to a `_starbuck` folder next to the manuscript. Inside the Sub-Sub folder or the working folder this needs no approval; elsewhere Sub-Sub asks first. Starbuck gets the contact email from the zotero-local-mcp env file. For the claim check, Sub-Sub's own model judges; Starbuck checks that every quoted passage is in the source.
 
 ---
 

package/dist/bench.js

@@ -20,8 +20,8 @@ import { expand, loadConfig, starbuckCommand, starbuckEnabled } from "./config.j
 import { findUv } from "./subsub.js";
 export const PACKAGE_DIR = resolve(dirname(fileURLToPath(import.meta.url)), "..");
 export const DEFAULT_MODELS = {
-    librarian: ["glm-5.3-flash", "deepseek-v4.1-flash", "qwen3.8-flash", "mimo-v2.6-flash", "minimax-m3", "mimo-v2.6-pro"],
-    researcher: ["mimo-v2.6-pro", "deepseek-v4-pro", "kimi-k2.6", "glm-5.3", "qwen3.7-plus", "minimax-m3"],
+    librarian: ["mimo-v2.6-flash", "glm-5.3-flash", "qwen3.8-flash", "gpt-5.6-luna", "hy3", "mimo-v2.6-pro"],
+    researcher: ["mimo-v2.6-pro", "qwen3.8-flash", "kimi-k3", "glm-5.3", "minimax-m3", "gpt-5.6-luna"],
 };
 export const TASKS = {
     librarian: ["tagging", "facet_fix", "import"],
@@ -81,7 +81,8 @@ const KEEP = new Set(["tool_execution_start", "tool_execution_end", "message_end
 export function runOne(opts) {
     mkdirSync(opts.out, { recursive: true });
     const args = ["--mode", "rpc", "--no-session", "--provider", opts.provider ?? "opencode-go", "--model", opts.model];
-    args.push("--librarian"); // library changes on for every task
+    if (opts.role === "librarian")
+        args.push("--librarian");
     const env = { ...process.env, ...opts.extraEnv, SUBSUB_BENCH_OUT: opts.out, SUBSUB_CONFIG: opts.configFile };
     const proc = spawn(process.execPath, [opts.cli ?? join(PACKAGE_DIR, "bin", "subsub.js"), ...args], { cwd: opts.cwd, env });
     const events = [];
@@ -557,7 +558,7 @@ export async function main(argv = process.argv.slice(2)) {
             if (!prompt)
                 return;
             const cf = join(cfgDir, `${j.code}.json`);
-            writeFileSync(cf, JSON.stringify({ ...userCfg, profile: "editor", model: `opencode-go/${j.model}`, models: undefined, libraryChanges: true }));
+            writeFileSync(cf, JSON.stringify({ ...userCfg, profile: "editor", models: { librarian: `opencode-go/${j.model}`, researcher: `opencode-go/${j.model}` }, model: undefined, libraryChanges: undefined }));
             const s = await runOne({ ...j, prompt, out, cwd: cfg.vault, configFile: cf, timeoutSec });
             n++;
             console.log(`${n}/${jobs.length}  ${j.code}  ${j.task}  ${s.seconds}s  ${s.error ?? (s.settled ? "done" : "?")}`);

