@tiagojct/subsub 0.11.1 → 0.11.2

package/README.md

@@ -25,8 +25,8 @@ Each mode can have its own model. Switch with `/researcher` and `/librarian`, or
 Every library change works the same way in both modes:
 
 - The Zotero server computes the change first. Sub-Sub shows it to you (added tags in green, removed tags in red) and applies it only when you select Yes. The check is in the program, so the model cannot skip it.
-- Each change sends the item's version, so an edit you make in Zotero at the same time is not overwritten.
-- Every change is journaled. `/undo` reverts it.
+- If you edit an item in Zotero while the preview is open, Sub-Sub shows you the new preview before it changes anything. Each change also sends the item's version, so a field you edit at the moment of writing is not overwritten.
+- Every change to an item is journaled. `/undo` reverts it. (A new collection is not; remove it in Zotero if you do not want it.)
 - Nothing is deleted: items go to the Zotero trash. Only tags from your tag list can be added.
 
 ## Profiles

package/dist/bridge.js

@@ -6,6 +6,7 @@
  */
 import { Client } from "@modelcontextprotocol/sdk/client/index.js";
 import { StdioClientTransport } from "@modelcontextprotocol/sdk/client/stdio.js";
+import { refreshedArgs } from "./config.js";
 function withTimeout(p, ms, what) {
     return new Promise((resolve, reject) => {
         const t = setTimeout(() => reject(new Error(`${what} did not answer within ${Math.round(ms / 1000)} s`)), ms);
@@ -56,13 +57,16 @@ export class Bridge {
             }
         }
         catch (err) {
-            this.errors[spec.name] = `${err.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] = `${err.message}${stderr ? `\n${stderr.trim()}` : ""}`;
         }
     }
     has(fullName) {

package/dist/config.js

@@ -33,7 +33,7 @@ export const DEFAULT_MODELS = {
 };
 export const PROFILES = ["reader", "scholar", "author", "editor"];
 /** The Zotero server release that this Sub-Sub version runs when there is no local server folder. */
-export const SERVER_VERSION = "0.5.1";
+export const SERVER_VERSION = "0.5.2";
 /** The Starbuck release (PyPI) that this Sub-Sub version runs when there is no local Starbuck folder. */
 export const STARBUCK_VERSION = "0.2.0";
 export const STARBUCK_SOURCE = `starbuck==${STARBUCK_VERSION}`;
@@ -171,6 +171,20 @@ export function serverCommand(cfg, program, args = [], env = process.env) {
     }
     return { command: uv, args: ["tool", "run", "--quiet", "--from", `zotero-local-mcp==${SERVER_VERSION}`, program, ...args] };
 }
+/**
+ * uv caches the PyPI index; right after a release it may not know the pinned version yet
+ * ("there is no version of zotero-local-mcp==0.5.2"). Then the same command runs again with
+ * the index for that package refreshed. Returns undefined when a retry would not help.
+ */
+export function refreshedArgs(args, stderr) {
+    if (!/there is no version of|no solution found/i.test(stderr))
+        return undefined;
+    const i = args.indexOf("--from");
+    if (args[0] !== "tool" || args[1] !== "run" || i < 0 || args.includes("--refresh-package"))
+        return undefined;
+    const pkg = args[i + 1].split(/[=<>!~]/)[0];
+    return [...args.slice(0, 2), "--refresh-package", pkg, ...args.slice(2)];
+}
 export function starbuckEnabled(cfg) {
     return (cfg.addons ?? []).includes("starbuck");
 }

