@tiagojct/subsub 0.10.0 → 0.11.1

package/dist/web.js

@@ -21,8 +21,8 @@ import { homedir } from "node:os";
 import { extname, join, normalize, resolve, sep } from "node:path";
 import { StringDecoder } from "node:string_decoder";
 import { agentDirFor, chooseCwd, PACKAGE_DIR, packageVersion } from "./cli.js";
-import { expand, loadConfig, saveConfig, withStarbuck } from "./config.js";
-import { TESTED_MODEL } from "./init.js";
+import { configPath, expand, loadConfig, readConfigFile, saveConfig, withStarbuck } from "./config.js";
+import { TESTED_MODELS } from "./init.js";
 import { obsidianRoot } from "./layout.js";
 import { realish, within } from "./paths.js";
 export function parseWebArgs(args) {
@@ -300,7 +300,7 @@ export async function startWeb(opts, env = process.env, log = () => { }) {
     const bin = join(PACKAGE_DIR, "bin", "subsub.js");
     env.PI_CODING_AGENT_DIR = agentDir; // for the session list below
     const childEnv = { ...env, SUBSUB_WEB: "1" };
-    const baseArgs = [bin, "--mode", "rpc", "--here", ...(opts.librarian ? ["--librarian"] : []), ...opts.piArgs];
+    const baseArgs = [bin, "--mode", "rpc", "--here", ...opts.piArgs];
     const agent = new Agent(process.execPath, baseArgs, cwd, childEnv);
     // ---- state shared with the pages
     const clients = new Set();
@@ -309,7 +309,19 @@ export async function startWeb(opts, env = process.env, log = () => { }) {
     let busy = false;
     let lastSeen = Date.now();
     let restarting = false;
+    let switching = false; // a restart for a new model, add-on or key is under way
+    let lastSession;
     let refreshAfterRun = false;
+    /** The mode to start pi in: the one on screen, else the --librarian flag. A session's own mode still wins. */
+    function modeArgs() {
+        const shown = subsubState?.mode;
+        if (shown === "librarian" || shown === "researcher")
+            return [`--${shown}`];
+        return opts.librarian ? ["--librarian"] : [];
+    }
+    function startAgent() {
+        agent.start([...modeArgs(), ...(lastSession && existsSync(lastSession) ? ["--session", lastSession] : [])]);
+    }
     function broadcast(ev) {
         const data = `data: ${JSON.stringify(ev)}\n\n`;
         for (const c of clients)
@@ -352,11 +364,13 @@ export async function startWeb(opts, env = process.env, log = () => { }) {
         if (restarting)
             return;
         busy = false;
+        for (const id of dialogs.keys())
+            broadcast({ type: "dialog_closed", id });
         dialogs.clear();
         broadcast({ type: "agent_exit", code, stderr: agent.stderr.slice(-1500) });
         log(`pi stopped (code ${code}).\n${agent.stderr.slice(-2000)}`);
     };
-    agent.start();
+    startAgent();
     async function snapshot() {
         const out = {
             type: "hello",
@@ -369,6 +383,7 @@ export async function startWeb(opts, env = process.env, log = () => { }) {
         };
         try {
             out.session = await agent.request({ type: "get_state" });
+            lastSession = out.session.sessionFile ?? lastSession;
             out.messages = (await agent.request({ type: "get_messages" })).messages;
             out.commands = (await agent.request({ type: "get_commands" })).commands;
         }
@@ -387,12 +402,11 @@ export async function startWeb(opts, env = process.env, log = () => { }) {
             .map((s) => ({ path: s.path, name: s.name ?? null, first: s.firstMessage.slice(0, 140), modified: s.modified, messages: s.messageCount }));
     }
     async function restartAgent() {
-        let sessionFile;
         try {
-            sessionFile = (await agent.request({ type: "get_state" })).sessionFile;
+            lastSession = (await agent.request({ type: "get_state" })).sessionFile ?? lastSession;
         }
         catch {
-            /* start fresh */
+            /* keep the last one known */
         }
         restarting = true;
         for (const id of dialogs.keys())
@@ -401,9 +415,23 @@ export async function startWeb(opts, env = process.env, log = () => { }) {
         await agent.stop();
         restarting = false;
         busy = false;
-        agent.start(sessionFile && existsSync(sessionFile) ? ["--session", sessionFile] : []);
+        startAgent();
         broadcast(await snapshot());
     }
+    /** Run a change that restarts pi, one at a time. */
+    async function withRestart(res, change) {
+        if (busy || switching)
+            return send(res, 409, { error: "busy" });
+        switching = true;
+        try {
+            await change();
+            await restartAgent();
+        }
+        finally {
+            switching = false;
+        }
+        return send(res, 200, { ok: true });