package/dist/config.js

@@ -6,13 +6,13 @@
  *   "profile": "scholar",
  *   "userName": "Ana", "about": "a master's student in health informatics", "language": "English",
  *   "vault": "~/Documents/Sub-Sub",
- *   "model": "opencode-go/mimo-v2.6-pro",
- *   "libraryChanges": true
+ *   "models": { "librarian": "opencode-go/mimo-v2.6-flash", "researcher": "opencode-go/mimo-v2.6-pro" },
+ *   "defaultMode": "researcher"
  * }
  *
- * Before 0.10 there were two modes, each with a model ("models": {"librarian",
- * "researcher"}) and "defaultMode". Those keys are still read: the researcher's
- * model becomes the model.
+ * Two modes: the Librarian manages the library; the Researcher does that too,
+ * and searches and writes notes. "model" (0.10) sets one model for both;
+ * "libraryChanges" (0.10) is no longer used.
  *
  * `subsub init` writes this file. Without "serverDir" (or when that folder does
  * not exist), the Zotero servers run from PyPI with uv.
@@ -26,8 +26,11 @@ import { existsSync, mkdirSync, readFileSync, writeFileSync } from "node:fs";
 import { homedir } from "node:os";
 import { dirname, join, resolve } from "node:path";
 import { isObsidianVault, settingsFile } from "./layout.js";
-/** The tested model (September 2026 model test). */
-export const DEFAULT_MODEL = "opencode-go/mimo-v2.6-pro";
+/** The tested models, one per mode (model test, see bench-results). */
+export const DEFAULT_MODELS = {
+    librarian: "opencode-go/mimo-v2.6-flash",
+    researcher: "opencode-go/mimo-v2.6-pro",
+};
 export const PROFILES = ["reader", "scholar", "author", "editor"];
 /** The Zotero server release that this Sub-Sub version runs when there is no local server folder. */
 export const SERVER_VERSION = "0.5.1";
@@ -107,10 +110,13 @@ export function loadConfig(env = process.env) {
     const envValues = envFile && existsSync(envFile) ? parseEnvFile(envFile) : {};
     const vaultRaw = user.vault ?? env.ZOTERO_VAULT ?? envValues.ZOTERO_VAULT;
     const vault = vaultRaw ? expand(vaultRaw, home) : undefined;
-    // Before 0.10: a model per mode, and themes per mode.
-    const legacyModels = user.models && typeof user.models === "object" ? user.models : undefined;
-    // "model": "" means: the user chooses in pi (/login, /model).
-    const model = "model" in user ? (typeof user.model === "string" && user.model) || undefined : legacyModels ? legacyModels.researcher || legacyModels.librarian || undefined : DEFAULT_MODEL;
+    // "models" per mode; "model" (0.10) for both; {} or "" means: the user chooses in pi (/login, /model).
+    const one = typeof user.model === "string" ? user.model : undefined;
+    const given = user.models && typeof user.models === "object" ? user.models : undefined;
+    const models = given ?? (one !== undefined ? { librarian: one || undefined, researcher: one || undefined } : { ...DEFAULT_MODELS });
+    for (const k of Object.keys(models))
+        if (!models[k])
+            delete models[k];
     const themes = user.themes === false ? false : typeof user.themes === "string" ? user.themes : user.themes?.researcher;
     return {
         configFile: file,
@@ -122,8 +128,8 @@ export function loadConfig(env = process.env) {
         serverDir: expand(user.serverDir ?? "~/Projects/zotero-local-mcp", home),
         envFile,
         vault,
-        model,
-        libraryChanges: user.libraryChanges !== false,
+        models,
+        defaultMode: user.defaultMode === "librarian" ? "librarian" : "researcher",
         // A Sub-Sub folder inside an Obsidian vault also reads the vault's context file.
         vaultContext: (user.vaultContext ??
             (vault ? [join(vault, ".claude", "CLAUDE.md"), ...(isObsidianVault(dirname(vault)) ? [join(dirname(vault), ".claude", "CLAUDE.md")] : [])] : [])).map((p) => expand(p, home)),

package/dist/doctor.js

@@ -104,7 +104,7 @@ export function runChecks(cfg, env, deps = {}) {
         out.push(starbuckCheck(cfg, env, run));
     const agentDir = deps.agentDir ?? (env.SUBSUB_AGENT_DIR ? env.SUBSUB_AGENT_DIR : join(homedir(), ".subsub", "agent"));
     out.push(hasLogin(agentDir)
-        ? { name: "Model login", ok: true, detail: cfg.model ?? "pi's default model" }
+        ? { name: "Model login", ok: true, detail: Object.keys(cfg.models).length ? Object.entries(cfg.models).map(([m, id]) => `${m} ${id}`).join(", ") : "pi's default model" }
         : { name: "Model login", ok: false, detail: "no model provider yet", fix: "Type subsub, then /login." });
     return out;
 }

