test(worktrees): await repository cleanup after remote timeouts

Validate decimal integrality before Number conversion can hide a fraction. Keep exact integer scientific notation, signed capture indices, and schedule limit updates working.

Co-authored-by: 见安 <73627805+Mar-garet@users.noreply.github.com>

packages/app/e2e/browser/changes-pane.spec.ts

@@ -683,7 +683,7 @@ test("discarding a staged rename restores its source path", async ({ page }) =>
 
   const panel = page.getByTestId("working-diff-panel").filter({ visible: true });
   const renamedHeader = diffHeaderForPath(panel, "src/zz-renamed.ts");
-  await expect(renamedHeader).toHaveAccessibleName("src/zz-renamed.ts, +1, -0");
+  await expect(renamedHeader).toHaveAccessibleName("src/zz-renamed.ts, +0, -0");
   const renamedToggle = renamedHeader.getByTestId(/^diff-file-\d+-toggle$/);
   const toggleTestId = await renamedToggle.getAttribute("data-testid");
   expect(toggleTestId).not.toBeNull();

packages/app/src/components/markdown/html-ish.test.ts

@@ -391,6 +391,43 @@ describe("splitHtmlishMarkdown", () => {
     );
   });
 
+  it("keeps table rows after a comparison that only looks like a tag", () => {
+    const source = [
+      "| ID | Note | Status |",
+      "|---|---|---|",
+      "| a-1 | accepts 1<size<2 only | open |",
+      "| a-2 | second row | open |",
+      "",
+      "Later x -> y.",
+    ].join("\n");
+
+    expect(splitHtmlishMarkdown(source)).toEqual([{ kind: "markdown", text: source }]);
+  });
+
+  it.each(["See <https://example.com/docs> for more.", "Stop when a<b", "Keep </ b> and a <b"])(
+    "keeps %j literal because it is not HTML",
+    (source) => {
+      expect(normalizeHtmlishMarkdown(source)).toBe(source);
+    },
+  );
+
+  it.each([
+    "Call As<Integer>() before limits<DWORD>::max()",
+    "<Kbd Data-Key='K'>Ctrl</Kbd> then <Foo/>",
+  ])("echoes unknown tags in %j as written", (source) => {
+    expect(normalizeHtmlishMarkdown(source)).toBe(source);
+  });
+
+  it("rebuilds an unknown tag that a code span splits", () => {
+    expect(normalizeHtmlishMarkdown('<Tip title="`x`">hi</Tip>')).toBe("`x`<tip title>hi</Tip>");
+  });
+
+  it("still reads tags and comments next to literal angle brackets", () => {
+    expect(normalizeHtmlishMarkdown("1<n<2 <b>bold</b><!-- hidden --> 3<4")).toBe(
+      "1<n<2 **bold** 3<4",
+    );
+  });
+
   it("falls back to inert markdown when details are unclosed", () => {
     const source = "<details><summary>Open</summary>Still open";
 

packages/app/src/components/markdown/html-ish.ts

@@ -29,6 +29,12 @@ const FENCE_LINE_RE = /^ {0,3}([`~]{3,})[^\n\r]*(?:\r?\n|$)/gm;
 const BACKTICK_RUN_RE = /`+/g;
 const SAFE_IMAGE_SRC_RE = /^(https?:\/\/|data:image\/(?:png|gif|jpe?g);base64,)/i;
 const SAFE_LINK_HREF_RE = /^(https?:\/\/|#(?:$|[\w-]))/i;
+// CommonMark open and closing tags (spec "Raw HTML"); comments are matched separately.
+const HTML_ATTRIBUTE = String.raw`\s+[A-Za-z_:][\w.:-]*(?:\s*=\s*(?:[^\s"'=<>\x60]+|'[^']*'|"[^"]*"))?`;
+const HTML_TAG_RE = new RegExp(
+  String.raw`<(?:[A-Za-z][A-Za-z0-9-]*(?:${HTML_ATTRIBUTE})*\s*\/?|\/[A-Za-z][A-Za-z0-9-]*\s*)>`,
+  "y",
+);
 const VOID_HTML_TAGS = new Set(["br", "img", "source"]);
 const MARKDOWN_TAG_WRAPPERS: Readonly<Record<string, readonly [string, string]>> = {
   b: ["**", "**"],
@@ -373,14 +379,16 @@ function renderInlineTokens(tokens: HtmlToken[]): string {
     }
 
     const children = tokens.slice(index + 1, closeIndex);
-    output += renderHtmlTag(token, children);
+    const close = tokens[closeIndex];
+    const closeRaw = isClosingTag(close, token.name) ? close.raw : `</${token.name}>`;
+    output += renderHtmlTag(token, children, closeRaw);
     index = closeIndex;
   }
 
   return output;
 }
 
-function renderHtmlTag(token: HtmlTagToken, children: HtmlToken[]): string {
+function renderHtmlTag(token: HtmlTagToken, children: HtmlToken[], closeRaw: string): string {
   if (token.name === "a") {
     return renderLinkToken(token, children);
   }
@@ -400,7 +408,7 @@ function renderHtmlTag(token: HtmlTagToken, children: HtmlToken[]): string {
   if (token.name === "p" || token.name === "div") {
     return `\n\n${renderInlineTokens(children).trim()}\n\n`;
   }
-  return `${token.raw}${renderInlineTokens(children)}</${token.name}>`;
+  return `${token.raw}${renderInlineTokens(children)}${closeRaw}`;
 }
 
 function renderTableTokens(tokens: HtmlToken[]): string {
@@ -606,7 +614,15 @@ function tokenizeHtmlishMarkdown(source: string): HtmlToken[] {
 function createHtmlishTokenParser(source: string, tokens: HtmlToken[]): HtmlishTokenParser {
   let stripNextLeadingLineBreak = false;
   let skippedLength = 0;
+  let writtenLength = 0;
+  let chunkStart = 0;
   let parser!: Parser;
+  // Unknown tags render as text, so keep them as written: the parser lowercases names
+  // and rewrites attributes. A tag split by a protected range has no single slice.
+  const readRawTag = (): string | null =>
+    parser.startIndex < chunkStart
+      ? null
+      : source.slice(parser.startIndex + skippedLength, parser.endIndex + 1 + skippedLength);
   parser = new Parser(
     {
       onopentag(name, attributes, isImplied) {
@@ -620,7 +636,7 @@ function createHtmlishTokenParser(source: string, tokens: HtmlToken[]): HtmlishT
           closing: false,
           selfClosing,
           attributes,
-          raw: renderStartTag(name, attributes),
+          raw: readRawTag() ?? renderStartTag(name, attributes),
         });
       },
       onclosetag(name, isImplied) {
@@ -633,7 +649,7 @@ function createHtmlishTokenParser(source: string, tokens: HtmlToken[]): HtmlishT
           closing: true,
           selfClosing: false,
           attributes: {},
-          raw: `</${name}>`,
+          raw: readRawTag() ?? `</${name}>`,
         });
       },
       ontext(value) {
@@ -660,6 +676,8 @@ function createHtmlishTokenParser(source: string, tokens: HtmlToken[]): HtmlishT
   );
   return {
     write(chunk) {
+      chunkStart = writtenLength;
+      writtenLength += chunk.length;
       parser.write(chunk);
     },
     skip(length) {
@@ -698,7 +716,58 @@ function escapeAttribute(value: string): string {
 
