@tiagojct/subsub 0.9.0 → 0.10.0

package/src/args.ts

@@ -62,3 +62,27 @@ export function coerceArgs(original: Schema, input: Record<string, unknown>): Re
 	}
 	return input;
 }
+
+/**
+ * Arguments that name a file in the user's working folder (a manuscript, a report
+ * folder, a bibliography to write). The servers run in their own working folder, so
+ * Sub-Sub makes these paths absolute against its own, as pi's file tools read them.
+ * Note paths (tag reviews, the import queue, linked notes) are not here: the servers
+ * read those from the Sub-Sub folder.
+ */
+export const CWD_PATH_ARGS: Record<string, string[]> = {
+	scholar_check_manuscript: ["path"],
+	scholar_export_bibliography: ["output_path"],
+	verify_check_manuscript: ["path", "report_dir"],
+	verify_prepare_claims: ["path", "report_dir"],
+	verify_record_claims: ["path", "report_dir"],
+};
+
+/** Make the working-folder paths of a tool call absolute. Changes input in place. */
+export function resolvePathArgs(tool: string, input: Record<string, unknown>, toAbsolute: (p: string) => string): Record<string, unknown> {
+	for (const k of CWD_PATH_ARGS[tool] ?? []) {
+		const v = input[k];
+		if (typeof v === "string" && v.trim()) input[k] = toAbsolute(v);
+	}
+	return input;
+}

package/src/bench.ts

@@ -3,7 +3,8 @@
  * with no changes applied. See docs/Subsub.md ("Model test").
  *
  *   subsub-bench prepare [--seed 7]        pick the tasks (read-only)
- *   subsub-bench run [--librarian a,b] [--researcher c,d] [--parallel 3] [--only task]
+ *   subsub-bench run [--models a,b] [--librarian a,b] [--researcher c,d] [--parallel 3] [--only task]
+ *   (--models sets the models for both task groups.)
  *   subsub-bench score                     objective checks -> results.md
  *
  * Results go to ~/Projects/subsub/bench-results/<date>/ (or --dir). Each model gets
@@ -16,7 +17,10 @@ import { spawn, spawnSync } from "node:child_process";
 import { existsSync, mkdirSync, readdirSync, readFileSync, writeFileSync } from "node:fs";
 import { dirname, join, resolve } from "node:path";
 import { fileURLToPath } from "node:url";
-import { expand, loadConfig, type Mode, starbuckCommand, starbuckEnabled } from "./config.ts";
+import { expand, loadConfig, starbuckCommand, starbuckEnabled } from "./config.ts";
+
+/** Task groups: library work and research. Every run has library changes on (each change is recorded, not applied). */
+export type Mode = "librarian" | "researcher";
 import { findUv } from "./subsub.ts";
 