package/dist/init.js

@@ -4,7 +4,7 @@
  *
  * Writes:
  * - the settings file (~/.config/subsub/config.json): profile, name, language,
- *   Sub-Sub folder, library changes, model;
+ *   Sub-Sub folder, models;
  * - the server settings file (~/.config/zotero-local-mcp/env, or the one that
  *   already exists): the Sub-Sub folder, tag list, alerts file, contact email.
  *   Other lines stay;
@@ -19,14 +19,14 @@
  * Flags (for scripts and tests): --yes (take every default), --setup
  * standard|fmup, --name, --about, --language, --folder (or --notes), --move
  * yes|no, --profile, --tags health-sciences|health-informatics|any-field,
- * --library on|off, --email, --starbuck on|off, --models keep|later|opencode-go.
+ * --email, --starbuck on|off, --models keep|later|opencode-go.
  */
 import { copyFileSync, existsSync, mkdirSync, readFileSync, writeFileSync } from "node:fs";
 import { homedir } from "node:os";
 import { dirname, join, resolve } from "node:path";
 import { createInterface } from "node:readline/promises";
 import { fileURLToPath } from "node:url";
-import { configPath, DEFAULT_MODEL, expand, isProfile, loadConfig, parseEnvFile, PROFILES, readConfigFile, saveConfig, starbuckEnabled, withStarbuck, } from "./config.js";
+import { configPath, DEFAULT_MODELS, expand, isProfile, loadConfig, parseEnvFile, PROFILES, readConfigFile, saveConfig, starbuckEnabled, withStarbuck, } from "./config.js";
 import { defaultRunner, starbuckCheck } from "./doctor.js";
 import { applyMoves, FOLDER_NAME, leftBehind, NOTE_DIRS, planMoves, SETTINGS_DIR, SETTINGS_FILES, subsubFolder } from "./layout.js";
 import { PROFILE_SPECS } from "./profiles.js";
@@ -36,7 +36,7 @@ export const STARTER_TAGS = {
     "health-informatics": "Health informatics: information systems, data, AI, digital health",
     "any-field": "Any field: methods and document types only; Sub-Sub proposes topics from your library",
 };
-export const TESTED_MODEL = DEFAULT_MODEL;
+export const TESTED_MODELS = DEFAULT_MODELS;
 /** Set KEY=VALUE lines in an env file text; other lines and comments stay. */
 export function upsertEnv(text, values) {
     const lines = text ? text.replace(/\n$/, "").split("\n") : [];
@@ -125,11 +125,6 @@ export async function runInit(io, flags, env = process.env, deps = {}) {
     explain("Profile", "The profile sets how much Sub-Sub writes for you and which tools it offers. Change it at any time with /profile.");
     const profileDefault = flags.profile ?? existing.profile ?? (fmup ? "reader" : "scholar");
     const profile = await io.choose("Profile", PROFILES.map((p) => ({ value: p, label: `${PROFILE_SPECS[p].label}: ${PROFILE_SPECS[p].summary}` })), isProfile(profileDefault) ? profileDefault : "scholar");
-    explain("Library changes", "With library changes on, Sub-Sub can import, tag and repair items in Zotero. It shows a preview of every change, and nothing changes until you select Yes. With them off, it only reads, searches and writes notes. Switch at any time with /library on or /library off.");
-    const library = await io.choose("Library changes", [
-        { value: "on", label: "On (recommended): every change shows a preview first" },
-        { value: "off", label: "Off: read, search and write notes only" },
-    ], flags.library ?? (existing.libraryChanges === false ? "off" : "on"));
     // The tag list: a custom path in the server settings stays; otherwise Zotero/Zotero tags.md (moved, kept or new).
     const vocabTarget = join(notes, SETTINGS_DIR, SETTINGS_FILES.tags);
     const oldDefaults = new Set([join(from, "Systems", SETTINGS_FILES.tags), join(from, SETTINGS_DIR, SETTINGS_FILES.tags)]);
@@ -155,16 +150,17 @@ export async function runInit(io, flags, env = process.env, deps = {}) {
         { value: "off", label: "Off" },
         { value: "on", label: "On (downloads Starbuck now; uses the email above)" },
     ], flags.starbuck ?? (starbuckEnabled(current) ? "on" : "off"));
-    explain("Models", "Sub-Sub needs an account with a model provider. You can connect one later in Sub-Sub with the model button (or /login in the terminal).");
+    explain("Models", "Sub-Sub needs an account with a model provider. Each mode can use its own model: the Librarian a fast, cheap one for tags and imports, the Researcher a stronger one for reading. You can connect a provider later in Sub-Sub with the model button (or /login in the terminal).");
     const hadModel = "model" in existing || "models" in existing;
+    const show = (m) => (Object.keys(m).length ? Object.entries(m).map(([k, v]) => `${k} ${v}`).join(", ") : "choose in Sub-Sub");
     const modelOptions = [
-        ...(hadModel ? [{ value: "keep", label: `Keep: ${current.model ?? "choose in Sub-Sub"}` }] : []),
+        ...(hadModel ? [{ value: "keep", label: `Keep: ${show(current.models)}` }] : []),
         { value: "later", label: "Choose later in Sub-Sub" },
-        { value: "opencode-go", label: `OpenCode Go, tested: ${TESTED_MODEL}` },
+        { value: "opencode-go", label: `OpenCode Go, tested: ${TESTED_MODELS.librarian} for the Librarian, ${TESTED_MODELS.researcher} for the Researcher` },
     ];
     const agentDir = initEnv.SUBSUB_AGENT_DIR ? expand(initEnv.SUBSUB_AGENT_DIR, home) : join(home, ".subsub", "agent");
     const modelDefault = hadModel ? "keep" : hasProvider(agentDir, "opencode") ? "opencode-go" : "later";
-    const models = await io.choose("Model", modelOptions, flags.models ?? modelDefault);
+    const models = await io.choose("Models", modelOptions, flags.models ?? modelDefault);
     // ---- write
     if (move === "yes")
         applyMoves(moves);
@@ -199,18 +195,17 @@ export async function runInit(io, flags, env = process.env, deps = {}) {
         setup: fmup ? "fmup" : undefined,
         vault: notes,
         envFile,
-        libraryChanges: library === "on",
-        defaultMode: undefined,
+        libraryChanges: undefined,
         addons: withStarbuck(current.addons, starbuck === "on"),
     };
-    // One model since 0.10: the per-mode models are replaced.
-    patch.models = undefined;
+    // A model per mode; "model" (0.10, one for both) is replaced.
+    patch.model = undefined;
     if (models === "keep")
-        patch.model = current.model ?? "";
+        patch.models = current.models;
     if (models === "later")
-        patch.model = "";
+        patch.models = {};
     if (models === "opencode-go")
-        patch.model = TESTED_MODEL;
+        patch.models = TESTED_MODELS;
     saveConfig(patch, initEnv);
     const zotero = await zoteroReachable(deps.fetch);
     const starbuckNote = starbuck === "on" && deps.prepareStarbuck ? deps.prepareStarbuck(loadConfig(initEnv)) : "";

