@tiagojct/subsub 0.11.0 → 0.11.2

package/dist/init.js

@@ -103,10 +103,12 @@ export async function runInit(io, flags, env = process.env, deps = {}) {
     // Without questions (--yes), an existing folder stays exactly as it is.
     const keepAsIs = Boolean(flags.yes) && !flags.folder && !flags.notes && oldFolder !== undefined;
     const folderDefault = flags.folder ?? flags.notes ?? (oldFolder ? (keepAsIs ? oldFolder : subsubFolder(oldFolder)) : join(home, "Documents", FOLDER_NAME));
-    const answer = expand((await io.ask("Sub-Sub folder (or an Obsidian vault)", folderDefault)).trim() || folderDefault, home);
-    const notes = keepAsIs && answer === oldFolder ? answer : subsubFolder(answer);
+    const answer = expand(cleanPath(await io.ask("Sub-Sub folder (or an Obsidian vault)", folderDefault)) || folderDefault, home);
+    let notes = keepAsIs && answer === oldFolder ? answer : subsubFolder(answer);
     if (notes !== answer)
         io.say(`That is an Obsidian vault. Sub-Sub will use ${notes}.`);
+    else if (notes !== folderDefault)
+        io.say(`Sub-Sub folder: ${notes}`);
     // ---- files of the old layout
     const from = oldFolder && existsSync(oldFolder) ? oldFolder : notes;
     const moves = planMoves(from, notes);
@@ -119,8 +121,14 @@ export async function runInit(io, flags, env = process.env, deps = {}) {
             io.say(`  and ${moves.length - 6} more`);
         move = await io.choose("Move them", [
             { value: "yes", label: "Move them (recommended)" },
-            { value: "no", label: from === notes ? "Leave them; Sub-Sub still reads them from Systems/" : "Leave them where they are" },
+            // In a new folder, files left behind would not be read: then "no" means keeping the old folder.
+            { value: "no", label: from === notes ? "Leave them; Sub-Sub still reads them from Systems/" : flags.folder || flags.notes ? "Leave them where they are" : `Leave them, and keep using ${from}` },
         ], flags.move ?? (flags.yes ? "no" : "yes"));
+        // A folder given on the command line (--folder, --notes) is a deliberate choice and stays.
+        if (move === "no" && from !== notes && !flags.folder && !flags.notes) {
+            notes = from;
+            io.say(`Sub-Sub keeps using ${notes}.`);
+        }
     }
     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");
@@ -143,7 +151,7 @@ export async function runInit(io, flags, env = process.env, deps = {}) {
         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 })), flags.tags ?? (fmup ? "health-sciences" : "any-field"));
     }
-    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.");
+    explain("Contact email", "Unpaywall needs an email address to find open-access PDFs. Sub-Sub sends it with its requests to PubMed, Europe PMC, OpenAlex, Crossref and Unpaywall, as they ask, and to nobody else.");
     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. Sub-Sub then has /verify.");
     const starbuck = await io.choose("Reference checks", [
@@ -226,6 +234,8 @@ export async function runInit(io, flags, env = process.env, deps = {}) {
     if (fmup)
         io.say("FMUP / U.Porto: the FMUP model service will come in a later version. Until then, connect a model provider yourself.");
     io.say("Next: type subsub web to open Sub-Sub in your browser (or subsub for the terminal). Connect a model provider with the model button (or /login in the terminal). To check the setup, type subsub doctor.");
+    if (tags === "any-field")
+        io.say('The tag list has no topics yet. Before you tag, ask Sub-Sub: "propose topics for my tag list".');
     return { configFile, envFile, notes, created, moved: move === "yes" ? moves.length : 0, zotero };
 }
 export function parseFlags(args) {
@@ -281,8 +291,10 @@ function terminalIO() {
 }
 export async function initMain(args, env = process.env) {
     const flags = parseFlags(args);
-    if (!process.stdin.isTTY)
-        flags.yes ??= "true";
+    if (!process.stdin.isTTY && flags.yes === undefined) {
+        flags.yes = "true";
+        console.log("Not a terminal: Sub-Sub takes the default answers (as with --yes).");
+    }
     const io = flags.yes ? defaultsIO((l) => console.log(l)) : terminalIO();
     try {
         await runInit(io, flags, env, { prepareStarbuck: (cfg) => {
@@ -300,3 +312,12 @@ export async function initMain(args, env = process.env) {
         io.close?.();
     }
 }
+/** A path as typed, dragged from Finder (spaces escaped) or copied from Explorer (in quotes). */
+export function cleanPath(raw) {
+    let p = raw.trim();
+    if (p.length > 1 && (p[0] === '"' || p[0] === "'") && p.at(-1) === p[0])
+        return p.slice(1, -1);
+    if (process.platform !== "win32")
+        p = p.replace(/\\([ '"()&])/g, "$1");
+    return p;
+}