package/dist/doctor.js

@@ -10,7 +10,7 @@ import { spawnSync } from "node:child_process";
 import { existsSync, readFileSync } from "node:fs";
 import { homedir } from "node:os";
 import { join } from "node:path";
-import { findUv, loadConfig, SERVER_VERSION, serverCommand, STARBUCK_SOURCE, starbuckCommand, starbuckEnabled, } from "./config.js";
+import { findUv, loadConfig, SERVER_VERSION, serverCommand, STARBUCK_SOURCE, starbuckCommand, starbuckEnabled, refreshedArgs, } from "./config.js";
 import { isObsidianVault, LEGACY_SETTINGS_DIR, SETTINGS_FILES, settingsFile } from "./layout.js";
 import { profileSpec } from "./profiles.js";
 export const defaultRunner = (command, args, env) => {
@@ -50,7 +50,11 @@ export function runChecks(cfg, env, deps = {}) {
     out.push({ name: "uv", ok: true, detail: uvRun.stdout.trim() });
     const cmd = serverCommand(cfg, "zotero-local-mcp", ["--check"], env);
     const local = cmd.args.includes("--directory");
-    const res = run(cmd.command, cmd.args, { ...env, ...(cfg.envFile ? { ZOTERO_MCP_ENV: cfg.envFile } : {}) });
+    const serverEnv = { ...env, ...(cfg.envFile ? { ZOTERO_MCP_ENV: cfg.envFile } : {}) };
+    let res = run(cmd.command, cmd.args, serverEnv);
+    const retry = res.status !== 0 ? refreshedArgs(cmd.args, res.stderr) : undefined;
+    if (retry)
+        res = run(cmd.command, retry, serverEnv);
     let st;
     try {
         st = JSON.parse(res.stdout);
@@ -106,7 +110,7 @@ export function runChecks(cfg, env, deps = {}) {
     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.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." });
+        : { name: "Model login", ok: false, detail: "no model provider yet", fix: "Open Sub-Sub (subsub web), select the model button and save an API key. In the terminal: type subsub, then /login." });
     return out;
 }
 /** The Starbuck add-on: can uv start it? (`starbuck --version`, from the local folder or the pinned release) */

package/dist/init.js

@@ -107,6 +107,8 @@ export async function runInit(io, flags, env = process.env, deps = {}) {
     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);
@@ -232,6 +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) {
@@ -287,8 +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) => {

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(`..${sep}`) && rel !== ".." && !isAbsolute(rel));
 }
 export function buildPolicy(opts) {
@@ -81,19 +85,22 @@ export function judgePath(target, policy) {
     const hit = policy.protectedPaths.find((p) => within(target, p));
     if (hit)
         return { ok: false, why: `it changes a protected file or folder (${hit})` };
+    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.
-    const hidden = target.split(/[\\/]/).find((part) => part.startsWith(".") && part !== "." && part !== "..");
+    // 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 (${hidden})` };
-    if (policy.allowed.some((a) => within(target, a)))
-        return { ok: true };
-    return { ok: false, why: "it is outside the vault and the working folder" };
+    return { ok: true };
 }
 /** Files with keys and passwords: the model may not read them, even when you ask. */
 export function secretPaths() {
     const home = realish(homedir());
     return [
         join(home, ".subsub", "agent", "auth.json"),
+        ...[process.env.SUBSUB_AGENT_DIR, process.env.PI_CODING_AGENT_DIR].filter((d) => !!d).map((d) => join(realish(d.replace(/^~(?=$|[\\/])/, home)), "auth.json")),
         join(home, ".pi", "agent", "auth.json"),
         join(home, ".config", "zotero-local-mcp", "env"),
         join(home, ".ssh"),
@@ -102,6 +109,6 @@ export function secretPaths() {
     ];
 }
 /** True if reading `target` would read a secret; for grep, also a folder that holds one. */
-export function isSecret(target, recursive = false) {
-    return secretPaths().some((p) => within(target, p) || (recursive && within(p, target)));
+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/subsub.js

@@ -245,14 +245,20 @@ export async function createSubsub(pi, deps = {}) {
             registerTools(b);
         }
         let restored;
-        let modelChosen = false; // the session already has a model: a resumed conversation keeps it
+        // 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")
-                modelChosen = true;
+                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);
@@ -265,6 +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");
         }
@@ -326,7 +334,8 @@ export async function createSubsub(pi, deps = {}) {
                 return { block: true, reason: why };
             }
         }
-        if (["read", "grep", "find", "ls"].includes(name) && typeof input.path === "string" && isSecret(normalizeToolPath(input.path, ctx.cwd), name === "grep")) {
+        // 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_"))
@@ -353,6 +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.` };
         }
@@ -368,8 +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) {

package/dist/web.js

@@ -412,8 +412,12 @@ export async function startWeb(opts, env = process.env, log = () => { }) {
         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;
         startAgent();
         broadcast(await snapshot());
@@ -520,7 +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":
@@ -585,9 +597,10 @@ export async function startWeb(opts, env = process.env, log = () => { }) {
                     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) });
+                        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": {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@tiagojct/subsub",
-  "version": "0.11.1",
+  "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",