+    }
     // ---- idle stop
     let closing = false;
     const idleTimer = setInterval(() => {
@@ -545,44 +573,50 @@ export async function startWeb(opts, env = process.env, log = () => { }) {
                     return send(res, 200, { models: Array.isArray(data) ? data : (data.models ?? []) });
                 }
                 case "POST /api/model": {
-                    if (busy)
+                    if (busy || switching)
                         return send(res, 409, { error: "busy" });
                     const body = await readJson(req);
                     const spec = `${String(body.provider)}/${String(body.id)}`;
-                    // Remember the model (and drop the per-mode models of versions before 0.10), then restart pi
-                    // so the extension reads the new setting.
-                    saveConfig({ model: spec, models: undefined }, env);
-                    await agent.request({ type: "set_model", provider: String(body.provider), modelId: String(body.id) });
-                    await restartAgent();
-                    return send(res, 200, { ok: true });
+                    // Remember the model for the current mode (or both), then restart pi so the extension reads it.
+                    const mode = subsubState?.mode === "librarian" ? "librarian" : "researcher";
+                    // Start from what the file says, not from the built-in defaults, so a model the user never chose is not saved.
+                    const raw = readConfigFile(configPath(env));
+                    const saved = raw.models && typeof raw.models === "object" ? raw.models : typeof raw.model === "string" && raw.model ? { librarian: raw.model, researcher: raw.model } : {};
+                    const models = { ...saved, [mode]: spec };
+                    if (body.both)
+                        models[mode === "librarian" ? "researcher" : "librarian"] = spec;
+                    saveConfig({ models, model: undefined }, env);
+                    return withRestart(res, async () => {
+                        await agent.request({ type: "set_model", provider: String(body.provider), modelId: String(body.id) });
+                    });
                 }
                 case "POST /api/addons": {
                     // Turn an add-on on or off, then restart pi so the extension starts or stops its server.
-                    if (busy)
+                    if (busy || switching)
                         return send(res, 409, { error: "busy" });
                     const body = await readJson(req);
                     if (typeof body.starbuck !== "boolean")
                         return send(res, 400, { error: "starbuck must be true or false" });
-                    saveConfig({ addons: withStarbuck(loadConfig(env).addons, body.starbuck) }, env);
-                    await restartAgent();
-                    return send(res, 200, { ok: true });
+                    return withRestart(res, () => {
+                        saveConfig({ addons: withStarbuck(loadConfig(env).addons, body.starbuck) }, env);
+                    });
                 }
                 case "POST /api/restart":
-                    if (agent.proc)
+                    if (agent.proc || switching)
                         return send(res, 200, { ok: true });
-                    agent.start();
+                    startAgent();
                     broadcast(await snapshot());
                     return send(res, 200, { ok: true });
                 case "POST /api/login": {
-                    if (busy)
+                    if (busy || switching)
                         return send(res, 409, { error: "busy" });
                     const body = await readJson(req);
-                    saveApiKey(agentDir, String(body.provider ?? ""), String(body.key ?? ""));
-                    const current = loadConfig(env);
-                    if (body.provider === "opencode-go" && !current.model)
-                        saveConfig({ model: TESTED_MODEL, models: undefined }, env);
-                    await restartAgent();
-                    return send(res, 200, { ok: true });
+                    return withRestart(res, () => {
+                        saveApiKey(agentDir, String(body.provider ?? ""), String(body.key ?? ""));
+                        const current = loadConfig(env);
+                        if (body.provider === "opencode-go" && Object.keys(current.models).length === 0)
+                            saveConfig({ models: TESTED_MODELS, model: undefined }, env);
+                    });
                 }
                 case "POST /api/open": {
                     const body = await readJson(req);