package/dist/paths.js

@@ -46,10 +46,14 @@ export function realish(abs) {
     }
     return tail.length ? join(real, ...tail) : real;
 }
+/** macOS and Windows file systems ignore case: ~/.SSH is ~/.ssh. */
+const FOLD_CASE = process.platform === "darwin" || process.platform === "win32";
 export function within(child, parent) {
     if (!parent)
         return false;
-    const rel = relative(parent, child);
+    // NFC: a name typed with combining accents is the same file as the precomposed one.
+    const [c, p] = [child.normalize("NFC"), parent.normalize("NFC")];
+    const rel = FOLD_CASE ? relative(p.toLowerCase(), c.toLowerCase()) : relative(p, c);
     return rel === "" || (!rel.startsWith(`..${sep}`) && rel !== ".." && !isAbsolute(rel));
 }
 export function buildPolicy(opts) {
@@ -81,7 +85,30 @@ export function judgePath(target, policy) {
     const hit = policy.protectedPaths.find((p) => within(target, p));
     if (hit)
         return { ok: false, why: `it changes a protected file or folder (${hit})` };
-    if (policy.allowed.some((a) => within(target, a)))
-        return { ok: true };
-    return { ok: false, why: "it is outside the vault and the working folder" };
+    const root = policy.allowed.find((a) => within(target, a));
+    if (!root)
+        return { ok: false, why: "it is outside the vault and the working folder" };
+    // Notes never live in hidden folders; .git/hooks, .obsidian/plugins or .vscode can run code.
+    // Only the part inside the folder counts, so a vault under ~/.something still works.
+    const hidden = relative(root, target).split(/[\\/]/).find((part) => part.startsWith(".") && part !== "." && part !== "..");
+    if (hidden)
+        return { ok: false, why: `it is in a hidden folder or file (${hidden})` };
+    return { ok: true };
+}
+/** Files with keys and passwords: the model may not read them, even when you ask. */
+export function secretPaths() {
+    const home = realish(homedir());
+    return [
+        join(home, ".subsub", "agent", "auth.json"),
+        ...[process.env.SUBSUB_AGENT_DIR, process.env.PI_CODING_AGENT_DIR].filter((d) => !!d).map((d) => join(realish(d.replace(/^~(?=$|[\\/])/, home)), "auth.json")),
+        join(home, ".pi", "agent", "auth.json"),
+        join(home, ".config", "zotero-local-mcp", "env"),
+        join(home, ".ssh"),
+        join(home, ".aws"),
+        join(home, ".netrc"),
+    ];
+}
+/** True if reading `target` would read a secret; for grep, also a folder that holds one. */
+export function isSecret(target, recursive = false, envFile) {
+    return [...secretPaths(), ...(envFile ? [realish(envFile)] : [])].some((p) => within(target, p) || (recursive && within(p, target)));
 }