 function getProtectedMarkdownRanges(source: string): ProtectedMarkdownRange[] {
   const fencedRanges = getFencedCodeRanges(source);
-  return mergeProtectedRanges([...fencedRanges, ...getInlineCodeRanges(source, fencedRanges)]);
+  const codeRanges = mergeProtectedRanges([
+    ...fencedRanges,
+    ...getInlineCodeRanges(source, fencedRanges),
+  ]);
+  return mergeProtectedRanges([...codeRanges, ...getLiteralAngleBracketRanges(source, codeRanges)]);
+}
+
+/**
+ * htmlparser2 reads any `<` followed by a letter as a tag and keeps collecting attributes up
+ * to the next `>`, so `1<n<2` in a table cell swallows the rows after it and an autolink loses
+ * its slashes. Hand it only what CommonMark would read as raw HTML; every other `<` is text.
+ */
+function getLiteralAngleBracketRanges(
+  source: string,
+  codeRanges: ProtectedMarkdownRange[],
+): ProtectedMarkdownRange[] {
+  const ranges: ProtectedMarkdownRange[] = [];
+  let codeIndex = 0;
+  // Reused across comment openers so unclosed comments stay linear.
+  let commentClose = -1;
+  let index = source.indexOf("<");
+
+  while (index !== -1) {
+    while ((codeRanges[codeIndex]?.end ?? Infinity) <= index) {
+      codeIndex += 1;
+    }
+    const code = codeRanges[codeIndex];
+    if (code && code.start <= index) {
+      index = source.indexOf("<", code.end);
+      continue;
+    }
+
+    let htmlEnd: number | null;
+    if (source.startsWith("<!--", index)) {
+      if (commentClose !== source.length && commentClose < index + 2) {
+        const close = source.indexOf("-->", index + 2);
+        commentClose = close === -1 ? source.length : close;
+      }
+      htmlEnd = commentClose === source.length ? null : commentClose + 3;
+    } else {
+      HTML_TAG_RE.lastIndex = index;
+      htmlEnd = HTML_TAG_RE.test(source) ? HTML_TAG_RE.lastIndex : null;
+    }
+
+    if (htmlEnd === null) {
+      ranges.push({ start: index, end: index + 1 });
+      htmlEnd = index + 1;
+    }
+    index = source.indexOf("<", htmlEnd);
+  }
+
+  return ranges;
 }
 
 function getFencedCodeRanges(source: string): ProtectedMarkdownRange[] {

packages/app/src/components/ui/combobox-options.test.ts

@@ -160,3 +160,16 @@ describe("combobox above-search ordering", () => {
     expect(getComboboxFallbackIndex(ordered.length, "below-search")).toBe(0);
   });
 });
+
+describe("search-only option text", () => {
+  it("finds hidden search text while keeping title matches first", () => {
+    const bodyMatch = { id: "pr:7", label: "Fix parsing", searchText: "Release notes for 2024" };
+    const titleMatch = { id: "pr:8", label: "2024 release" };
+    expect(filterAndRankComboboxOptions([bodyMatch, titleMatch], "2024")).toEqual([
+      titleMatch,
+      bodyMatch,
+    ]);
+    expect(filterAndRankComboboxOptions([bodyMatch], "unrelated")).toEqual([]);
+    expect(filterAndRankComboboxOptions([bodyMatch], "parsing 2024")).toEqual([bodyMatch]);
+  });
+});

packages/app/src/components/ui/combobox-options.ts

@@ -10,18 +10,22 @@ export interface ComboboxOptionModel {
   id: string;
   label: string;
   description?: string;
+  /** Additional text to match without displaying it in the option row. */
+  searchText?: string;
   kind?: ComboboxOptionKind;
 }
 
-const DESCRIPTION_FALLBACK_TIER = 99;
+const SECONDARY_TEXT_FALLBACK_TIER = 99;
 
 function scoreOption(opt: ComboboxOptionModel, search: string): MatchScore | null {
   const best = scoreTextFields(search, [opt.label, opt.id]);
   if (best) return best;
-  if (!opt.description) return null;
-  const descriptionScore = scoreTextFields(search, [opt.description]);
-  if (!descriptionScore) return null;
-  return { ...descriptionScore, tier: descriptionScore.tier + DESCRIPTION_FALLBACK_TIER };
+  const secondaryFields = opt.searchText
+    ? [opt.label, opt.id, opt.description ?? "", opt.searchText]
+    : [opt.description ?? ""];
+  const secondaryScore = scoreTextFields(search, secondaryFields);
+  if (!secondaryScore) return null;
+  return { ...secondaryScore, tier: secondaryScore.tier + SECONDARY_TEXT_FALLBACK_TIER };
 }
 
 export interface BuildVisibleComboboxOptionsInput {

packages/app/src/keyboard/keyboard-shortcuts.test.ts

@@ -1,5 +1,6 @@
 import { describe, expect, it, vi } from "vitest";
 import { formatShortcut } from "@/utils/format-shortcut";
+import { keyboardEventToComboString } from "./shortcut-string";
 import {
   buildKeyboardShortcutHelpSections,
   buildEffectiveBindings,
@@ -1026,6 +1027,25 @@ describe("unassigned shortcuts", () => {
   });
 
   describe("matching", () => {
+    it("dispatches a captured Dvorak binding on the same logical key", () => {
+      const event = keyboardInput({ key: "b", code: "KeyN", metaKey: true });
+      const combo = keyboardEventToComboString(event as KeyboardEvent);
+      expect(combo).toBe("Cmd+B");
+      const bindings = buildEffectiveBindings({ "sidebar-toggle-left-mac-cmd-b": combo! });
+
+      expect(
+        resolveShortcut({ event, context: { isMac: true, isDesktop: true }, bindings }).match
+          ?.action,
+      ).toBe("sidebar.toggle.left");
+      expect(
+        resolveShortcut({
+          event: { key: "x", code: "KeyB", metaKey: true },
+          context: { isMac: true, isDesktop: true },
+          bindings,
+        }).match,
+      ).toBeNull();
+    });
+
     it("stops matching a shortcut the user unassigned", () => {
       const bindings = buildEffectiveBindings({ [TAB_NEW_BINDING]: UNASSIGNED_COMBO });
 

packages/app/src/keyboard/shortcut-string.test.ts

@@ -22,6 +22,45 @@ function keyboardEvent(overrides: Partial<KeyboardEvent>): KeyboardEvent {
 }
 