package/dist/look.js

@@ -63,7 +63,7 @@ export function libraryLine(st) {
 export function headerLines(opts) {
     const p = opts.paint ?? plain;
     const w = Math.max(10, opts.width);
-    const modeLabel = `Assistant${opts.profile ? `, ${opts.profile}` : ""}${opts.libraryChanges ? "" : ", read only"}`;
+    const modeLabel = (opts.mode === "librarian" ? "Librarian" : "Researcher") + (opts.profile ? `, ${opts.profile}` : "");
     const lib = libraryLine(opts.library);
     if (w < BANNER[0].length + 2) {
         return [p.mark(cut(`Sub-Sub ${opts.version}`, w)), p.text(cut(`${modeLabel} | ${opts.model}`, w)), (lib.warn ? p.warn : p.muted)(cut(lib.text, w))];
@@ -78,7 +78,7 @@ export function headerLines(opts) {
         else
             out.push(p.dim(cut(`"${opts.quote[0]}"`, w)), p.dim(cut(`  (${opts.quote[1]})`, w)));
     }
-    out.push(p.dim(cut("/library  /profile  /history  /undo  |  / for all commands", w)), "");
+    out.push(p.dim(cut("/researcher  /librarian  /profile  /history  /undo  |  / for all commands", w)), "");
     return out;
 }
 /**