package/dist/preview.js

@@ -7,6 +7,11 @@ function s(v, n = 90) {
     const t = typeof v === "string" ? v : JSON.stringify(v);
     return t.length > n ? `${t.slice(0, n - 3)}...` : t;
 }
+/** What will be written: shown whole up to a large limit, and the rest is counted, never silently cut. */
+function whole(v, n = 3000) {
+    const t = typeof v === "string" ? v : JSON.stringify(v);
+    return t.length > n ? `${t.slice(0, n)} [${t.length - n} more characters not shown]` : t;
+}
 function list(rows, total) {
     const out = rows.slice(0, MAX_LINES);
     const rest = (total ?? rows.length) - out.length;
@@ -25,7 +30,7 @@ function describeChange(c) {
             continue;
         if (v && typeof v === "object" && "after" in v) {
             const b = v.before;
-            parts.push(`${k}: ${s(b || "(empty)", 40)} -> ${s(v.after, 60)}`);
+            parts.push(`${k}: ${s(b || "(empty)", 40)} -> ${whole(v.after)}`);
         }
     }
     return `${s(c.item ?? c.key, 60)}: ${parts.join("; ") || "(change)"}`;
@@ -69,7 +74,7 @@ export function formatPreview(tool, preview) {
         if (p.item || p.parent)
             lines.push(`Note on: ${s(p.item ?? p.parent, 90)}`);
         if (p.summary || p.note_preview)
-            lines.push(s(p.summary ?? p.note_preview, 600));
+            lines.push(whole(p.summary ?? p.note_preview));
         if (p.link)
             lines.push(`Link: ${p.link}`);
     }

package/dist/prompt.js

@@ -54,6 +54,9 @@ export function roleText(mode, cfg) {
 export function systemAddition(mode, cfg, cwd) {
     const user = who(cfg);
     const parts = [`# Sub-Sub: ${mode === "librarian" ? "Librarian" : "Researcher"} mode`, roleText(mode, cfg)];
+    if (cfg.vault) {
+        parts.push("# The Sub-Sub folder", `The Sub-Sub folder is ${cfg.vault}. Folder names in these instructions (Inbox/, Literature/, Syntheses/, Research/, Zotero/) are inside it. Write notes there with absolute paths, even when the working folder is somewhere else.`);
+    }
     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/shortcut.js

@@ -64,7 +64,7 @@ export function desktopEntry(p) {
         "[Desktop Entry]",
         "Type=Application",
         "Name=Sub-Sub",
-        "Comment=Zotero librarian and research assistant",
+        "Comment=Research assistant for your Zotero library",
         `Exec=${desktopQuote(p.node)} ${desktopQuote(p.bin)} web`,
         `Path=${p.home}`,
         `Icon=${join(p.packageDir, "assets", "icon.png")}`,
@@ -85,7 +85,7 @@ export function windowsScript(p) {
         `  $s.Arguments = ${psQuote(`"${p.bin}" web`)}`,
         `  $s.WorkingDirectory = ${psQuote(p.home)}`,
         `  $s.IconLocation = ${psQuote(join(p.packageDir, "assets", "icon.ico"))}`,
-        "  $s.Description = 'Sub-Sub: Zotero librarian and research assistant'",
+        "  $s.Description = 'Sub-Sub: research assistant for your Zotero library'",
         "  $s.WindowStyle = 7",
         "  $s.Save()",
         "  Write-Output (Join-Path $dir 'Sub-Sub.lnk')",