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@tiagojct/subsub",
-  "version": "0.10.0",
-  "description": "Sub-Sub: a Zotero librarian and research assistant in the browser or the terminal, built on pi",
+  "version": "0.11.1",
+  "description": "Sub-Sub: a research assistant that works from your own Zotero library, in the browser or the terminal, built on pi",
   "type": "module",
   "license": "MIT",
   "author": "Tiago Jacinto",
@@ -49,7 +49,6 @@
     "assets",
     "bin",
     "dist",
-    "docs",
     "extensions",
     "prompts",
     "roles",

package/prompts/lit-note.md

@@ -2,4 +2,4 @@
 description: "Literature note for one item"
 argument-hint: "<citekey or title words>"
 ---
-Make a literature note for $ARGUMENTS in Resources/Zotero/, following the template in the shared rules. Read the full text if it is indexed. Then offer to link it in Zotero.
+Make a literature note for $ARGUMENTS in Literature/ in the Sub-Sub folder, following the template in the shared rules. Read the full text if it is indexed. Then offer to link it in Zotero.

package/roles/librarian.md

@@ -0,0 +1,46 @@
+You are Sub-Sub, the librarian for {{user}}'s Zotero library. {{about}} Reply briefly. No emojis.
+
+You change the library through the zotero_ tools. You have no web access; outside metadata reaches you only through the import and repair tools. For literature searches and notes, {{user}} switches to the Researcher (/researcher), which also does everything you do.
+
+## How changes work
+
+- Call a write tool with dry_run=false when you intend the change. Sub-Sub shows {{user}} the server's preview and applies it only on approval.
+- If a call is blocked because {{user}} did not approve, ask what to change. Do not retry the same call.
+- Report the journal_id after each applied change. {{User}} can revert with /undo or ask you to use undo.
+- Start a session with zotero_status. If Zotero is not reachable, stop and tell {{user}}.
+
+## How to tag
+
+- A tag must be supported by the item itself: title and abstract, or the full text. If you are unsure, leave the tag out. Fewer correct tags are better than many loose ones.
+- type/ says what the document is, not what it is about. A review of trials is type/narrative-review or type/systematic-review, not type/rct. A paper about guidelines is not type/guideline.
+- method/ says how the work was done. A paper or book about statistics gets topic/statistics, not method/statistical-modelling.
+- When an item already has tags, judge each existing topic/, method/ and type/ tag. Remove the ones the item does not support: call zotero_tag_items with replace=["topic","method","type"] and the complete set in add.
+- The server refuses more tags than max_per_facet allows (topic 4, type 2). Do not work around it; choose.
+- Do not change status/ tags unless {{user}} says so.
+
+## A tag list without topics
+
+If zotero_get_vocabulary has no topic/ tags, propose topics before tagging: read the titles of 100 to 200 items (zotero_find_items, several pages), write Inbox/Zotero topic proposal.md with 15 to 30 topics (tag, one-line description, how many items it would fit), and ask {{user}} to copy the chosen ones into the tag list file. You cannot edit that file.
+
+## Tagging untagged items
+
+1. zotero_find_items with missing_facet="topic", detail=true, limit={{batch}}, offset=0.
+2. Call zotero_write_tag_review with the name "Zotero tag review NN" (NN: the next free number; ls Inbox/ first) and one row per item: key, the complete topic/, method/ and type/ set, and a short reason. The tool fills in the citekey, item and current tags and checks every row. Do not write the table by hand.
+3. Tell {{user}} the file name. {{User}} edits the Proposed tags column.
+4. When {{user}} approves, call zotero_apply_tag_review with the note path. It applies the column exactly as {{user}} left it and removes the review marker. Do not copy rows into zotero_tag_items. If the preview shows changed_since_note or already_applied, tell {{user}} before you apply. For many notes at once, {{user}} can run `subsub review apply NN-MM` (note numbers) in a terminal.
+5. Report the missing_facet counts from zotero_library_overview.
+
+## Re-tagging and cleaning
+
+1. zotero_tag_audit: items over the limits, pairs of tags that almost always appear together (batch tagging), items without the review marker.
+2. For the flagged items, write review notes with zotero_write_tag_review as above ({{batch}} items each, grouped by subject), with a complete new set for each item.
+3. After {{user}}'s edits, zotero_apply_tag_review, one note at a time. Run zotero_tag_audit again at the end.
+4. Old tags outside the vocabulary: zotero_list_tags with outside_vocabulary=true, then Inbox/Zotero tag mapping.md (old tag, item count, proposed action). Check that the meaning fits: a subject tag such as "rct" or "guidelines" is not a document type, and tags that were put on whole groups of items should be removed, not renamed. After approval: zotero_rename_tags and zotero_remove_tags.
+
+## Imports, metadata, PDFs
+
+- Import the ticked lines of the queue or an alert note with zotero_import_queue; single works with zotero_import_identifiers.
+- zotero_audit_metadata, then zotero_repair_metadata in batches of 25. Mention matches with confidence below 1.0. Journal articles of 1 or 2 pages are often letters, editorials or book reviews: check their type/ tag.
+- zotero_find_duplicates: give {{user}} each group with its evidence (identifiers, fields, files, citekeys) and the fullest record. Do not call items duplicates on a similar title alone. When the item types differ, say that Zotero's Duplicate Items view will not show the group. {{User}} merges in Zotero.
+- zotero_check_retractions: call again while still_unchecked > 0. Propose the tag _retracted for retracted items.
+- zotero_missing_pdfs, then zotero_attach_oa_pdfs in batches of 25. Say when a file is an accepted manuscript.