 export const PACKAGE_DIR = resolve(dirname(fileURLToPath(import.meta.url)), "..");
@@ -134,7 +138,7 @@ export function runOne(opts: {
 }): Promise<RunSummary> {
 	mkdirSync(opts.out, { recursive: true });
 	const args = ["--mode", "rpc", "--no-session", "--provider", opts.provider ?? "opencode-go", "--model", opts.model];
-	if (opts.role === "librarian") args.push("--librarian");
+	args.push("--librarian"); // library changes on for every task
 	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: any[] = [];
@@ -584,9 +588,10 @@ export async function main(argv: string[] = process.argv.slice(2)): Promise<void
 		if (!existsSync(tasksFile)) throw new Error(`No tasks in ${dir}. Run: subsub-bench prepare`);
 		if (!cfg.vault) throw new Error("No vault configured (ZOTERO_VAULT).");
 		const t: Tasks = JSON.parse(readFileSync(tasksFile, "utf8"));
+		const both = arg(argv, "models")?.split(",").filter(Boolean);
 		const lists: Record<Mode, string[]> = {
-			librarian: arg(argv, "librarian")?.split(",").filter(Boolean) ?? DEFAULT_MODELS.librarian,
-			researcher: arg(argv, "researcher")?.split(",").filter(Boolean) ?? DEFAULT_MODELS.researcher,
+			librarian: arg(argv, "librarian")?.split(",").filter(Boolean) ?? both ?? DEFAULT_MODELS.librarian,
+			researcher: arg(argv, "researcher")?.split(",").filter(Boolean) ?? both ?? DEFAULT_MODELS.researcher,
 		};
 		const only = arg(argv, "only")?.split(",");
 		const codes = codesFor([...new Set([...lists.librarian, ...lists.researcher])], dir);
@@ -606,7 +611,7 @@ export async function main(argv: string[] = process.argv.slice(2)): Promise<void
 			const prompt = promptFor(j.task, t, j.code, out);
 			if (!prompt) return;
 			const cf = join(cfgDir, `${j.code}.json`);
-			writeFileSync(cf, JSON.stringify({ ...userCfg, profile: "editor", models: { librarian: `opencode-go/${j.model}`, researcher: `opencode-go/${j.model}` } }));
+			writeFileSync(cf, JSON.stringify({ ...userCfg, profile: "editor", model: `opencode-go/${j.model}`, models: undefined, libraryChanges: true }));
 			const s = await runOne({ ...j, prompt, out, cwd: cfg.vault!, configFile: cf, timeoutSec });
 			n++;
 			console.log(`${n}/${jobs.length}  ${j.code}  ${j.task}  ${s.seconds}s  ${s.error ?? (s.settled ? "done" : "?")}`);
@@ -634,6 +639,6 @@ export async function main(argv: string[] = process.argv.slice(2)): Promise<void
 		console.log(`Wrote ${join(dir, "results.md")}`);
 		return;
 	}
-	console.log("Usage: subsub-bench prepare | run [--librarian a,b] [--researcher c,d] [--only task] [--parallel 3] | score  [--dir DIR]");
+	console.log("Usage: subsub-bench prepare | run [--models a,b] [--librarian a,b] [--researcher c,d] [--only task] [--parallel 3] | score  [--dir DIR]");
 }
 

package/src/bridge.ts

@@ -1,6 +1,6 @@
 /**
- * Bridge to the Python MCP servers of zotero-local-mcp (librarian "zotero" and
- * researcher "scholar"). Starts them over stdio, lists their tools, and calls them.
+ * Bridge to the Python MCP servers of zotero-local-mcp ("zotero" for the library,
+ * "scholar" for searches and notes). Starts them over stdio, lists their tools, and calls them.
  * All safety logic (dry runs, version checks, journal, vocabulary, the researcher's
  * note-only client) stays in the Python servers.
  */

package/src/config.ts

@@ -6,10 +6,14 @@
  *   "profile": "scholar",
  *   "userName": "Ana", "about": "a master's student in health informatics", "language": "English",
  *   "vault": "~/Documents/Sub-Sub",
- *   "models": { "librarian": "opencode-go/glm-5.3-flash", "researcher": "opencode-go/mimo-v2.6-pro" },
- *   "defaultMode": "researcher"
+ *   "model": "opencode-go/mimo-v2.6-pro",
+ *   "libraryChanges": true
  * }
  *
+ * 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.
+ *
  * `subsub init` writes this file. Without "serverDir" (or when that folder does
  * not exist), the Zotero servers run from PyPI with uv.
  *
@@ -24,12 +28,13 @@ import { homedir } from "node:os";
 import { dirname, join, resolve } from "node:path";
 import { isObsidianVault, settingsFile } from "./layout.ts";
 
-export type Mode = "librarian" | "researcher";
+/** The tested model (September 2026 model test). */
+export const DEFAULT_MODEL = "opencode-go/mimo-v2.6-pro";
 export type Profile = "reader" | "scholar" | "author" | "editor";
 export const PROFILES: Profile[] = ["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 = "0.5.0";
+export const SERVER_VERSION = "0.5.1";
 