package/dist/subsub.js

@@ -1,5 +1,5 @@
 /**
- * Sub-Sub: a Zotero librarian and research assistant for pi.
+ * Sub-Sub: a research assistant for pi that works from your own Zotero library.
  *
  * - Two modes: the Librarian manages the library (Zotero tools only); the
  *   Researcher does the same and also searches PubMed, Europe PMC and OpenAlex
@@ -23,7 +23,7 @@ import { expand, findUv, isProfile, loadConfig, parseEnvFile, saveConfig, server
 import { profileList, profileSpec, promptBlocked } from "./profiles.js";
 import { coerceArgs, loosenArrays, resolvePathArgs } from "./args.js";
 import { applyEdits, checkLiteratureNote } from "./notes.js";
-import { buildPolicy, judgePath, normalizeToolPath, realish, within } from "./paths.js";
+import { buildPolicy, isSecret, judgePath, normalizeToolPath, realish, within } from "./paths.js";
 import { describeArgs, formatPreview } from "./preview.js";
 import { headerLines, paintPreview, QUOTES, schemeFromAnsi, themeName } from "./look.js";
 import { systemAddition } from "./prompt.js";
@@ -104,6 +104,7 @@ export async function createSubsub(pi, deps = {}) {
     if (deps.bridge)
         registerTools(deps.bridge);
     pi.registerFlag("librarian", { description: "Start Sub-Sub in the Librarian mode", type: "boolean", default: false });
+    pi.registerFlag("researcher", { description: "Start Sub-Sub in the Researcher mode", type: "boolean", default: false });
     let mode = cfg.defaultMode;
     const benchRun = Boolean(process.env.SUBSUB_BENCH_OUT);
     const toolOpts = () => ({ profile, bench: benchRun });
@@ -220,11 +221,12 @@ export async function createSubsub(pi, deps = {}) {
         webCtx = ctx;
         emitWeb();
     }
-    async function applyMode(ctx, next, remember) {
+    /** Set the mode's tools and, unless `switchModel` is false, the mode's model. */
+    async function applyMode(ctx, next, remember, switchModel = true) {
         mode = next;
         pi.setActiveTools(toolsFor(mode, registered(), toolOpts()));
         const spec = cfg.models[mode];
-        if (spec) {
+        if (spec && switchModel) {
             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;
@@ -243,16 +245,25 @@ export async function createSubsub(pi, deps = {}) {
             registerTools(b);
         }
         let restored;
+        // A resumed conversation keeps its model. pi records a model for every new session too,
+        // so only a session with messages counts (pi's own test for an existing session).
+        let hasModel = false;
+        let hasMessages = false;
         for (const e of ctx.sessionManager.getBranch()) {
             const m = e.customType === MODE_ENTRY ? e.data?.mode : undefined;
             if (m === "librarian" || m === "researcher")
                 restored = m;
+            if (e.type === "model_change")
+                hasModel = true;
+            if (e.type === "message")
+                hasMessages = true;
         }
+        const modelChosen = hasModel && hasMessages;
         // Judge light or dark before Sub-Sub changes the theme.
         if (lookOn(ctx))
             scheme ??= schemeFromAnsi(ctx.ui.theme.getFgAnsi("text"), ctx.ui.theme.name);
         applyTheme(ctx);
-        await applyMode(ctx, restored ?? (pi.getFlag("librarian") ? "librarian" : cfg.defaultMode), false);
+        await applyMode(ctx, restored ?? (pi.getFlag("librarian") ? "librarian" : pi.getFlag("researcher") ? "researcher" : cfg.defaultMode), false, !modelChosen);
         if (lookOn(ctx)) {
             setHeader(ctx);
             void refreshLibrary();
@@ -260,6 +271,8 @@ export async function createSubsub(pi, deps = {}) {
         else if (webView) {
             void refreshLibrary();
         }
+        if (!ctx.model && !webView)
+            ctx.ui.notify("Sub-Sub: no model is connected yet. Type /login and select a provider (or use the model button in subsub web).", "warning");
         for (const [name, err] of Object.entries(bridge.errors)) {
             ctx.ui.notify(`Sub-Sub: the ${name} server did not start: ${err.split("\n")[0]}`, "error");
         }
@@ -271,10 +284,28 @@ export async function createSubsub(pi, deps = {}) {
         bridge = undefined;
         await b?.close();
     });
+    /** Prompt commands for the Researcher; the Librarian has the library ones (tag-batch, clean-tags, import-queue). */
+    const RESEARCH_PROMPTS = ["lit", "compare", "lit-note", "synthesis", "gaps", "manuscript", "verify", "review", "alert", "request-copy", "digest"];
+    // /tree moves to another branch: take that branch's mode (pi restores its model itself).
+    pi.on("session_tree", async (_event, ctx) => {
+        let m;
+        for (const e of ctx.sessionManager.getBranch()) {
+            const x = e.customType === MODE_ENTRY ? e.data?.mode : undefined;
+            if (x === "librarian" || x === "researcher")
+                m = x;
+        }
+        if (m && m !== mode)