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()}` : ""}`;
 		}
 	}
 

package/src/config.ts

@@ -39,7 +39,7 @@ 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 = "0.5.1";
+export const SERVER_VERSION = "0.5.2";
 
 /** The Starbuck release (PyPI) that this Sub-Sub version runs when there is no local Starbuck folder. */
 export const STARBUCK_VERSION = "0.2.0";
@@ -225,6 +225,19 @@ export function serverCommand(
 	return { command: uv, args: ["tool", "run", "--quiet", "--from", `zotero-local-mcp==${SERVER_VERSION}`, program, ...args] };
 }
 
+/**
+ * uv caches the PyPI index; right after a release it may not know the pinned version yet
+ * ("there is no version of zotero-local-mcp==0.5.2"). Then the same command runs again with
+ * the index for that package refreshed. Returns undefined when a retry would not help.
+ */
+export function refreshedArgs(args: string[], stderr: string): string[] | undefined {
+	if (!/there is no version of|no solution found/i.test(stderr)) return undefined;
+	const i = args.indexOf("--from");
+	if (args[0] !== "tool" || args[1] !== "run" || i < 0 || args.includes("--refresh-package")) return undefined;
+	const pkg = args[i + 1].split(/[=<>!~]/)[0];
+	return [...args.slice(0, 2), "--refresh-package", pkg, ...args.slice(2)];
+}
+
 export function starbuckEnabled(cfg: Pick<SubsubConfig, "addons">): boolean {
 	return (cfg.addons ?? []).includes("starbuck");
 }

package/src/doctor.ts

@@ -20,6 +20,7 @@ import {
 	starbuckCommand,
 	starbuckEnabled,
 	type SubsubConfig,
+	refreshedArgs,
 } from "./config.ts";
 import { isObsidianVault, LEGACY_SETTINGS_DIR, SETTINGS_FILES, settingsFile } from "./layout.ts";
 import { profileSpec } from "./profiles.ts";
@@ -92,7 +93,10 @@ export function runChecks(
 
 	const cmd = serverCommand(cfg, "zotero-local-mcp", ["--check"], env);
 	const local = cmd.args.includes("--directory");
-	const res = run(cmd.command, cmd.args, { ...env, ...(cfg.envFile ? { ZOTERO_MCP_ENV: cfg.envFile } : {}) });
+	const serverEnv = { ...env, ...(cfg.envFile ? { ZOTERO_MCP_ENV: cfg.envFile } : {}) };
+	let res = run(cmd.command, cmd.args, serverEnv);
+	const retry = res.status !== 0 ? refreshedArgs(cmd.args, res.stderr) : undefined;
+	if (retry) res = run(cmd.command, retry, serverEnv);
 	let st: Record<string, any> | undefined;
 	try {
 		st = JSON.parse(res.stdout);
@@ -150,7 +154,7 @@ export function runChecks(
 	out.push(
 		hasLogin(agentDir)
 			? { 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." },
+			: { name: "Model login", ok: false, detail: "no model provider yet", fix: "Open Sub-Sub (subsub web), select the model button and save an API key. In the terminal: type subsub, then /login." },
 	);
 	return out;
 }

package/src/init.ts

@@ -155,6 +155,7 @@ export async function runInit(
 	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;
@@ -301,6 +302,7 @@ export async function runInit(
 	if (starbuck === "on") io.say(starbuckNote || "Reference checks: on. The first start downloads Starbuck.");
 	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 };
 }
 
@@ -354,7 +356,10 @@ function terminalIO(): InitIO & { close(): void } {
 
 export async function initMain(args: string[], env: NodeJS.ProcessEnv = process.env): Promise<number> {
 	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) => {

package/src/paths.ts

@@ -45,9 +45,14 @@ export function realish(abs: string): string {
 	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: string, parent: string | undefined): boolean {
 	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));
 }
 