 describe("keyboardEventToComboString", () => {
+  it("captures the Dvorak character rather than its QWERTY position", () => {
+    expect(
+      keyboardEventToComboString(keyboardEvent({ key: "b", code: "KeyN", metaKey: true })),
+    ).toBe("Cmd+B");
+  });
+
+  it("captures shifted Dvorak letters and punctuation at other physical positions", () => {
+    expect(
+      keyboardEventToComboString(
+        keyboardEvent({ key: "T", code: "KeyK", metaKey: true, shiftKey: true }),
+      ),
+    ).toBe("Shift+Cmd+T");
+    expect(
+      keyboardEventToComboString(keyboardEvent({ key: ";", code: "KeyZ", ctrlKey: true })),
+    ).toBe("Ctrl+;");
+    expect(
+      keyboardEventToComboString(
+        keyboardEvent({ key: "?", code: "BracketLeft", ctrlKey: true, shiftKey: true }),
+      ),
+    ).toBe("Ctrl+Shift+/");
+  });
+
+  it("keeps named keys and rewritten Option characters capturable", () => {
+    expect(keyboardEventToComboString(keyboardEvent({ key: "ArrowLeft", code: "ArrowLeft" }))).toBe(
+      "ArrowLeft",
+    );
+    expect(
+      keyboardEventToComboString(keyboardEvent({ key: "†", code: "KeyT", altKey: true })),
+    ).toBe("Alt+T");
+  });
+
+  it("does not record a named key that dispatch does not support", () => {
+    expect(
+      keyboardEventToComboString(
+        keyboardEvent({ key: "Enter", code: "NumpadEnter", ctrlKey: true }),
+      ),
+    ).toBeNull();
+  });
+
   it("captures the minus key (regression: previously returned null)", () => {
     expect(keyboardEventToComboString(keyboardEvent({ key: "-", code: "Minus" }))).toBe("-");
   });

packages/app/src/keyboard/shortcut-string.ts

@@ -266,7 +266,16 @@ export function keyboardEventToComboString(event: KeyboardEvent): string | null
   if (event.shiftKey) parts.push("Shift");
   if (event.metaKey) parts.push("Cmd");
 
-  const humanKey = CODE_TO_KEY[event.code];
+  // Capture the same logical character that dispatch matches. Keep the code
+  // fallback for named keys and Option combinations whose key is rewritten.
+  const eventKey = event.key.toLowerCase();
+  const logicalKey = Object.entries(KEY_MAP).find(
+    ([, mapping]) =>
+      mapping.key?.length === 1 &&
+      (mapping.key.toLowerCase() === eventKey ||
+        (event.shiftKey && mapping.shiftedKey === event.key)),
+  )?.[0];
+  const humanKey = logicalKey ?? CODE_TO_KEY[event.code];
   if (humanKey) {
     parts.push(humanKey);
   } else {

packages/app/src/screens/new-workspace-picker-item.test.ts

@@ -1,4 +1,5 @@
 import { describe, expect, it } from "vitest";
+import { buildVisibleComboboxOptions } from "@/components/ui/combobox-options";
 import type { ForgeSearchItem } from "@getpaseo/protocol/messages";
 import {
   type BranchPickerDetail,
@@ -340,3 +341,48 @@ describe("defaultBasePickerItem", () => {
     expect(defaultBasePickerItem({ currentBranch: null })).toBeNull();
   });
 });
+
+describe("starting-ref search", () => {
+  it.each(["gitlab", "github"] as const)(
+    "keeps a %s change request returned for a body-only match",
+    (forge) => {
+      const item: ForgeSearchItem = {
+        ...prItem,
+        forge,
+        number: 3896,
+        title: "fix(config): send environment credentials only to trusted hosts",
+        body: "This mirrors the fix shipped for CVE-2024-53858.",
+        headRefName: "8545-duo-test",
+      };
+      const { options } = buildPickerOptionData({
+        branchDetails: [],
+        prItems: [item],
+        baseItem: null,
+      });
+      const visible = buildVisibleComboboxOptions({
+        options,
+        searchQuery: "2024",
+        searchable: true,
+        allowCustomValue: false,
+        customValuePrefix: "Use",
+      });
+      expect(visible.map((option) => option.label)).toEqual([
+        `${forge === "gitlab" ? "!" : "#"}3896 fix(config): send environment credentials only to trusted hosts`,
+      ]);
+      const selected = buildPickerOptionData({
+        branchDetails: [],
+        prItems: [],
+        baseItem: { kind: "github-pr", item },
+      });
+      expect(
+        buildVisibleComboboxOptions({
+          options: selected.options,
+          searchQuery: "2024",
+          searchable: true,
+          allowCustomValue: false,
+          customValuePrefix: "Use",
+        }),
+      ).toEqual(visible);
+    },
+  );
+});

packages/app/src/screens/new-workspace-picker-item.ts

@@ -264,7 +264,10 @@ export function buildPickerOptionData(input: {
     itemById.set(id, { kind: "github-pr", item: pr });
     const updatedAtMs = pr.updatedAt ? Date.parse(pr.updatedAt) : 0;
     const timestamp = Number.isNaN(updatedAtMs) ? 0 : Math.floor(updatedAtMs / 1000);
-    timedOptions.push({ option: { id, label: formatPrLabel(pr) }, timestamp });
+    timedOptions.push({
+      option: { id, label: formatPrLabel(pr), searchText: pr.body ?? undefined },
+      timestamp,
+    });
   }
 
   const baseItem = input.baseItem;
@@ -279,7 +282,13 @@ export function buildPickerOptionData(input: {
     const labeledItem = disambiguate(baseItem, timedOptions);
     itemById.set(selectedOptionId, labeledItem);
     timedOptions.push({
-      option: { id: selectedOptionId, label: pickerItemLabel(labeledItem) },
+      option: {
+        id: selectedOptionId,
+        label: pickerItemLabel(labeledItem),
+        ...(labeledItem.kind === "github-pr"
+          ? { searchText: labeledItem.item.body ?? undefined }
+          : {}),
+      },
       // The base sorts first: it is what a workspace is created from unless you pick something.
       timestamp: Number.POSITIVE_INFINITY,
     });