+            await applyMode(ctx, m, false, false);
+    });
     pi.on("model_select", async (_event, ctx) => status(ctx));
     // Prompt commands that the profile does not run (/lit for Reader, /review for Reader and Scholar).
     // The input event comes before pi expands a prompt template.
     pi.on("input", async (event, ctx) => {
+        const cmd = /^\/([\w-]+)(?:\s|$)/.exec(event.text.trim())?.[1];
+        if (mode === "librarian" && cmd && RESEARCH_PROMPTS.includes(cmd)) {
+            ctx.ui.notify(`Sub-Sub: /${cmd} is part of the Researcher. Switch with /researcher.`, "warning");
+            return { action: "handled" };
+        }
         const why = promptBlocked(event.text, profile);
         if (!why)
             return { action: "continue" };
@@ -303,6 +334,10 @@ export async function createSubsub(pi, deps = {}) {
                 return { block: true, reason: why };
             }
         }
+        // grep, find and ls search the working folder when no path is given.
+        if (["read", "grep", "find", "ls"].includes(name) && isSecret(normalizeToolPath(typeof input.path === "string" ? input.path : ".", ctx.cwd), name === "grep", cfg.envFile)) {
+            return { block: true, reason: "That file holds keys or passwords. Sub-Sub does not read it." };
+        }
         if (name.startsWith("verify_"))
             return verifyGate(name, input, ctx);
         const kind = benchOut && name === "scholar_queue_imports" ? "confirm" : gateKind(name, input);
@@ -327,6 +362,12 @@ export async function createSubsub(pi, deps = {}) {
             return { block: true, reason: `Library changes need ${user}'s approval, which needs an interactive session.` };
         }
         if (kind === "confirm") {
+            // A file the tool writes is judged like any file write: protected files stay protected.
+            if (typeof input.output_path === "string") {
+                const verdict = judgePath(normalizeToolPath(input.output_path, ctx.cwd), buildPolicy({ vault: cfg.vault, cwd: ctx.cwd, serverDir: cfg.serverDir, packageDir: PACKAGE_DIR }));
+                if (!verdict.ok && /protected|hidden/.test(verdict.why))
+                    return { block: true, reason: `Sub-Sub does not write there: ${verdict.why}.` };
+            }
             const ok = await ctx.ui.confirm(`Sub-Sub: run ${name}?`, describeArgs(input));
             return ok ? undefined : { block: true, reason: `${user} did not approve. Ask what to change.` };
         }
@@ -342,8 +383,29 @@ export async function createSubsub(pi, deps = {}) {
         }
         if (preview.isError)
             return { block: true, reason: preview.text };
-        const ok = await ctx.ui.confirm(`Sub-Sub: apply ${name.replace(/^(zotero|scholar)_/, "")}?`, paintFor(ctx)(formatPreview(name, preview.data ?? preview.text)));
-        return ok ? undefined : { block: true, reason: `${user} did not approve this change. Ask what to change; do not retry the same call.` };
+        const title = `Sub-Sub: apply ${name.replace(/^(zotero|scholar)_/, "")}?`;
+        let shown = formatPreview(name, preview.data ?? preview.text);
+        // The dialog may stay open for minutes. Before applying, compute the preview again: if the
+        // library changed meanwhile (an edit in Zotero, new items), show the new preview instead.
+        for (let round = 0; round < 3; round++) {
+            const ok = await ctx.ui.confirm(round ? `${title} (the library changed; this is the new preview)` : title, paintFor(ctx)(shown));
+            if (!ok)
+                return { block: true, reason: `${user} did not approve this change. Ask what to change; do not retry the same call.` };
+            let again;
+            try {
+                again = await current().call(name, { ...input, dry_run: true }, ctx.signal);
+            }
+            catch (err) {
+                return { block: true, reason: `Preview failed: ${err.message}` };
+            }
+            if (again.isError)
+                return { block: true, reason: again.text };
+            const now = formatPreview(name, again.data ?? again.text);
+            if (now === shown)
+                return undefined;
+            shown = now;
+        }
+        return { block: true, reason: "The library kept changing while the preview was open. Nothing was applied; try again." };
     });
     /** A literature note (front matter with a citekey) must state its evidence; see notes.ts. */
     function literatureNoteProblem(name, target, input) {
@@ -453,7 +515,7 @@ export async function createSubsub(pi, deps = {}) {
             catch (err) {
                 saved = ` Not saved: ${err.message}`;
             }
-            await applyMode(ctx, mode, false);
+            await applyMode(ctx, mode, false, false);
             ctx.ui.notify(`Sub-Sub: ${profileSpec(profile).label} profile (${profileSpec(profile).summary}).${saved}`, "info");
         },
     });