 /** The Starbuck release (PyPI) that this Sub-Sub version runs when there is no local Starbuck folder. */
 export const STARBUCK_VERSION = "0.2.0";
@@ -51,8 +56,10 @@ export interface SubsubConfig {
 	serverDir: string;
 	envFile?: string;
 	vault?: string;
-	models: Partial<Record<Mode, string>>;
-	defaultMode: Mode;
+	/** The model, as provider/id. Undefined: pi's own choice (the user picks with /model). */
+	model?: string;
+	/** Library changes on: the Zotero write tools are offered, each with a preview. */
+	libraryChanges: boolean;
 	/** Extra context files added to the system prompt when pi runs inside the vault. */
 	vaultContext: string[];
 	/** Shared rules file (tag system, citekeys, note formats). */
@@ -65,8 +72,8 @@ export interface SubsubConfig {
 	look?: boolean;
 	/** A line from Moby-Dick under the banner (default true). */
 	quotes?: boolean;
-	/** Theme per mode, without -dark/-light; false keeps your pi theme. */
-	themes?: Partial<Record<Mode, string>> | false;
+	/** Theme, without -dark/-light; false keeps your pi theme. */
+	themes?: string | false;
 	/** Optional servers to start, e.g. ["starbuck"]. */
 	addons?: string[];
 	/** Local Starbuck folder (used when it has a pyproject.toml). */
@@ -125,7 +132,7 @@ export function isProfile(x: unknown): x is Profile {
 export function loadConfig(env: NodeJS.ProcessEnv = process.env): SubsubConfig {
 	const home = env.HOME;
 	const file = configPath(env);
-	let user: Partial<SubsubConfig> = {};
+	let user: Record<string, any> = {};
 	if (existsSync(file)) {
 		try {
 			user = JSON.parse(readFileSync(file, "utf8"));
@@ -145,7 +152,11 @@ export function loadConfig(env: NodeJS.ProcessEnv = process.env): SubsubConfig {
 	const envValues = envFile && existsSync(envFile) ? parseEnvFile(envFile) : {};
 	const vaultRaw = user.vault ?? env.ZOTERO_VAULT ?? envValues.ZOTERO_VAULT;
 	const vault = vaultRaw ? expand(vaultRaw, home) : undefined;
-	const mode = user.defaultMode === "librarian" ? "librarian" : "researcher";
+	// Before 0.10: a model per mode, and themes per mode.
+	const legacyModels = user.models && typeof user.models === "object" ? (user.models as Record<string, string>) : 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;
+	const themes = user.themes === false ? false : typeof user.themes === "string" ? user.themes : user.themes?.researcher;
 	return {
 		configFile: file,
 		profile: isProfile(user.profile) ? user.profile : "scholar",
@@ -156,16 +167,13 @@ export function loadConfig(env: NodeJS.ProcessEnv = process.env): SubsubConfig {
 		serverDir: expand(user.serverDir ?? "~/Projects/zotero-local-mcp", home),
 		envFile,
 		vault,
-		models: user.models ?? {
-			librarian: "opencode-go/glm-5.3-flash",
-			researcher: "opencode-go/mimo-v2.6-pro",
-		},
-		defaultMode: mode,
+		model,
+		libraryChanges: user.libraryChanges !== false,
 		// 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)),
+		).map((p: string) => expand(p, home)),
 		sharedRules: user.sharedRules
 			? expand(user.sharedRules, home)
 			: vault
@@ -175,7 +183,7 @@ export function loadConfig(env: NodeJS.ProcessEnv = process.env): SubsubConfig {
 		uvPath: user.uvPath ? expand(user.uvPath, home) : undefined,
 		look: user.look,
 		quotes: user.quotes,
-		themes: user.themes,
+		themes,
 		addons: Array.isArray(user.addons) ? user.addons.filter((a): a is string => typeof a === "string") : [],
 		starbuckDir: expand(user.starbuckDir ?? "~/Projects/starbuck", home),
 	};

package/src/doctor.ts

@@ -134,7 +134,7 @@ export function runChecks(
 			fix: v.problems?.length
 				? `Fix these lines in the tag list: ${v.problems.slice(0, 3).join("; ")}`
 				: noTopics
-					? "In Sub-Sub (librarian), ask: propose topics for my tag list."
+					? "In Sub-Sub, ask: propose topics for my tag list."
 					: undefined,
 		});
 	}
@@ -148,7 +148,7 @@ export function runChecks(
 	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: Object.keys(cfg.models).length ? Object.values(cfg.models).join(", ") : "pi's default model" }
+			? { name: "Model login", ok: true, detail: cfg.model ?? "pi's default model" }
 			: { name: "Model login", ok: false, detail: "no model provider yet", fix: "Type subsub, then /login." },
 	);
 	return out;

package/src/init.ts

@@ -4,7 +4,7 @@
  *
  * Writes:
  * - the settings file (~/.config/subsub/config.json): profile, name, language,
- *   notes folder, models;
+ *   Sub-Sub folder, library changes, model;
  * - 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;
@@ -19,7 +19,7 @@
  * 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,
- * --email, --starbuck on|off, --models keep|later|opencode-go.
+ * --library on|off, --email, --starbuck on|off, --models keep|later|opencode-go.
  */
 