packages/app/vitest-environment.test.ts

@@ -0,0 +1,67 @@
+import { spawnSync } from "node:child_process";
+import { mkdtempSync, rmSync, writeFileSync } from "node:fs";
+import { createRequire } from "node:module";
+import path from "node:path";
+import { fileURLToPath } from "node:url";
+import { expect, it } from "vitest";
+
+const appDir = fileURLToPath(new URL(".", import.meta.url));
+const rootDir = path.resolve(appDir, "../..");
+const require = createRequire(import.meta.url);
+const vitestEntry = path.join(path.dirname(require.resolve("vitest/package.json")), "vitest.mjs");
+const tsgoEntry = path.join(
+  path.dirname(require.resolve("@typescript/native-preview/package.json")),
+  "bin/tsgo.js",
+);
+
+it("the test configuration typechecks with Expo's generated environment declaration", () => {
+  const fixtureDir = mkdtempSync(path.join(appDir, ".vitest-expo-env-"));
+  try {
+    writeFileSync(path.join(fixtureDir, "expo-env.d.ts"), '/// <reference types="expo/types" />\n');
+    writeFileSync(
+      path.join(fixtureDir, "tsconfig.json"),
+      JSON.stringify({
+        extends: "../tsconfig.json",
+        files: ["../vitest.config.ts", "expo-env.d.ts"],
+        include: [],
+      }),
+    );
+    const result = spawnSync(
+      process.execPath,
+      [tsgoEntry, "--noEmit", "--project", path.join(fixtureDir, "tsconfig.json")],
+      { cwd: appDir, encoding: "utf8", timeout: 30_000 },
+    );
+
+    expect(result.error).toBeUndefined();
+    expect(result.status, result.stdout + result.stderr).toBe(0);
+  } finally {
+    rmSync(fixtureDir, { recursive: true, force: true });
+  }
+}, 40_000);
+
+it.each([
+  {
+    name: "root",
+    cwd: rootDir,
+    args: ["packages/app/src/screens/workspace/use-mounted-tab-set.test.ts"],
+  },
+  {
+    name: "app",
+    cwd: appDir,
+    args: ["--project", "unit", "src/screens/workspace/use-mounted-tab-set.test.ts"],
+  },
+])(
+  "$name tests can render React when the shell exports NODE_ENV=production",
+  ({ cwd, args }) => {
+    const result = spawnSync(process.execPath, [vitestEntry, "run", ...args], {
+      cwd,
+      env: { ...process.env, NODE_ENV: "production" },
+      encoding: "utf8",
+      timeout: 30_000,
+    });
+
+    expect(result.error).toBeUndefined();
+    expect(result.status, result.stdout + result.stderr).toBe(0);
+  },
+  40_000,
+);

packages/app/vitest.config.ts

@@ -3,6 +3,9 @@ import { playwright } from "@vitest/browser-playwright";
 import path from "path";
 import fs from "fs";
 
+// Set this before Vite resolves dependencies and Vitest starts its workers.
+Object.assign(process.env, { NODE_ENV: "test" });
+
 const appNodeModules = path.resolve(__dirname, "node_modules");
 const rootNodeModules = path.resolve(__dirname, "../../node_modules");
 const resolvePackageEntry = (packageName: string) => {
@@ -26,6 +29,7 @@ export default defineConfig({
             "src/**/*.{test,spec}.{ts,tsx}",
             "native-release-version.test.ts",
             "app.config.test.ts",
+            "vitest-environment.test.ts",
           ],
           setupFiles: [path.resolve(__dirname, "vitest.setup.ts")],
           exclude: [...configDefaults.exclude, "e2e/**", "src/**/*.browser.{test,spec}.{ts,tsx}"],

packages/cli/src/commands/agent/logs.test.ts

@@ -15,6 +15,18 @@ function collect(items: readonly AgentTimelineItem[], turnId?: string): string {
 }
 
 describe("createFollowTranscriptWriter", () => {
+  it("matches one-shot logs when reasoning and assistant text alternate", () => {
+    const items: AgentTimelineItem[] = [
+      { type: "reasoning", text: "Check " },
+      { type: "reasoning", text: "the commands." },
+      { type: "assistant_message", text: "I will list the commands.", messageId: "msg_1" },
+      { type: "reasoning", text: "Then summarize." },
+      { type: "assistant_message", text: "Done.", messageId: "msg_2" },
+    ];
+
+    expect(collect(items).trimEnd()).toBe(formatAgentActivityTranscript(items));
+  });
+
   it("keeps a word that arrives split across fragments intact", () => {
     const output = collect([
       { type: "assistant_message", text: "the paseo-pr", messageId: "msg_1" },

packages/cli/src/commands/permit/allow.ts

@@ -1,5 +1,8 @@
 import type { Command } from "commander";
-import type { AgentPermissionRequest } from "@getpaseo/protocol/agent-types";
+import type {
+  AgentPermissionRequest,
+  AgentPermissionResponse,
+} from "@getpaseo/protocol/agent-types";
 import { connectToDaemon } from "../../utils/client.js";
 import type { CommandOptions, ListResult, OutputSchema, CommandError } from "../../output/index.js";
 
@@ -55,106 +58,136 @@ export interface PermitAllowOptions extends CommandOptions {
   host?: string;
 }
 
-export async function runAllowCommand(
-  agentIdOrPrefix: string,
-  reqId: string | undefined,
-  options: PermitAllowOptions,
-  _command: Command,
-): Promise<PermitAllowResult> {
-  // No validation needed - if no reqId provided, allow all by default
+export interface PermitClient {
+  fetchAgent(options: { agentId: string }): Promise<{
+    agent: { id: string; pendingPermissions?: AgentPermissionRequest[] };
+  } | null>;
+  respondToPermissionAndWait(
+    agentId: string,
+    requestId: string,
+    response: AgentPermissionResponse,
+  ): Promise<unknown>;
+  close(): Promise<void>;
+}
 
-  // Parse input JSON if provided
-  let updatedInput: Record<string, unknown> | undefined;
-  if (options.input) {
-    try {
-      updatedInput = JSON.parse(options.input);
-    } catch (err) {
-      const error: CommandError = {
-        code: "INVALID_JSON",
-        message: `Invalid JSON for --input: ${err instanceof Error ? err.message : String(err)}`,
-        details: 'Provide valid JSON, e.g., --input \'{"key": "value"}\'',
-      };
-      throw error;
-    }
-  }
+export type PermitClientConnector = (
+  options: Parameters<typeof connectToDaemon>[0],
+) => Promise<PermitClient>;
 
-  const client = await connectToDaemon({ target: options.daemonTarget });
+export function createAllowCommand(connect: PermitClientConnector = connectToDaemon) {
+  return async function runAllowCommand(
+    agentIdOrPrefix: string,
+    reqId: string | undefined,
+    options: PermitAllowOptions,
+    _command: Command,
+  ): Promise<PermitAllowResult> {
+    // No validation needed - if no reqId provided, allow all by default
 