package/roles/{assistant.md → researcher.md}

@@ -1,6 +1,6 @@
-You are Sub-Sub, the librarian and research assistant for {{user}}'s Zotero library. {{about}} Reply briefly. No emojis.
+You are Sub-Sub, the researcher for {{user}}'s Zotero library. You also do the librarian's work. {{about}} Reply briefly. No emojis.
 
-You read the Zotero library (zotero_ tools), search PubMed, Europe PMC and OpenAlex (scholar_ tools), write notes in the Sub-Sub folder and, when library changes are on, change the library through the zotero_ write tools. Every library change goes through Sub-Sub's preview and {{user}}'s approval.
+You read the Zotero library (zotero_ tools), search PubMed, Europe PMC and OpenAlex (scholar_ tools), write notes in the Sub-Sub folder and change the library through the zotero_ write tools. Every library change goes through Sub-Sub's preview and {{user}}'s approval.
 
 ## Always
 
@@ -22,8 +22,7 @@ You read the Zotero library (zotero_ tools), search PubMed, Europe PMC and OpenA
 - If a call is blocked because {{user}} did not approve, ask what to change. Do not retry the same call.
 - Report the journal_id after each applied change. {{User}} can revert with /undo or ask you to use undo.
 - Start work on the library with zotero_status. If Zotero is not reachable, stop and tell {{user}}.
-- If library changes are off, a write tool is not available: say what you would change and ask {{user}} to turn library changes on.
-- Older shared rules may speak of a librarian and a researcher, and of handing works over between them. Those were two modes of Sub-Sub before version 0.10; you do both.
+- Older shared rules may say that the researcher cannot change the library and hands works over to the librarian. That was before version 0.10: you do both.
 
 ## Questions about the library
 
@@ -35,7 +34,7 @@ You read the Zotero library (zotero_ tools), search PubMed, Europe PMC and OpenA
 2. Search with scholar_search_multi (three or four phrasings, all sources in one call). Use scholar_search_pubmed, scholar_search_europepmc or scholar_search_openalex alone only for a precise query in that service's syntax. Report total hits and how many are already in the library.
 3. Read open-access full text with scholar_read_oa_fulltext: first the section list, then only the sections you need. When a work you need is not open access, say that it may open through {{user}}'s institution (the DOI link, opened on the institution's network), and offer /request-copy to ask the author for a copy. Never point to unlicensed copies (Sci-Hub, LibGen and similar).
 4. List the most relevant works not in the library, one line each on why it matters.
-5. Ask which to add. Import the chosen works with zotero_import_identifiers (one preview for all), then offer to tag them. When {{user}} wants to choose later, or library changes are off, put them in the import queue with scholar_queue_imports; {{user}} ticks the lines and you import them with zotero_import_queue.
+5. Ask which to add. Import the chosen works with zotero_import_identifiers (one preview for all), then offer to tag them. When {{user}} wants to choose later, put them in the import queue with scholar_queue_imports; {{user}} ticks the lines and you import them with zotero_import_queue.
 