 import { copyFileSync, existsSync, mkdirSync, readFileSync, writeFileSync } from "node:fs";
@@ -29,6 +29,7 @@ import { createInterface } from "node:readline/promises";
 import { fileURLToPath } from "node:url";
 import {
 	configPath,
+	DEFAULT_MODEL,
 	expand,
 	isProfile,
 	loadConfig,
@@ -49,10 +50,10 @@ const TEMPLATES = resolve(dirname(fileURLToPath(import.meta.url)), "..", "templa
 export const STARTER_TAGS: Record<string, string> = {
 	"health-sciences": "Health sciences: clinical areas, public health, methods and study designs",
 	"health-informatics": "Health informatics: information systems, data, AI, digital health",
-	"any-field": "Any field: methods and document types only; the librarian proposes topics from your library",
+	"any-field": "Any field: methods and document types only; Sub-Sub proposes topics from your library",
 };
 
-export const TESTED_MODELS = { librarian: "opencode-go/glm-5.3-flash", researcher: "opencode-go/mimo-v2.6-pro" };
+export const TESTED_MODEL = DEFAULT_MODEL;
 
 export interface InitIO {
 	ask(question: string, def: string): Promise<string>;
@@ -184,6 +185,19 @@ export async function runInit(
 		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)]);
@@ -198,7 +212,7 @@ export async function runInit(
 		io.say("");
 		io.say(`Tag list: keeping ${vocab}.`);
 	} else {
-		explain("Tag list", `The librarian tags items only with the tags in this list. Pick a start; you edit the list later in ${SETTINGS_DIR}/${SETTINGS_FILES.tags}.`);
+		explain("Tag list", `Sub-Sub tags items only with the tags in this list. Pick a start; you edit the list later in ${SETTINGS_DIR}/${SETTINGS_FILES.tags}.`);
 		tags = await io.choose(
 			"Starter tag list",
 			Object.entries(STARTER_TAGS).map(([value, label]) => ({ value, label })),
@@ -209,7 +223,7 @@ export async function runInit(
 	explain("Contact email", "Unpaywall needs an email address to find open-access PDFs. Sub-Sub sends it only to Unpaywall, Crossref, OpenAlex and PubMed, as they ask.");
 	const email = (await io.ask("Email (optional)", flags.email ?? envValues.ZOTERO_CONTACT_EMAIL ?? "")).trim();
 
-	explain("Reference checks (Starbuck)", "An optional add-on for manuscripts: it checks that each cited work exists, matches its citation and was not retracted. The researcher then has /verify.");
+	explain("Reference checks (Starbuck)", "An optional add-on for manuscripts: it checks that each cited work exists, matches its citation and was not retracted. Sub-Sub then has /verify.");
 	const starbuck = await io.choose(
 		"Reference checks",
 		[
@@ -220,14 +234,15 @@ export async function runInit(
 	);
 
 	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).");
+	const hadModel = "model" in existing || "models" in existing;
 	const modelOptions = [
-		...(existing.models ? [{ value: "keep", label: `Keep: ${JSON.stringify(existing.models)}` }] : []),
+		...(hadModel ? [{ value: "keep", label: `Keep: ${current.model ?? "choose in Sub-Sub"}` }] : []),
 		{ value: "later", label: "Choose later in Sub-Sub" },
-		{ value: "opencode-go", label: `OpenCode Go, tested: ${TESTED_MODELS.librarian} for the librarian, ${TESTED_MODELS.researcher} for the researcher` },
+		{ value: "opencode-go", label: `OpenCode Go, tested: ${TESTED_MODEL}` },
 	];
 	const agentDir = initEnv.SUBSUB_AGENT_DIR ? expand(initEnv.SUBSUB_AGENT_DIR, home) : join(home, ".subsub", "agent");
-	const modelDefault = existing.models ? "keep" : hasProvider(agentDir, "opencode") ? "opencode-go" : "later";
-	const models = await io.choose("Models", modelOptions, flags.models ?? modelDefault);
+	const modelDefault = hadModel ? "keep" : hasProvider(agentDir, "opencode") ? "opencode-go" : "later";
+	const models = await io.choose("Model", modelOptions, flags.models ?? modelDefault);
 