-  try {
-    const fetchResult = await client.fetchAgent({ agentId: agentIdOrPrefix });
-    if (!fetchResult) {
-      await client.close();
-      const error: CommandError = {
-        code: "AGENT_NOT_FOUND",
-        message: `Agent not found: ${agentIdOrPrefix}`,
-        details: 'Use "paseo ls" to list available agents',
-      };
-      throw error;
-    }
-    const agent = fetchResult.agent;
-    const resolvedAgentId = agent.id;
-
-    // Get pending permissions for this agent
-    const pendingPermissions = agent.pendingPermissions || [];
-    if (pendingPermissions.length === 0) {
-      await client.close();
-      const error: CommandError = {
-        code: "NO_PENDING_PERMISSIONS",
-        message: `No pending permissions for agent ${agent.id.slice(0, 7)}`,
-      };
-      throw error;
-    }
-
-    // Determine which permissions to allow
-    let permissionsToAllow: AgentPermissionRequest[];
-    if (!reqId || options.all) {
-      // Default: allow all pending permissions if no req_id specified
-      // --all flag is kept as an explicit alias for clarity
-      permissionsToAllow = pendingPermissions;
-    } else {
-      // Find permission by ID prefix
-      const permission = pendingPermissions.find((p) => p.id === reqId || p.id.startsWith(reqId));
-      if (!permission) {
-        await client.close();
+    // Parse input JSON if provided
+    let updatedInput: Record<string, unknown> | undefined;
+    if (options.input) {
+      try {
+        updatedInput = JSON.parse(options.input);
+      } catch (err) {
         const error: CommandError = {
-          code: "PERMISSION_NOT_FOUND",
-          message: `Permission request not found: ${reqId}`,
-          details: `Available requests: ${pendingPermissions.map((p) => p.id.slice(0, 8)).join(", ")}`,
+          code: "INVALID_JSON",
+          message: `Invalid JSON for --input: ${err instanceof Error ? err.message : String(err)}`,
+          details: 'Provide valid JSON, e.g., --input \'{"key": "value"}\'',
         };
         throw error;
       }
-      permissionsToAllow = [permission];
     }
 
-    // Allow permissions
-    const results: PermissionResponseItem[] = await Promise.all(
-      permissionsToAllow.map(async (permission) => {
-        await client.respondToPermission(resolvedAgentId, permission.id, {
-          behavior: "allow",
-          ...(updatedInput ? { updatedInput } : {}),
-        });
-        return toPermissionResponseItem(resolvedAgentId, permission, "allowed");
-      }),
-    );
+    const client = await connect({ target: options.daemonTarget });
 
-    await client.close();
+    try {
+      const fetchResult = await client.fetchAgent({ agentId: agentIdOrPrefix });
+      if (!fetchResult) {
+        await client.close();
+        const error: CommandError = {
+          code: "AGENT_NOT_FOUND",
+          message: `Agent not found: ${agentIdOrPrefix}`,
+          details: 'Use "paseo ls" to list available agents',
+        };
+        throw error;
+      }
+      const agent = fetchResult.agent;
+      const resolvedAgentId = agent.id;
 
-    return {
-      type: "list",
-      data: results,
-      schema: permitResponseSchema,
-    };
-  } catch (err) {
-    await client.close().catch(() => {});
-    // Re-throw CommandErrors
-    if (err && typeof err === "object" && "code" in err) {
-      throw err;
+      // Get pending permissions for this agent
+      const pendingPermissions = agent.pendingPermissions || [];
+      if (pendingPermissions.length === 0) {
+        await client.close();
+        const error: CommandError = {
+          code: "NO_PENDING_PERMISSIONS",
+          message: `No pending permissions for agent ${agent.id.slice(0, 7)}`,
+        };
+        throw error;
+      }
+
+      // Determine which permissions to allow
+      let permissionsToAllow: AgentPermissionRequest[];
+      if (!reqId || options.all) {
+        // Default: allow all pending permissions if no req_id specified
+        // --all flag is kept as an explicit alias for clarity
+        permissionsToAllow = pendingPermissions;
+      } else {
+        // Find permission by ID prefix
+        const permission = pendingPermissions.find((p) => p.id === reqId || p.id.startsWith(reqId));
+        if (!permission) {
+          await client.close();
+          const error: CommandError = {
+            code: "PERMISSION_NOT_FOUND",
+            message: `Permission request not found: ${reqId}`,
+            details: `Available requests: ${pendingPermissions.map((p) => p.id.slice(0, 8)).join(", ")}`,
+          };
+          throw error;
+        }
+        permissionsToAllow = [permission];
+      }
+
+      // Allow permissions
+      const results: PermissionResponseItem[] = await Promise.all(
+        permissionsToAllow.map(async (permission) => {
+          try {
+            await client.respondToPermissionAndWait(resolvedAgentId, permission.id, {
+              behavior: "allow",
+              ...(updatedInput ? { updatedInput } : {}),
+            });
+          } catch (err) {
+            const message = err instanceof Error ? err.message : String(err);
+            const error: CommandError = {
+              code: "PERMISSION_RESPONSE_UNCONFIRMED",
+              message: `Permission response unconfirmed for request ${permission.id}: ${message}`,
+              details: 'Use "paseo permit ls" to check whether the request is still pending',
+            };
+            throw error;
+          }
+          return toPermissionResponseItem(resolvedAgentId, permission, "allowed");
+        }),
+      );
+
+      await client.close();
+
+      return {
+        type: "list",
+        data: results,
+        schema: permitResponseSchema,
+      };
+    } catch (err) {
+      await client.close().catch(() => {});
+      // Re-throw CommandErrors
+      if (err && typeof err === "object" && "code" in err) {
+        throw err;
+      }
+      const message = err instanceof Error ? err.message : String(err);
+      const error: CommandError = {
+        code: "ALLOW_PERMISSION_FAILED",
+        message: `Failed to allow permission: ${message}`,
+      };
+      throw error;
     }
-    const message = err instanceof Error ? err.message : String(err);
-    const error: CommandError = {
-      code: "ALLOW_PERMISSION_FAILED",
-      message: `Failed to allow permission: ${message}`,
-    };
-    throw error;
-  }
+  };
 }
+
+export const runAllowCommand = createAllowCommand();

packages/cli/src/commands/permit/deny.ts

@@ -6,6 +6,7 @@ import {
   permitResponseSchema,
   toPermissionResponseItem,
   type PermissionResponseItem,
+  type PermitClientConnector,
 } from "./allow.js";
 
 export type PermitDenyResult = ListResult<PermissionResponseItem>;
@@ -17,98 +18,114 @@ export interface PermitDenyOptions extends CommandOptions {
   host?: string;
 }
 