 ## Imports, metadata, PDFs
 

package/src/bench.ts

@@ -1,6 +1,6 @@
 /**
  * subsub-bench: the same tasks for several models, against the real library,
- * with no changes applied. See docs/Subsub.md ("Model test").
+ * with no changes applied. See docs/model-test.md.
  *
  *   subsub-bench prepare [--seed 7]        pick the tasks (read-only)
  *   subsub-bench run [--models a,b] [--librarian a,b] [--researcher c,d] [--parallel 3] [--only task]
@@ -17,17 +17,14 @@ 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, 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 { expand, loadConfig, type Mode, starbuckCommand, starbuckEnabled } from "./config.ts";
 import { findUv } from "./subsub.ts";
 
 export const PACKAGE_DIR = resolve(dirname(fileURLToPath(import.meta.url)), "..");
 
 export const DEFAULT_MODELS: Record<Mode, string[]> = {
-	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: Record<Mode, string[]> = {
@@ -82,7 +79,7 @@ export function promptFor(task: string, t: Tasks, code: string, out: string): st
 		case "lit_note":
 			return t.lit_note
 				? `Make a literature note for ${t.lit_note.citekey}, following the literature-note format in the shared rules. Read the full text. ` +
-						`This is a model test: save the note as ${join(out, `${t.lit_note.citekey}.md`)} instead of Resources/Zotero/, and do not attach anything to Zotero.`
+						`This is a model test: save the note as ${join(out, `${t.lit_note.citekey}.md`)} instead of Literature/ in the Sub-Sub folder, and do not attach anything to Zotero.`
 				: undefined;
 		case "synthesis":
 			return t.synthesis
@@ -138,7 +135,7 @@ 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];
-	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: any[] = [];
@@ -611,7 +608,7 @@ 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, `${j.code}.json`);
-			writeFileSync(cf, JSON.stringify({ ...userCfg, profile: "editor", model: `opencode-go/${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/src/cli.ts

@@ -134,12 +134,38 @@ export function reviewCommand(args: string[], cfg: SubsubConfig, env: NodeJS.Pro
 	};
 }
 
+const HELP = `Sub-Sub: your research assistant, working from your own Zotero library.
+
+Usage:
+  subsub                 Start Sub-Sub in the terminal
+  subsub --librarian     Start in the Librarian, which only manages the library
+  subsub web             Open Sub-Sub in the browser
+  subsub init            Set up or change the settings (folder, tag list, profile, models)
+  subsub doctor          Check the set-up; each line marked FIX says what to do
+  subsub shortcut        Add a Sub-Sub shortcut (--remove takes it away)
+  subsub review preview|apply <note>
+                         Check or apply a tag review note from Inbox/
+  subsub --version       Show the versions
+
+Options:
+  --here                 Work in the current folder, not in the Sub-Sub folder
+
+In Sub-Sub, type /subsub for the state, /researcher or /librarian to switch modes,
+/profile to change the profile, /undo to undo the last change, and / for all commands.
+Sub-Sub runs on pi: pi's options (for example --model, --resume) also work.
+
+Docs: https://subsub.tiagojacinto.eu`;
+
 export async function run(argv: string[] = process.argv.slice(2)): Promise<void> {
 	const env = process.env;
 	const home = homedir();
 	const here = argv.includes("--here");
 	const args = argv.filter((a) => a !== "--here");
 
+	if (args[0] === "--help" || args[0] === "-h" || args[0] === "help") {
+		console.log(HELP);
+		return;
+	}
 	if (args[0] === "--version" || args[0] === "-v") {
 		const piPkg = join(dirname(fileURLToPath(import.meta.resolve("@earendil-works/pi-coding-agent"))), "..");
 		console.log(`subsub ${packageVersion()} (pi ${packageVersion(piPkg)})`);
@@ -173,7 +199,12 @@ export async function run(argv: string[] = process.argv.slice(2)): Promise<void>
 		return;
 	}
 	if (isSelfUpdate(args)) {
-		console.log(`Sub-Sub is not updated with "update". Its code is in ${PACKAGE_DIR}; after new code arrives, run "npm install" there.`);
+		if (PACKAGE_DIR.split(/[\\/]/).includes("node_modules")) {
+			console.log("Sub-Sub is not updated with \"update\". To update it, run the installer again (https://subsub.tiagojacinto.eu/install/);");
+			console.log("if you installed it with npm, type: npm install -g @tiagojct/subsub");
+		} else {
+			console.log(`Sub-Sub is not updated with "update". Its code is in ${PACKAGE_DIR}; after new code arrives, run "npm install" there.`);
+		}
 		console.log('To update packages added to Sub-Sub, use "subsub update --extensions".');
 		process.exitCode = 1;
 		return;
@@ -206,6 +237,8 @@ export async function run(argv: string[] = process.argv.slice(2)): Promise<void>
 	env.SUBSUB_CLI = "1";
 	// pi's update notice would point to the global pi, not to this copy.
 	env.PI_SKIP_VERSION_CHECK ??= "1";
+	// pi reports a first install to pi.dev and names itself to some providers; Sub-Sub sends no usage data.
+	env.PI_TELEMETRY ??= "0";
 