 	// ---- write
 	if (move === "yes") applyMoves(moves);
@@ -263,10 +278,15 @@ export async function runInit(
 		setup: fmup ? "fmup" : undefined,
 		vault: notes,
 		envFile,
+		libraryChanges: library === "on",
+		defaultMode: undefined,
 		addons: withStarbuck(current.addons, starbuck === "on"),
 	};
-	if (models === "later") patch.models = {};
-	if (models === "opencode-go") patch.models = TESTED_MODELS;
+	// One model since 0.10: the per-mode models are replaced.
+	patch.models = undefined;
+	if (models === "keep") patch.model = current.model ?? "";
+	if (models === "later") patch.model = "";
+	if (models === "opencode-go") patch.model = TESTED_MODEL;
 	saveConfig(patch, initEnv);
 
 	const zotero = await zoteroReachable(deps.fetch);

package/src/layout.ts

@@ -30,6 +30,14 @@ export function isObsidianVault(dir: string): boolean {
 	return existsSync(join(dir, ".obsidian"));
 }
 
+/** The Obsidian vault that holds a folder: the folder itself or the nearest parent with .obsidian/. */
+export function obsidianRoot(dir: string): string | undefined {
+	for (let d = dir; ; d = dirname(d)) {
+		if (isObsidianVault(d)) return d;
+		if (dirname(d) === d) return undefined;
+	}
+}
+
 /** The folder that a user's answer means: a vault root becomes <vault>/Sub-Sub. */
 export function subsubFolder(answer: string): string {
 	return isObsidianVault(answer) && basename(answer) !== FOLDER_NAME ? join(answer, FOLDER_NAME) : answer;

package/src/look.ts

@@ -4,7 +4,6 @@
  * Only used when Sub-Sub runs as its own command in the terminal UI.
  */
 
-import type { Mode } from "./config.ts";
 
 export const BANNER = [
 	"╔═╗╦ ╦╔╗    ╔═╗╦ ╦╔╗",
@@ -25,7 +24,8 @@ export const QUOTES: Array<[string, string]> = [
 	["Call me Ishmael.", "Moby-Dick, ch. 1"],
 ];
 
-export const MODE_THEMES: Record<Mode, string> = { librarian: "subsub-try-works", researcher: "subsub-glauca" };
+/** The terminal theme, without -dark/-light. subsub-try-works is the other one shipped. */
+export const DEFAULT_THEME = "subsub-glauca";
 
 export type Scheme = "dark" | "light";
 
@@ -47,8 +47,7 @@ export function schemeFromAnsi(fgAnsi: string, themeName?: string): Scheme {
 	return "dark";
 }
 
-export function themeName(mode: Mode, scheme: Scheme, map: Partial<Record<Mode, string>> = MODE_THEMES): string | undefined {
-	const base = map[mode];
+export function themeName(scheme: Scheme, base: string | undefined = DEFAULT_THEME): string | undefined {
 	return base ? `${base}-${scheme}` : undefined;
 }
 
@@ -84,7 +83,8 @@ export function libraryLine(st: LibraryState): { text: string; warn: boolean } {
 /** Header lines. Each line is cut to the width before it is coloured. */
 export function headerLines(opts: {
 	version: string;
-	mode: Mode;
+	/** Library changes on (false: read only). */
+	libraryChanges: boolean;
 	/** Profile label, e.g. "Scholar". */
 	profile?: string;
 	model: string;
@@ -95,7 +95,7 @@ export function headerLines(opts: {
 }): string[] {
 	const p = opts.paint ?? plain;
 	const w = Math.max(10, opts.width);
-	const modeLabel = (opts.mode === "librarian" ? "Librarian" : "Researcher") + (opts.profile ? `, ${opts.profile}` : "");
+	const modeLabel = `Assistant${opts.profile ? `, ${opts.profile}` : ""}${opts.libraryChanges ? "" : ", read only"}`;
 	const lib = libraryLine(opts.library);
 	if (w < BANNER[0].length + 2) {
 		return [p.mark(cut(`Sub-Sub ${opts.version}`, w)), p.text(cut(`${modeLabel} | ${opts.model}`, w)), (lib.warn ? p.warn : p.muted)(cut(lib.text, w))];
@@ -108,7 +108,7 @@ export function headerLines(opts: {
 		if ([...one].length <= w) out.push(p.dim(one));
 		else out.push(p.dim(cut(`"${opts.quote[0]}"`, w)), p.dim(cut(`  (${opts.quote[1]})`, w)));
 	}
-	out.push(p.dim(cut("/researcher  /librarian  /profile  /history  /undo  |  / for all commands", w)), "");
+	out.push(p.dim(cut("/library  /profile  /history  /undo  |  / for all commands", w)), "");
 	return out;
 }
 