@@ -92,11 +97,13 @@ export type PathVerdict = { ok: true } | { ok: false; why: string };
 export function judgePath(target: string, policy: PathPolicy): PathVerdict {
 	const hit = policy.protectedPaths.find((p) => within(target, p));
 	if (hit) return { ok: false, why: `it changes a protected file or folder (${hit})` };
+	const root = policy.allowed.find((a) => within(target, a));
+	if (!root) return { ok: false, why: "it is outside the vault and the working folder" };
 	// Notes never live in hidden folders; .git/hooks, .obsidian/plugins or .vscode can run code.
-	const hidden = target.split(/[\\/]/).find((part) => part.startsWith(".") && part !== "." && part !== "..");
+	// Only the part inside the folder counts, so a vault under ~/.something still works.
+	const hidden = relative(root, target).split(/[\\/]/).find((part) => part.startsWith(".") && part !== "." && part !== "..");
 	if (hidden) return { ok: false, why: `it is in a hidden folder or file (${hidden})` };
-	if (policy.allowed.some((a) => within(target, a))) return { ok: true };
-	return { ok: false, why: "it is outside the vault and the working folder" };
+	return { ok: true };
 }
 
 /** Files with keys and passwords: the model may not read them, even when you ask. */
@@ -104,6 +111,7 @@ export function secretPaths(): string[] {
 	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 is string => !!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"),
@@ -113,6 +121,6 @@ export function secretPaths(): string[] {
 }
 
 /** True if reading `target` would read a secret; for grep, also a folder that holds one. */
-export function isSecret(target: string, recursive = false): boolean {
-	return secretPaths().some((p) => within(target, p) || (recursive && within(p, target)));
+export function isSecret(target: string, recursive = false, envFile?: string): boolean {
+	return [...secretPaths(), ...(envFile ? [realish(envFile)] : [])].some((p) => within(target, p) || (recursive && within(p, target)));
 }

package/src/preview.ts

@@ -12,6 +12,12 @@ function s(v: unknown, n = 90): string {
 	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: unknown, n = 3000): string {
+	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: string[], total?: number): string[] {
 	const out = rows.slice(0, MAX_LINES);
 	const rest = (total ?? rows.length) - out.length;
@@ -27,7 +33,7 @@ function describeChange(c: Obj): string {
 		if (["key", "item", "added", "removed", "tags_after"].includes(k)) continue;
 		if (v && typeof v === "object" && "after" in (v as Obj)) {
 			const b = (v as Obj).before;
-			parts.push(`${k}: ${s(b || "(empty)", 40)} -> ${s((v as Obj).after, 60)}`);
+			parts.push(`${k}: ${s(b || "(empty)", 40)} -> ${whole((v as Obj).after)}`);
 		}
 	}
 	return `${s(c.item ?? c.key, 60)}: ${parts.join("; ") || "(change)"}`;
@@ -83,7 +89,7 @@ export function formatPreview(tool: string, preview: unknown): string {
 	}
 	if (tool.endsWith("attach_note") || tool.endsWith("create_note")) {
 		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));
+		if (p.summary || p.note_preview) lines.push(whole(p.summary ?? p.note_preview));
 		if (p.link) lines.push(`Link: ${p.link}`);
 	}
 	const skipped = p.skipped as Obj | undefined;

package/src/subsub.ts

@@ -276,12 +276,17 @@ export async function createSubsub(pi: ExtensionAPI, deps: SubsubDeps = {}): Pro
 			registerTools(b);
 		}
 		let restored: Mode | undefined;
-		let modelChosen = false; // the session already has a model: a resumed conversation keeps it
+		// 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() as Array<{ type?: string; customType?: string; data?: { mode?: unknown } }>) {
 			const m = e.customType === MODE_ENTRY ? e.data?.mode : undefined;
 			if (m === "librarian" || m === "researcher") restored = m;
-			if (e.type === "model_change") modelChosen = true;
+			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);
@@ -292,6 +297,7 @@ export async function createSubsub(pi: ExtensionAPI, deps: SubsubDeps = {}): Pro
 		} 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");
 		}
@@ -355,7 +361,8 @@ export async function createSubsub(pi: ExtensionAPI, deps: SubsubDeps = {}): Pro
 				return { block: true, reason: why };
 			}
 		}
-		if (["read", "grep", "find", "ls"].includes(name) && typeof input.path === "string" && isSecret(normalizeToolPath(input.path, ctx.cwd), name === "grep")) {
+		// 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);
@@ -376,6 +383,11 @@ export async function createSubsub(pi: ExtensionAPI, deps: SubsubDeps = {}): Pro
 			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.` };
 		}
@@ -389,11 +401,25 @@ export async function createSubsub(pi: ExtensionAPI, deps: SubsubDeps = {}): Pro
 			return { block: true, reason: `Preview failed: ${(err as Error).message}` };
 		}
 		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 as Error).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. */