 	process.argv = [process.argv[0], process.argv[1], ...args];
 	const index = fileURLToPath(import.meta.resolve("@earendil-works/pi-coding-agent"));

package/src/config.ts

@@ -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.
@@ -28,8 +28,13 @@ import { homedir } from "node:os";
 import { dirname, join, resolve } from "node:path";
 import { isObsidianVault, settingsFile } from "./layout.ts";
 
-/** The tested model (September 2026 model test). */
-export const DEFAULT_MODEL = "opencode-go/mimo-v2.6-pro";
+export type Mode = "librarian" | "researcher";
+
+/** The tested models, one per mode (model test, see bench-results). */
+export const DEFAULT_MODELS: Record<Mode, string> = {
+	librarian: "opencode-go/mimo-v2.6-flash",
+	researcher: "opencode-go/mimo-v2.6-pro",
+};
 export type Profile = "reader" | "scholar" | "author" | "editor";
 export const PROFILES: Profile[] = ["reader", "scholar", "author", "editor"];
 
@@ -56,10 +61,9 @@ export interface SubsubConfig {
 	serverDir: string;
 	envFile?: string;
 	vault?: string;
-	/** 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;
+	/** The model of each mode, as provider/id. Missing: pi's own choice (the user picks with /model). */
+	models: Partial<Record<Mode, string>>;
+	defaultMode: Mode;
 	/** Extra context files added to the system prompt when pi runs inside the vault. */
 	vaultContext: string[];
 	/** Shared rules file (tag system, citekeys, note formats). */
@@ -152,10 +156,13 @@ 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;
-	// 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;
+	// "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 as Record<string, string>) : undefined;
+	// Without a settings file (no subsub init yet), the user chooses in pi: no default that may lack a key.
+	const fallback = existsSync(file) ? { ...DEFAULT_MODELS } : {};
+	const models: Partial<Record<Mode, string>> = given ?? (one !== undefined ? { librarian: one || undefined, researcher: one || undefined } : fallback);
+	for (const k of Object.keys(models) as Mode[]) if (!models[k]) delete models[k];
 	const themes = user.themes === false ? false : typeof user.themes === "string" ? user.themes : user.themes?.researcher;
 	return {
 		configFile: file,
@@ -167,8 +174,8 @@ export function loadConfig(env: NodeJS.ProcessEnv = process.env): SubsubConfig {
 		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 ??

package/src/doctor.ts

@@ -123,7 +123,8 @@ export function runChecks(
 	);
 	const v = st.vocabulary ?? {};
 	if (v.loaded === false || !v.tags) {
-		out.push({ name: "Tag list", ok: false, detail: v.path ? `cannot read ${v.path}` : "not set", fix: "Type subsub init: it creates a starter tag list." });
+		const path = v.path && v.path !== "None" ? v.path : undefined; // the server writes Python's None when unset
+		out.push({ name: "Tag list", ok: false, detail: path ? `cannot read ${path}` : "not set", fix: "Type subsub init: it creates a starter tag list." });
 	} else {
 		const noTopics = Array.isArray(v.facets) && !v.facets.includes("topic");
 		out.push({
@@ -148,7 +149,7 @@ export function runChecks(
 	const agentDir = deps.agentDir ?? (env.SUBSUB_AGENT_DIR ? env.SUBSUB_AGENT_DIR : join(homedir(), ".subsub", "agent"));
 	out.push(
 		hasLogin(agentDir)
-			? { name: "Model login", ok: true, detail: cfg.model ?? "pi's default model" }
+			? { name: "Model login", ok: true, detail: Object.keys(cfg.models).length ? Object.entries(cfg.models).map(([m, id]) => `${m} ${id}`).join(", ") : "pi's default model" }
 			: { name: "Model login", ok: false, detail: "no model provider yet", fix: "Type subsub, then /login." },
 	);
 	return out;