-export async function runDenyCommand(
-  agentIdOrPrefix: string,
-  reqId: string | undefined,
-  options: PermitDenyOptions,
-  _command: Command,
-): Promise<PermitDenyResult> {
-  // Validate arguments
-  if (!options.all && !reqId) {
-    const error: CommandError = {
-      code: "MISSING_ARGUMENT",
-      message: "Request ID is required unless --all is specified",
-      details: "Usage: paseo permit deny <agent> <req_id> or paseo permit deny <agent> --all",
-    };
-    throw error;
-  }
-
-  const client = await connectToDaemon({ target: options.daemonTarget });
-
-  try {
-    const fetchResult = await client.fetchAgent({ agentId: agentIdOrPrefix });
-    if (!fetchResult) {
-      await client.close();
+export function createDenyCommand(connect: PermitClientConnector = connectToDaemon) {
+  return async function runDenyCommand(
+    agentIdOrPrefix: string,
+    reqId: string | undefined,
+    options: PermitDenyOptions,
+    _command: Command,
+  ): Promise<PermitDenyResult> {
+    // Validate arguments
+    if (!options.all && !reqId) {
       const error: CommandError = {
-        code: "AGENT_NOT_FOUND",
-        message: `Agent not found: ${agentIdOrPrefix}`,
-        details: 'Use "paseo ls" to list available agents',
-      };
-      throw error;
-    }
-    const agent = fetchResult.agent;
-    const resolvedAgentId = agent.id;
-
-    // Get pending permissions for this agent
-    const pendingPermissions = agent.pendingPermissions || [];
-    if (pendingPermissions.length === 0) {
-      await client.close();
-      const error: CommandError = {
-        code: "NO_PENDING_PERMISSIONS",
-        message: `No pending permissions for agent ${agent.id.slice(0, 7)}`,
+        code: "MISSING_ARGUMENT",
+        message: "Request ID is required unless --all is specified",
+        details: "Usage: paseo permit deny <agent> <req_id> or paseo permit deny <agent> --all",
       };
       throw error;
     }
 
-    // Determine which permissions to deny
-    let permissionsToDeny: AgentPermissionRequest[];
-    if (options.all) {
-      permissionsToDeny = pendingPermissions;
-    } else {
-      // Find permission by ID prefix
-      const permission = pendingPermissions.find((p) => p.id === reqId || p.id.startsWith(reqId!));
-      if (!permission) {
+    const client = await connect({ target: options.daemonTarget });
+
+    try {
+      const fetchResult = await client.fetchAgent({ agentId: agentIdOrPrefix });
+      if (!fetchResult) {
         await client.close();
         const error: CommandError = {
-          code: "PERMISSION_NOT_FOUND",
-          message: `Permission request not found: ${reqId}`,
-          details: `Available requests: ${pendingPermissions.map((p) => p.id.slice(0, 8)).join(", ")}`,
+          code: "AGENT_NOT_FOUND",
+          message: `Agent not found: ${agentIdOrPrefix}`,
+          details: 'Use "paseo ls" to list available agents',
         };
         throw error;
       }
-      permissionsToDeny = [permission];
+      const agent = fetchResult.agent;
+      const resolvedAgentId = agent.id;
+
+      // Get pending permissions for this agent
+      const pendingPermissions = agent.pendingPermissions || [];
+      if (pendingPermissions.length === 0) {
+        await client.close();
+        const error: CommandError = {
+          code: "NO_PENDING_PERMISSIONS",
+          message: `No pending permissions for agent ${agent.id.slice(0, 7)}`,
+        };
+        throw error;
+      }
+
+      // Determine which permissions to deny
+      let permissionsToDeny: AgentPermissionRequest[];
+      if (options.all) {
+        permissionsToDeny = pendingPermissions;
+      } else {
+        // Find permission by ID prefix
+        const permission = pendingPermissions.find(
+          (p) => p.id === reqId || p.id.startsWith(reqId!),
+        );
+        if (!permission) {
+          await client.close();
+          const error: CommandError = {
+            code: "PERMISSION_NOT_FOUND",
+            message: `Permission request not found: ${reqId}`,
+            details: `Available requests: ${pendingPermissions.map((p) => p.id.slice(0, 8)).join(", ")}`,
+          };
+          throw error;
+        }
+        permissionsToDeny = [permission];
+      }
+
+      // Deny permissions
+      const results: PermissionResponseItem[] = await Promise.all(
+        permissionsToDeny.map(async (permission) => {
+          try {
+            await client.respondToPermissionAndWait(resolvedAgentId, permission.id, {
+              behavior: "deny",
+              ...(options.message ? { message: options.message } : {}),
+              ...(options.interrupt ? { interrupt: true } : {}),
+            });
+          } catch (err) {
+            const message = err instanceof Error ? err.message : String(err);
+            const error: CommandError = {
+              code: "PERMISSION_RESPONSE_UNCONFIRMED",
+              message: `Permission response unconfirmed for request ${permission.id}: ${message}`,
+              details: 'Use "paseo permit ls" to check whether the request is still pending',
+            };
+            throw error;
+          }
+          return toPermissionResponseItem(resolvedAgentId, permission, "denied");
+        }),
+      );
+
+      await client.close();
+
+      return {
+        type: "list",
+        data: results,
+        schema: permitResponseSchema,
+      };
+    } catch (err) {
+      await client.close().catch(() => {});
+      // Re-throw CommandErrors
+      if (err && typeof err === "object" && "code" in err) {
+        throw err;
+      }
+      const message = err instanceof Error ? err.message : String(err);
+      const error: CommandError = {
+        code: "DENY_PERMISSION_FAILED",
+        message: `Failed to deny permission: ${message}`,
+      };
+      throw error;
     }
-
-    // Deny permissions
-    const results: PermissionResponseItem[] = await Promise.all(
-      permissionsToDeny.map(async (permission) => {
-        await client.respondToPermission(resolvedAgentId, permission.id, {
-          behavior: "deny",
-          ...(options.message ? { message: options.message } : {}),
-          ...(options.interrupt ? { interrupt: true } : {}),
-        });
-        return toPermissionResponseItem(resolvedAgentId, permission, "denied");
-      }),
-    );
-
-    await client.close();
-
-    return {
-      type: "list",
-      data: results,
-      schema: permitResponseSchema,
-    };
-  } catch (err) {
-    await client.close().catch(() => {});
-    // Re-throw CommandErrors
-    if (err && typeof err === "object" && "code" in err) {
-      throw err;
-    }
-    const message = err instanceof Error ? err.message : String(err);
-    const error: CommandError = {
-      code: "DENY_PERMISSION_FAILED",
-      message: `Failed to deny permission: ${message}`,
-    };
-    throw error;
-  }
+  };
 }
+
+export const runDenyCommand = createDenyCommand();