package/src/web.ts

@@ -444,8 +444,11 @@ export async function startWeb(opts: WebOptions, env: NodeJS.ProcessEnv = proces
 		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;
 		startAgent();
 		broadcast(await snapshot());
@@ -547,7 +550,13 @@ export async function startWeb(opts: WebOptions, env: NodeJS.ProcessEnv = proces
 					const body = await readJson(req);
 					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 as Error).message)) return send(res, 409, { error: "nomodel" });
+						throw err;
+					}
 					return send(res, 200, { ok: true });
 				}
 				case "POST /api/abort":
@@ -601,9 +610,10 @@ export async function startWeb(opts: WebOptions, env: NodeJS.ProcessEnv = proces
 					const saved = raw.models && typeof raw.models === "object" ? (raw.models as Record<string, string>) : typeof raw.model === "string" && raw.model ? { librarian: raw.model, researcher: raw.model } : {};
 					const models: Record<string, string> = { ...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) });
+						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": {

package/web/app.css

@@ -158,6 +158,7 @@ button:disabled { opacity: 0.45; cursor: default; }
 .icon-btn:hover { color: var(--text); background: var(--surface); }
 .icon-btn[aria-pressed="true"] { color: var(--accent); background: var(--accent-soft); }
 
+.model-btn.needs { color: var(--warn); border-color: var(--warn); font-family: var(--sans); }
 .chip-btn {
 	max-width: 16rem;
 	overflow: hidden;

package/web/app.js

@@ -183,7 +183,9 @@ function renderHeader() {
 	$("starbuck-toggle").checked = Boolean(state?.starbuck);
 	$("starbuck-label").title = t("starbuckHint");
 	const m = state?.model ?? session?.model;
-	$("model-btn").textContent = $("model-btn-side").textContent = m ? m.id : t("noModel");
+	const none = !m || !m.id || m.id === "unknown";
+	$("model-btn").textContent = $("model-btn-side").textContent = none ? t("noModel") : m.id;
+	for (const b of [$("model-btn"), $("model-btn-side")]) b.classList.toggle("needs", none);
 	const lib = $("library");
 	const txt = lib.querySelector(".library-text") ?? lib;
 	const L = state?.library;
@@ -862,7 +864,8 @@ function nextDialog() {
 	dlg.onkeydown = (e) => {
 		if (d.method === "confirm") {
 			if (e.repeat || performance.now() - openedAt < 700) {
-				if (!e.metaKey && !e.ctrlKey && e.key.length === 1) e.preventDefault();
+				// Escape still declines (through oncancel); Enter and Space would press the focused button.
+				if (e.key !== "Escape" && e.key !== "Tab") e.preventDefault();
 				return;
 			}
 			if (yesKeys.includes(e.key) || (e.key === "Enter" && (e.metaKey || e.ctrlKey))) {
@@ -981,6 +984,16 @@ async function sendMessage(text) {
 		return true;
 	} catch (err) {
 		if (isTemplate) sentTemplates.pop();
+		if (err.message === "nomodel") {
+			// Keep what the user wrote, and show where to connect a provider.
+			if (!input.value.trim()) {
+				input.value = message;
+				autosize();
+			}
+			note(t("noModelSend"), "warning");
+			showModels();
+			return false;
+		}
 		note(err.message, "error");
 		return false;
 	}

package/web/i18n.js

@@ -5,7 +5,8 @@ export const STRINGS = {
 	en: {
 		profile: "Profile",
 		model: "Model",
-		noModel: "No model",
+		noModel: "Connect a model",
+		noModelSend: "No model is connected yet. Choose a provider and save its key; your message is still in the box.",
 		newConversation: "New conversation",
 		actions: "Actions",
 		conversations: "Conversations",
@@ -97,7 +98,8 @@ export const STRINGS = {
 	pt: {
 		profile: "Perfil",
 		model: "Modelo",
-		noModel: "Sem modelo",
+		noModel: "Ligar um modelo",
+		noModelSend: "Ainda não há um modelo ligado. Escolha um fornecedor e guarde a chave; a sua mensagem continua na caixa.",
 		newConversation: "Nova conversa",
 		actions: "Ações",
 		conversations: "Conversas",