package/dist/prompt.js

@@ -47,16 +47,13 @@ export function fill(text, cfg) {
         .replaceAll("{{batch}}", String(profileSpec(cfg.profile).batch))
         .replace(/[ \t]+\n/g, "\n");
 }
-export function roleText(cfg) {
-    const raw = readIf(join(ROLE_DIR, "assistant.md")) ?? "You are Sub-Sub, a Zotero librarian and research assistant.";
+export function roleText(mode, cfg) {
+    const raw = readIf(join(ROLE_DIR, `${mode}.md`)) ?? `You are Sub-Sub, the ${mode}.`;
     return cfg ? fill(raw, cfg) : raw;
 }
-export function systemAddition(cfg, cwd, libraryChanges = cfg.libraryChanges) {
+export function systemAddition(mode, cfg, cwd) {
     const user = who(cfg);
-    const parts = ["# Sub-Sub", roleText(cfg)];
-    if (!libraryChanges) {
-        parts.push(`Library changes are off: you read the library, search, write notes and queue imports. To import, tag or change items, ask ${user} to turn library changes on (/library on, or the switch in the browser view).`);
-    }
+    const parts = [`# Sub-Sub: ${mode === "librarian" ? "Librarian" : "Researcher"} mode`, roleText(mode, cfg)];
     const shared = readIf(cfg.sharedRules);
     if (shared) {
         parts.push("# Shared Zotero rules (from the Sub-Sub folder)", shared, `Sub-Sub note: in Sub-Sub you do not need a separate dry run before a change. Call the write tool with dry_run=false; Sub-Sub shows ${user} the server's preview and applies it only on approval. This replaces the dry-run steps above.`);

package/dist/roles.js

@@ -1,9 +1,9 @@
 /**
- * Which tools the Assistant may use, and which calls need the user's approval.
+ * Which tools each mode may use, and which calls need the user's approval.
  */
 import { profileSpec } from "./profiles.js";
 export const FILE_TOOLS = ["read", "edit", "write", "grep", "find", "ls"];
-/** Prefixes of the tools that Sub-Sub's servers provide (the gate checks the switch and the profile for these). */
+/** Prefixes of the tools that Sub-Sub's servers provide (the gate checks the mode and the profile for these). */
 export const SERVER_PREFIXES = ["zotero_", "scholar_", "verify_"];
 export const ZOTERO_READ = [
     "status",
@@ -43,33 +43,33 @@ export const CONFIRM_WRITES = new Set(["scholar_export_bibliography"]);
 /** Zotero tools that look at the library or write only a note in the Sub-Sub folder. */
 export const ZOTERO_CHECKS = ["tag_audit", "audit_metadata", "find_duplicates", "check_retractions", "missing_pdfs", "write_tag_review"].map((n) => `zotero_${n}`);
 /**
- * The Assistant's tools: reading the library, searching, notes and reference
- * checks always; the Zotero write tools when library changes are on. The profile
- * then removes tools.
+ * The tools of a mode. The Librarian manages the library: Zotero tools and files.
+ * The Researcher has the same, plus searches, notes and reference checks. The
+ * profile then removes tools. Every library change is still previewed (gateKind).
  */
-export function toolsFor(registered, opts) {
+export function toolsFor(mode, registered, opts = {}) {
     const has = new Set(registered);
     const without = new Set(profileSpec(opts.profile ?? "editor").without);
     const zotero = registered.filter((n) => n.startsWith("zotero_") && (opts.bench || !n.startsWith("zotero_bakeoff_")));
     const wanted = [
         ...ZOTERO_READ,
         ...ZOTERO_CHECKS,
-        ...(opts.libraryChanges ? zotero : []),
-        ...registered.filter((n) => n.startsWith("scholar_") || n.startsWith("verify_")),
+        ...zotero,
+        ...(mode === "researcher" ? registered.filter((n) => n.startsWith("scholar_") || n.startsWith("verify_")) : []),
         ...FILE_TOOLS,
     ];
     return [...new Set(wanted)].filter((n) => has.has(n) && !without.has(n));
 }
 /** Why a Sub-Sub tool is not available now, or undefined when it is. */
-export function unavailableReason(name, registered, opts) {
-    if (toolsFor(registered, opts).includes(name))
+export function unavailableReason(name, mode, registered, opts = {}) {
+    if (toolsFor(mode, registered, opts).includes(name))
         return undefined;
     const profile = opts.profile ?? "editor";
     if (profileSpec(profile).without.includes(name)) {
         return `${name} is not part of the ${profileSpec(profile).label} profile. The user can change the profile with /profile.`;
     }
-    if (!opts.libraryChanges && toolsFor(registered, { ...opts, libraryChanges: true }).includes(name)) {
-        return `${name} changes the library, and library changes are off. The user can turn them on with /library on.`;
+    if (mode === "librarian" && toolsFor("researcher", registered, opts).includes(name)) {
+        return `${name} is part of the Researcher, which also does everything the Librarian does. The user can switch with /researcher.`;
     }
     return `${name} is not available.`;
 }