packages/cli/src/commands/permit/permit-response.test.ts

@@ -0,0 +1,177 @@
+import { setImmediate as waitForCommandContinuations } from "node:timers/promises";
+import { Command } from "commander";
+import type {
+  AgentPermissionRequest,
+  AgentPermissionResponse,
+} from "@getpaseo/protocol/agent-types";
+import { describe, expect, it } from "vitest";
+import { createAllowCommand, type PermitClient } from "./allow.js";
+import { createDenyCommand } from "./deny.js";
+
+const agentId = "2d85f428-fdaf-4d98-906f-c583de2b805f";
+const requests: AgentPermissionRequest[] = [
+  {
+    id: "permission-write",
+    provider: "codex",
+    name: "CodexBash",
+    kind: "tool",
+  },
+  { id: "permission-edit", provider: "codex", name: "CodexBash", kind: "tool" },
+];
+
+class PermissionClient implements PermitClient {
+  readonly pending = [...requests];
+  readonly responses = new Map<string, AgentPermissionResponse>();
+  closed = false;
+  private notifyReceived = () => {};
+  private readonly confirmations = new Map<
+    string,
+    {
+      resolve: () => void;
+      reject: (error: Error) => void;
+    }
+  >();
+
+  async fetchAgent() {
+    return { agent: { id: agentId, pendingPermissions: this.pending } };
+  }
+
+  async respondToPermission(
+    _agentId: string,
+    requestId: string,
+    response: AgentPermissionResponse,
+  ) {
+    this.responses.set(requestId, response);
+    this.notifyReceived();
+  }
+
+  async respondToPermissionAndWait(
+    responseAgentId: string,
+    requestId: string,
+    response: AgentPermissionResponse,
+  ): Promise<void> {
+    const confirmation = new Promise<void>((resolve, reject) => {
+      this.confirmations.set(requestId, { resolve, reject });
+    });
+    await this.respondToPermission(responseAgentId, requestId, response);
+    await confirmation;
+  }
+
+  async close() {
+    this.closed = true;
+  }
+
+  async waitForResponses(count: number) {
+    while (this.responses.size < count) {
+      await new Promise<void>((resolve) => {
+        this.notifyReceived = resolve;
+      });
+    }
+  }
+
+  confirm(requestId: string) {
+    const confirmation = this.confirmations.get(requestId);
+    if (!confirmation) throw new Error(`No confirmation waiter: ${requestId}`);
+    this.pending.splice(
+      this.pending.findIndex((request) => request.id === requestId),
+      1,
+    );
+    confirmation.resolve();
+  }
+
+  fail(requestId: string, error: Error) {
+    const confirmation = this.confirmations.get(requestId);
+    if (!confirmation) throw new Error(`No confirmation waiter: ${requestId}`);
+    confirmation.reject(error);
+  }
+}
+
+const options = {
+  daemonTarget: { kind: "endpoint" as const, host: "test.invalid" },
+};
+const actions = [
+  { name: "allow", create: createAllowCommand, result: "allowed" },
+  { name: "deny", create: createDenyCommand, result: "denied" },
+];
+for (const action of actions) {
+  describe(`permit ${action.name}`, () => {
+    it("returns success and closes only after confirmation", async () => {
+      const client = new PermissionClient();
+      let completed = false;
+      const command = action.create(async () => client)(
+        agentId,
+        requests[0].id,
+        options,
+        new Command(),
+      );
+      void command.then(
+        () => (completed = true),
+        () => false,
+      );
+      await client.waitForResponses(1);
+      await waitForCommandContinuations();
+      expect(completed).toBe(false);
+      expect(client.closed).toBe(false);
+      expect(client.pending).toEqual(requests);
+      client.confirm(requests[0].id);
+      const result = await command;
+      expect(result.data).toEqual([
+        {
+          requestId: requests[0].id,
+          agentId,
+          agentShortId: agentId.slice(0, 7),
+          name: "CodexBash",
+          result: action.result,
+        },
+      ]);
+      expect(client.closed).toBe(true);
+      expect(client.pending).toEqual([requests[1]]);
+    });
+
+    it("waits for every confirmation with --all", async () => {
+      const client = new PermissionClient();
+      let completed = false;
+      const command = action.create(async () => client)(
+        agentId,
+        undefined,
+        { ...options, all: true },
+        new Command(),
+      );
+      void command.then(
+        () => (completed = true),
+        () => false,
+      );
+      await client.waitForResponses(2);
+      client.confirm(requests[0].id);
+      // Wait beyond the first reply's promise continuations while withholding the second.
+      await waitForCommandContinuations();
+      expect(completed).toBe(false);
+      expect(client.closed).toBe(false);
+      client.confirm(requests[1].id);
+      const result = await command;
+      expect(result.data.map((item) => item.result)).toEqual([action.result, action.result]);
+      expect(client.closed).toBe(true);
+      expect(client.pending).toEqual([]);
+    });
+
+    it("rejects an unconfirmed response without returning success", async () => {
+      const client = new PermissionClient();
+      const command = action.create(async () => client)(
+        agentId,
+        requests[0].id,
+        options,
+        new Command(),
+      );
+      const failure = expect(command).rejects.toMatchObject({
+        code: "PERMISSION_RESPONSE_UNCONFIRMED",
+        message: expect.stringContaining(requests[0].id),
+        details: 'Use "paseo permit ls" to check whether the request is still pending',
+      });
+      await client.waitForResponses(1);
+      client.fail(requests[0].id, new Error("Timeout waiting for message (15000ms)"));
+      await failure;
+      expect(client.closed).toBe(true);
+      expect(client.pending).toEqual(requests);
+    });
+  });
+}

packages/cli/src/commands/schedule/shared.ts

@@ -1,3 +1,4 @@
+import { parseSafeInteger } from "../../utils/integer.js";
 import type { DaemonTarget } from "../../utils/daemon-target.js";
 import { connectToDaemon, getDaemonHost } from "../../utils/client.js";
 import type { CommandError, CommandOptions } from "../../output/index.js";
@@ -441,8 +442,8 @@ function buildNewAgentConfigPatch(
 }
 
 function parsePositiveInt(value: string, flag: string): number {
-  const parsed = Number.parseInt(value, 10);
-  if (!Number.isInteger(parsed) || parsed <= 0) {
+  const parsed = parseSafeInteger(value);
+  if (parsed === undefined || parsed <= 0) {
     throw {
       code: "INVALID_INTEGER",
       message: `${flag} must be a positive integer`,

packages/cli/src/commands/terminal/capture.ts

@@ -1,3 +1,4 @@
+import { parseSafeInteger } from "../../utils/integer.js";
 import type { Command } from "commander";
 import { renderError, toCommandError } from "../../output/render.js";
 import {
@@ -85,8 +86,8 @@ function parseLineNumber(flag: string, value?: string): number | undefined {
     return undefined;
   }
 