package/src/profiles.ts

@@ -5,7 +5,7 @@
  *
  * - reader:  explains each step; reading notes are quotes with page numbers and
  *            questions; no summaries or syntheses; no bulk library changes.
- * - scholar: literature notes, syntheses, searches, alerts; the full librarian.
+ * - scholar: literature notes, syntheses, searches, alerts; all library changes.
  * - author:  scholar plus manuscript work: citation check, bibliography, comments
  *            on the argument. Does not write the manuscript's paragraphs.
  * - editor:  everything, including drafting text for a manuscript on request.
@@ -46,13 +46,13 @@ export const PROFILE_SPECS: Record<Profile, ProfileSpec> = {
 			"- A literature note is a reading note: the full reference, then direct quotes with page numbers (or section names), and under each quote one question for {{user}} to answer. Do not write summaries, syntheses, conclusions or paragraphs that {{user}} could hand in as their own text. When a prompt or the shared rules ask for a literature note or a synthesis, make a reading note instead and say so.",
 			"- For searches, list works with one line each on what they study, not on what they conclude.",
 			"- If {{user}} asks for a summary, a synthesis or text for an assignment, say that the Reader profile does not write these, and offer quotes and questions. {{User}} can change the profile with /profile.",
-			"- Librarian: at most 10 items per review note. Explain each proposed tag in the Reason column.",
+			"- Tag review notes: at most 10 items. Explain each proposed tag in the Reason column.",
 		].join("\n"),
 	},
 	scholar: {
 		name: "scholar",
 		label: "Scholar",
-		summary: "literature notes, syntheses, searches and alerts; the full librarian",
+		summary: "literature notes, syntheses, searches and alerts; all library changes",
 		without: MANUSCRIPT,
 		withoutPrompts: ["review"],
 		batch: 25,
@@ -60,7 +60,7 @@ export const PROFILE_SPECS: Record<Profile, ProfileSpec> = {
 			"Profile: Scholar.",
 			"- Write literature notes and syntheses from what you read, with a source for every claim.",
 			"- Do not draft text for {{user}}'s manuscripts, theses or assignments. If asked, say that the Author and Editor profiles help with manuscripts (/profile).",
-			"- Librarian: 25 items per review note.",
+			"- Tag review notes: 25 items.",
 		].join("\n"),
 	},
 	author: {
@@ -75,7 +75,7 @@ export const PROFILE_SPECS: Record<Profile, ProfileSpec> = {
 			"- Write literature notes and syntheses from what you read, with a source for every claim.",
 			"- Help with {{user}}'s manuscripts: check citations against the library, export the bibliography, and comment on the argument, the structure and the evidence that is missing, with the sources that could support each point.",
 			"- Do not write the manuscript's paragraphs. Say what is missing and where the support is; {{user}} writes the text. The Editor profile drafts text (/profile).",
-			"- Librarian: 25 items per review note.",
+			"- Tag review notes: 25 items.",
 		].join("\n"),
 	},
 	editor: {
@@ -89,7 +89,7 @@ export const PROFILE_SPECS: Record<Profile, ProfileSpec> = {
 			"Profile: Editor. All tools.",
 			"- Write literature notes and syntheses from what you read, with a source for every claim.",
 			"- When {{user}} asks, draft text for a manuscript: cite library items as [@citekey], use only claims from sources you read, and mark drafted text clearly so that {{user}} can check it.",
-			"- Librarian: 25 items per review note unless {{user}} asks for more.",
+			"- Tag review notes: 25 items unless {{user}} asks for more.",
 		].join("\n"),
 	},
 };

package/src/prompt.ts

@@ -10,7 +10,7 @@
 import { existsSync, readFileSync } from "node:fs";
 import { dirname, isAbsolute, join, relative, resolve } from "node:path";
 import { fileURLToPath } from "node:url";
-import { type Mode, type SubsubConfig, who } from "./config.ts";
+import { type SubsubConfig, who } from "./config.ts";
 import { profileSpec } from "./profiles.ts";
 
 const ROLE_DIR = join(dirname(fileURLToPath(import.meta.url)), "..", "roles");
@@ -52,14 +52,19 @@ export function fill(text: string, cfg: Pick<SubsubConfig, "userName" | "about"
 		.replace(/[ \t]+\n/g, "\n");
 }
 