package/dist/subsub.js

@@ -1,15 +1,14 @@
 /**
  * Sub-Sub: a Zotero librarian and research assistant for pi.
  *
- * - One assistant: it reads the library, searches PubMed, Europe PMC and
- *   OpenAlex, writes notes in the Sub-Sub folder and, with library changes on,
- *   changes the library. /library on|off is the switch (saved in the settings).
+ * - Two modes: the Librarian manages the library (Zotero tools only); the
+ *   Researcher does the same and also searches PubMed, Europe PMC and OpenAlex
+ *   and writes notes. Each mode can have its own model.
  * - An approval gate: every library change is previewed by the server (dry run)
  *   and shown to the user; nothing is applied without a yes.
  * - Profiles (reader, scholar, author, editor) set what Sub-Sub writes and which
  *   tools it offers; /profile changes it.
- * - Commands: /library, /profile, /subsub, /history, /undo. /librarian and
- *   /researcher (the two modes before 0.10) turn library changes on and off.
+ * - Commands: /librarian, /researcher, /profile, /subsub, /history, /undo.
  * - Add-on: with "addons": ["starbuck"], Starbuck runs as a third server
  *   ("verify") for reference checks.
  *
@@ -29,6 +28,7 @@ import { describeArgs, formatPreview } from "./preview.js";
 import { headerLines, paintPreview, QUOTES, schemeFromAnsi, themeName } from "./look.js";
 import { systemAddition } from "./prompt.js";
 import { gateKind, SERVER_PREFIXES, toolsFor, unavailableReason } from "./roles.js";
+const MODE_ENTRY = "subsub-mode";
 const PACKAGE_DIR = join(dirname(fileURLToPath(import.meta.url)), "..");
 const BENCH_ENTRY = "subsub-bench";
 function ownVersion() {
@@ -103,11 +103,10 @@ export async function createSubsub(pi, deps = {}) {
     }
     if (deps.bridge)
         registerTools(deps.bridge);
-    pi.registerFlag("read-only", { description: "Start Sub-Sub with library changes off (this run only)", type: "boolean", default: false });
-    pi.registerFlag("librarian", { description: "Start Sub-Sub with library changes on (this run only)", type: "boolean", default: false });
-    let libraryChanges = cfg.libraryChanges;
+    pi.registerFlag("librarian", { description: "Start Sub-Sub in the Librarian mode", type: "boolean", default: false });
+    let mode = cfg.defaultMode;
     const benchRun = Boolean(process.env.SUBSUB_BENCH_OUT);
-    const toolOpts = () => ({ libraryChanges, profile, bench: benchRun });
+    const toolOpts = () => ({ profile, bench: benchRun });
     let profile = cfg.profile;
     const user = who(cfg);
     /** True when started with the `subsub` command (not as a package inside plain pi). */
@@ -129,7 +128,7 @@ export async function createSubsub(pi, deps = {}) {
             return;
         const down = bridge ? Object.keys(bridge.errors) : ["zotero", "scholar"];
         const state = {
-            libraryChanges,
+            mode,
             profile,
             profileLabel: profileSpec(profile).label,
             model: ctx.model ? { provider: ctx.model.provider, id: ctx.model.id } : null,
@@ -192,7 +191,7 @@ export async function createSubsub(pi, deps = {}) {
                     const th = ctx.ui.theme;
                     return headerLines({
                         version,
-                        libraryChanges,
+                        mode,
                         profile: profileSpec(profile).label,
                         model: modelId,
                         library,
@@ -214,38 +213,28 @@ export async function createSubsub(pi, deps = {}) {
     function status(ctx) {
         modelId = ctx.model ? `${ctx.model.id}` : "no model";
         const down = bridge ? Object.keys(bridge.errors) : ["zotero", "scholar"];
-        const lib = libraryChanges ? "library changes on" : "read only";