package/dist/web.js

@@ -21,7 +21,7 @@ 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 { 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";
@@ -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;
         }
@@ -387,23 +402,40 @@ 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())
             broadcast({ type: "dialog_closed", id });
         dialogs.clear();
-        await agent.stop();
-        restarting = false;
+        try {
+            await agent.stop();
+        }
+        finally {
+            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(() => {
@@ -492,7 +524,15 @@ export async function startWeb(opts, env = process.env, log = () => { }) {
                     const message = String(body.message ?? "").trim();
                     if (!message)
                         return send(res, 400, { error: "empty message" });
-                    await agent.request({ type: "prompt", message, ...(busy ? { streamingBehavior: "followUp" } : {}) });
+                    try {
+                        await agent.request({ type: "prompt", message, ...(busy ? { streamingBehavior: "followUp" } : {}) });
+                    }
+                    catch (err) {
+                        // No provider yet: the page opens the model dialog instead of showing pi's text.
+                        if (/no api key|no model|no models available/i.test(err.message))
+                            return send(res, 409, { error: "nomodel" });
+                        throw err;
+                    }
                     return send(res, 200, { ok: true });
                 }
                 case "POST /api/abort":
@@ -545,47 +585,51 @@ 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 for the current mode (or both), then restart pi so the extension reads it.
                     const mode = subsubState?.mode === "librarian" ? "librarian" : "researcher";
-                    const models = { ...(loadConfig(env).models ?? {}), [mode]: spec };
+                    // 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);
-                    await agent.request({ type: "set_model", provider: String(body.provider), modelId: String(body.id) });
-                    await restartAgent();
-                    return send(res, 200, { ok: true });
+                    return withRestart(res, async () => {
+                        saveConfig({ models, model: undefined }, env);
+                        // The open conversation records the new model, so it keeps it after the restart.
+                        await agent.request({ type: "set_model", provider: String(body.provider), modelId: String(body.id) }).catch(() => { });
+                    });
                 }
                 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" && Object.keys(current.models).length === 0)
-                        saveConfig({ models: TESTED_MODELS, model: 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": "0.11.0",
-  "description": "Sub-Sub: a Zotero librarian and research assistant in the browser or the terminal, built on pi",
+  "version": "0.11.2",
+  "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/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]
@@ -79,7 +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

package/src/bridge.ts

@@ -7,6 +7,7 @@
 
 import { Client } from "@modelcontextprotocol/sdk/client/index.js";
 import { StdioClientTransport } from "@modelcontextprotocol/sdk/client/stdio.js";
+import { refreshedArgs } from "./config.ts";
 
 export interface ServerSpec {
 	name: string; // tool prefix: "zotero" or "scholar"
@@ -85,12 +86,14 @@ export class Bridge {
 				});
 			}
 		} catch (err) {
-			this.errors[spec.name] = `${(err as Error).message}${stderr ? `\n${stderr.trim()}` : ""}`;
 			try {
 				await client.close();
 			} catch {
 				/* ignore */
 			}
+			const retry = refreshedArgs(spec.args, stderr);
+			if (retry) return this.startOne({ ...spec, args: retry }, timeoutMs);
+			this.errors[spec.name] = `${(err as Error).message}${stderr ? `\n${stderr.trim()}` : ""}`;
 		}
 	}