-export function roleText(mode: Mode, cfg?: Pick<SubsubConfig, "userName" | "about" | "profile">): string {
-	const raw = readIf(join(ROLE_DIR, `${mode}.md`)) ?? `You are the ${mode}.`;
+export function roleText(cfg?: Pick<SubsubConfig, "userName" | "about" | "profile">): string {
+	const raw = readIf(join(ROLE_DIR, "assistant.md")) ?? "You are Sub-Sub, a Zotero librarian and research assistant.";
 	return cfg ? fill(raw, cfg) : raw;
 }
 
-export function systemAddition(mode: Mode, cfg: SubsubConfig, cwd: string): string {
+export function systemAddition(cfg: SubsubConfig, cwd: string, libraryChanges: boolean = cfg.libraryChanges): string {
 	const user = who(cfg);
-	const parts = [`# Sub-Sub: ${mode} mode`, roleText(mode, 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 shared = readIf(cfg.sharedRules);
 	if (shared) {
 		parts.push(

package/src/roles.ts

@@ -1,13 +1,13 @@
 /**
- * Which tools each mode may use, and which calls need the user's approval.
+ * Which tools the Assistant may use, and which calls need the user's approval.
  */
 
-import type { Mode, Profile } from "./config.ts";
+import type { Profile } from "./config.ts";
 import { profileSpec } from "./profiles.ts";
 
 export const FILE_TOOLS = ["read", "edit", "write", "grep", "find", "ls"];
 
-/** Prefixes of the tools that Sub-Sub's servers provide (the gate checks the mode for these). */
+/** Prefixes of the tools that Sub-Sub's servers provide (the gate checks the switch and the profile for these). */
 export const SERVER_PREFIXES = ["zotero_", "scholar_", "verify_"];
 
 export const ZOTERO_READ = [
@@ -48,27 +48,49 @@ export const PREVIEW_WRITES = new Set([
 /** Writes without a dry run that still need a yes. */
 export const CONFIRM_WRITES = new Set(["scholar_export_bibliography"]);
 
-export function toolsFor(mode: Mode, registered: string[], profile: Profile = "editor"): string[] {
+/** 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}`,
+);
+
+export interface ToolOptions {
+	/** Library changes on: the Zotero write tools are offered (each still previewed). */
+	libraryChanges: boolean;
+	profile?: Profile;
+	/** The model test: also the bakeoff_ tools. */
+	bench?: boolean;
+}
+
+/**
+ * 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.
+ */
+export function toolsFor(registered: string[], opts: ToolOptions): string[] {
 	const has = new Set(registered);
-	const without = new Set(profileSpec(profile).without);
-	const wanted =
-		mode === "librarian"
-			? [...registered.filter((n) => n.startsWith("zotero_")), ...FILE_TOOLS]
-			: [
-					...ZOTERO_READ,
-					...registered.filter((n) => n.startsWith("scholar_") || n.startsWith("verify_")),
-					...FILE_TOOLS,
-				];
+	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_")),
+		...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: string, mode: Mode, registered: string[], profile: Profile): string | undefined {
-	if (toolsFor(mode, registered, profile).includes(name)) return undefined;
+export function unavailableReason(name: string, registered: string[], opts: ToolOptions): string | undefined {
+	if (toolsFor(registered, opts).includes(name)) return undefined;
+	const profile = opts.profile ?? "editor";
 	if (profileSpec(profile).without.includes(name)) {
 		return `${name} is not part of the ${profileSpec(profile).label} profile. The user can change the profile with /profile.`;
 	}
-	return `${name} is not available in ${mode} mode. The user can switch with /${otherMode(mode)}.`;
+	if (!opts.libraryChanges && toolsFor(registered, { ...opts, libraryChanges: true }).includes(name)) {
+		return `${name} changes the library, and library changes are off. The user can turn them on with /library on.`;
+	}
+	return `${name} is not available.`;
 }
 
 export type GateKind = "preview" | "confirm" | "path" | null;
@@ -84,7 +106,3 @@ export function gateKind(toolName: string, input: Record<string, unknown>): Gate
 	if (toolName === "write" || toolName === "edit") return "path";
 	return null;
 }
-
-export function otherMode(mode: Mode): Mode {
-	return mode === "librarian" ? "researcher" : "librarian";
-}