-        ctx.ui.setStatus("subsub", `Sub-Sub: ${lib} | ${profileSpec(profile).label} | ${modelId}${down.length ? ` | not running: ${down.join(", ")}` : ""}`);
+        ctx.ui.setStatus("subsub", `Sub-Sub: ${mode} | ${profileSpec(profile).label} | ${modelId}${down.length ? ` | not running: ${down.join(", ")}` : ""}`);
         if (standalone)
-            ctx.ui.setTitle(libraryChanges ? "Sub-Sub" : "Sub-Sub (read only)");
+            ctx.ui.setTitle(`Sub-Sub: ${mode}`);
         headerTui?.requestRender();
         webCtx = ctx;
         emitWeb();
     }
-    /** Set the tools for the switch and the profile; save the switch when asked. */
-    function applyLibrary(ctx, on, save) {
-        libraryChanges = on;
-        pi.setActiveTools(toolsFor(registered(), toolOpts()));
-        if (save) {
-            try {
-                saveConfig({ libraryChanges: on });
-            }
-            catch (err) {
-                ctx.ui.notify(`Sub-Sub: the setting was not saved: ${err.message}`, "warning");
-            }
+    async function applyMode(ctx, next, remember) {
+        mode = next;
+        pi.setActiveTools(toolsFor(mode, registered(), toolOpts()));
+        const spec = cfg.models[mode];
+        if (spec) {
+            const i = spec.indexOf("/");
+            const model = i > 0 ? ctx.modelRegistry.find(spec.slice(0, i), spec.slice(i + 1)) : undefined;
+            const ok = model ? await pi.setModel(model) : false;
+            if (!ok)
+                ctx.ui.notify(`Sub-Sub: cannot use ${spec} (unknown model or no key); keeping the current model.`, "warning");
         }
+        if (remember)
+            pi.appendEntry(MODE_ENTRY, { mode });
         status(ctx);
     }
-    async function applyModel(ctx) {
-        const spec = cfg.model;
-        if (!spec)
-            return;
-        const i = spec.indexOf("/");
-        const model = i > 0 ? ctx.modelRegistry.find(spec.slice(0, i), spec.slice(i + 1)) : undefined;
-        const ok = model ? await pi.setModel(model) : false;
-        if (!ok)
-            ctx.ui.notify(`Sub-Sub: cannot use ${spec} (unknown model or no key); keeping the current model.`, "warning");
-    }
     pi.on("session_start", async (_event, ctx) => {
         if (!bridge) {
             const b = new Bridge();
@@ -253,13 +242,17 @@ export async function createSubsub(pi, deps = {}) {
             bridge = b;
             registerTools(b);
         }
+        let restored;
+        for (const e of ctx.sessionManager.getBranch()) {
+            const m = e.customType === MODE_ENTRY ? e.data?.mode : undefined;
+            if (m === "librarian" || m === "researcher")
+                restored = m;
+        }
         // Judge light or dark before Sub-Sub changes the theme.
         if (lookOn(ctx))
             scheme ??= schemeFromAnsi(ctx.ui.theme.getFgAnsi("text"), ctx.ui.theme.name);
-        await applyModel(ctx);
         applyTheme(ctx);
-        // The flags change this run only; the saved setting stays.
-        applyLibrary(ctx, pi.getFlag("read-only") ? false : pi.getFlag("librarian") ? true : cfg.libraryChanges, false);
+        await applyMode(ctx, restored ?? (pi.getFlag("librarian") ? "librarian" : cfg.defaultMode), false);
         if (lookOn(ctx)) {
             setHeader(ctx);
             void refreshLibrary();
@@ -289,7 +282,7 @@ export async function createSubsub(pi, deps = {}) {
         return { action: "handled" };
     });
     pi.on("before_agent_start", async (event, ctx) => ({
-        systemPrompt: `${event.systemPrompt}\n\n${systemAddition({ ...cfg, profile }, ctx.cwd, libraryChanges)}`,
+        systemPrompt: `${event.systemPrompt}\n\n${systemAddition(mode, { ...cfg, profile }, ctx.cwd)}`,
     }));
     /** Model test (subsub-bench): record every change instead of asking, and apply none. */
     const benchOut = process.env.SUBSUB_BENCH_OUT ? expand(process.env.SUBSUB_BENCH_OUT) : undefined;
@@ -303,7 +296,7 @@ export async function createSubsub(pi, deps = {}) {
             coerceArgs(schema, input);
         resolvePathArgs(name, input, (p) => normalizeToolPath(p, ctx.cwd));
         if (SERVER_PREFIXES.some((p) => name.startsWith(p))) {
-            const why = unavailableReason(name, registered(), toolOpts());
+            const why = unavailableReason(name, mode, registered(), toolOpts());
             if (why) {
                 if (benchOut)
                     record({ kind: "wrong_mode", tool: name, input });
@@ -426,35 +419,18 @@ export async function createSubsub(pi, deps = {}) {
                 `for ${user}.${shown}`,
         };
     }
-    const libraryNote = (on) => on
-        ? "Sub-Sub: library changes on. Every change shows a preview first."
-        : "Sub-Sub: library changes off. Sub-Sub reads, searches and writes notes; it does not change the library.";
-    pi.registerCommand("library", {
-        description: "Sub-Sub: turn library changes on or off (/library on, /library off)",
-        handler: async (args, ctx) => {
-            const a = args.trim().toLowerCase();
-            const on = a === "on" ? true : a === "off" ? false : a === "" ? !libraryChanges : undefined;
-            if (on === undefined) {
-                ctx.ui.notify("Type /library on or /library off.", "warning");
-                return;
-            }
-            applyLibrary(ctx, on, true);
-            ctx.ui.notify(libraryNote(on), "info");
-        },
-    });
-    // The two modes before 0.10, kept so that old habits and notes still work.
     pi.registerCommand("librarian", {
-        description: "Sub-Sub: same as /library on",
+        description: "Sub-Sub: switch to the Librarian (manages the library: tags, imports, metadata, PDFs)",
         handler: async (_args, ctx) => {
-            applyLibrary(ctx, true, true);
-            ctx.ui.notify(`${libraryNote(true)} (/librarian is now /library on.)`, "info");
+            await applyMode(ctx, "librarian", true);
+            ctx.ui.notify("Sub-Sub: Librarian mode. For searches and notes, switch to /researcher.", "info");
         },
     });
     pi.registerCommand("researcher", {
-        description: "Sub-Sub: same as /library off",
+        description: "Sub-Sub: switch to the Researcher (searches, notes, reviews, and everything the Librarian does)",
         handler: async (_args, ctx) => {
-            applyLibrary(ctx, false, true);
-            ctx.ui.notify(`${libraryNote(false)} (/researcher is now /library off.)`, "info");
+            await applyMode(ctx, "researcher", true);
+            ctx.ui.notify("Sub-Sub: Researcher mode. It searches, writes notes and also changes the library, with a preview.", "info");
         },
     });
     pi.registerCommand("profile", {
@@ -477,14 +453,14 @@ export async function createSubsub(pi, deps = {}) {
             catch (err) {
                 saved = ` Not saved: ${err.message}`;
             }
-            applyLibrary(ctx, libraryChanges, false);
+            await applyMode(ctx, mode, false);
             ctx.ui.notify(`Sub-Sub: ${profileSpec(profile).label} profile (${profileSpec(profile).summary}).${saved}`, "info");
         },
     });
     pi.registerCommand("subsub", {
         description: "Sub-Sub: Zotero connection and library overview",
         handler: async (_args, ctx) => {
-            const lines = [`Library changes: ${libraryChanges ? "on" : "off"}. Profile: ${profileSpec(profile).label}. Model: ${ctx.model?.id ?? "none"}.`];
+            const lines = [`Mode: ${mode}. Profile: ${profileSpec(profile).label}. Model: ${ctx.model?.id ?? "none"}.`];
             if (!bridge) {
                 ctx.ui.notify(`${lines[0]}\nThe Zotero servers are not running. Try /reload.`, "warning");
                 return;