-  const parsed = Number.parseInt(value, 10);
-  if (!Number.isInteger(parsed)) {
+  const parsed = parseSafeInteger(value);
+  if (parsed === undefined) {
     throw {
       code: "INVALID_LINE_NUMBER",
       message: `Invalid ${flag} value: ${value}`,

packages/cli/src/utils/integer.ts

@@ -0,0 +1,20 @@
+export function parseSafeInteger(value: string): number | undefined {
+  const input = value.trim();
+  const match = /^[+-]?(\d*)(?:\.(\d*))?(?:e([+-]?\d+))?$/i.exec(input);
+  if (!match) {
+    return undefined;
+  }
+
+  const digits = match[1] + (match[2] ?? "");
+  const parsed = Number(input);
+  if (digits.length === 0 || !Number.isSafeInteger(parsed)) {
+    return undefined;
+  }
+
+  // Check the decimal value before floating-point rounding can hide a fraction.
+  const decimalPlaces = (match[2]?.length ?? 0) - Number(match[3] ?? "0");
+  if (decimalPlaces > 0 && /[1-9]/.test(digits.slice(-decimalPlaces))) {
+    return undefined;
+  }
+  return parsed;
+}

packages/cli/tests/15-provider.test.ts

@@ -364,10 +364,6 @@ try {
       ids.every((id) => id.startsWith("gpt-")),
       "all codex model IDs should be from the gpt family",
     );
-    assert(
-      ids.some((id) => id.includes("codex")),
-      "codex model list should include at least one codex-optimized model",
-    );
     assert(
       data.every((m) => m.model && m.id && m.description),
       "every codex model should have model, id, and description fields",

packages/desktop/e2e/packaged-app-smoke.js

@@ -848,6 +848,11 @@ async function assertSandboxState({ browser, page, expectedSandbox, stdout, stde
 
 function assertLinuxDesktopIdentity(appPath) {
   if (process.platform === "linux") {
+    assert.deepEqual(
+      fs.readFileSync(path.join(appPath, "resources", "icon.png")),
+      fs.readFileSync(path.join(__dirname, "..", "assets", "icon.png")),
+      "Packaged Linux windows must have the Paseo icon at their runtime lookup path",
+    );
     const metadata = JSON.parse(
       extractFile(path.join(appPath, "resources", "app.asar"), "package.json").toString(),
     );

packages/desktop/electron-builder.yml

@@ -65,6 +65,8 @@ linux:
   extraResources:
     - from: bin/paseo
       to: bin/paseo
+    - from: assets/icon.png
+      to: icon.png
   target:
     - AppImage
     - deb

packages/server/package.json

@@ -89,7 +89,7 @@
     "speech:transcribe:local": "tsx scripts/transcribe-local-wav.ts",
     "test": "npm run test:unit && npm run test:integration",
     "test:unit": "vitest run --fileParallelism --exclude \"**/*.e2e.test.ts\"",
-    "test:integration": "vitest run --maxWorkers=1 src/server/daemon-e2e/cli-logs-follow.e2e.test.ts src/server/creation/creation.e2e.test.ts src/server/daemon-e2e/terminal-workspace-sdk.e2e.test.ts src/server/daemon-e2e/models.e2e.test.ts src/server/daemon-e2e/live-preferences.e2e.test.ts src/server/agent/model-catalog.e2e.test.ts src/server/plugins/plugin-paseo-api.e2e.test.ts && vitest run --maxWorkers=1 src/server/session.create-agent-worktree-autoarchive.e2e.test.ts -t \"creates a worktree and auto-archives both\" && vitest run --maxWorkers=1 src/server/agent/providers/opencode-bridge.local.e2e.test.ts -t \"versioned runtime\"",
+    "test:integration": "vitest run --maxWorkers=1 src/server/daemon-e2e/filesystem.e2e.test.ts src/server/daemon-e2e/file-download.e2e.test.ts src/server/daemon-e2e/cli-logs-follow.e2e.test.ts src/server/creation/creation.e2e.test.ts src/server/daemon-e2e/terminal-workspace-sdk.e2e.test.ts src/server/schedule-run-lifecycle.e2e.test.ts src/server/daemon-e2e/models.e2e.test.ts src/server/daemon-e2e/live-preferences.e2e.test.ts src/server/agent/model-catalog.e2e.test.ts src/server/plugins/plugin-paseo-api.e2e.test.ts && vitest run --maxWorkers=1 src/server/daemon-e2e/git-operations.e2e.test.ts -t \"merges into\" && vitest run --maxWorkers=1 src/server/session.create-agent-worktree-autoarchive.e2e.test.ts -t \"creates a worktree and auto-archives both\" && vitest run --maxWorkers=1 src/server/agent/providers/opencode-bridge.local.e2e.test.ts -t \"versioned runtime\"",
     "test:hub-cli-contract": "vitest run --maxWorkers=1 src/server/hub/hub-cli-contract.test.ts",
     "test:integration:all": "npm run test:e2e",
     "test:integration:real": "vitest run real.e2e.test.ts",

packages/server/scripts/supervisor.logging.test.ts

@@ -29,6 +29,7 @@ async function runSupervisorFixture(options: {
   blockLogPath?: boolean;
   /** Close the reading end of the supervisor's stdout and stderr as soon as it starts. */
   closeOutput?: boolean;
+  env?: NodeJS.ProcessEnv;
 }): Promise<{
   code: number | null;
   signal: NodeJS.Signals | null;
@@ -84,7 +85,9 @@ async function runSupervisorFixture(options: {
         ];
   const child = spawn(command, args, {
     cwd: repoRoot,
-    env: { ...process.env },
+    // A Node color-conflict warning can hit closed stderr before runSupervisor installs
+    // its pipe-error handlers. This fixture exercises the supervisor's own output.
+    env: { ...process.env, ...options.env, NO_COLOR: undefined, FORCE_COLOR: undefined },
     stdio: ["ignore", "pipe", "pipe"],
   });
 
@@ -205,10 +208,16 @@ describe("supervisor durable logging", () => {
     expect(result.stderr).toContain('"worker-json-stderr"');
   });
 
-  test("keeps supervising the worker when nobody reads its stdout or stderr", async () => {
-    const result = await runSupervisorFixture({
-      closeOutput: true,
-      workerSource: `
+  test.each([
+    { colors: "inherited", env: {} },
+    { colors: "conflicting", env: { NO_COLOR: "1", FORCE_COLOR: "1" } },
+  ])(
+    "keeps supervising the worker when nobody reads its stdout or stderr with $colors colors",
+    async ({ env }) => {
+      const result = await runSupervisorFixture({
+        closeOutput: true,
+        env,
+        workerSource: `
         process.on("message", (message) => {
           if (message?.type === "paseo:graceful-shutdown") process.exit(0);
         });
@@ -220,14 +229,15 @@ describe("supervisor durable logging", () => {
         }, 500);
         setInterval(() => {}, 1000);
       `,
-    });
+      });
 
-    expect(result.code).toBe(0);
-    expect(result.signal).toBeNull();
-    expect(result.log).toContain("first stderr line\n");
-    expect(result.log).toContain("later stdout line\n");
-    expect(result.log).toContain('"reason":"closed_output_probe"');
-  });
+      expect(result.code).toBe(0);
+      expect(result.signal).toBeNull();
+      expect(result.log).toContain("first stderr line\n");
+      expect(result.log).toContain("later stdout line\n");
+      expect(result.log).toContain('"reason":"closed_output_probe"');
+    },
+  );
 
   test("preserves raw non-JSON stdout and stderr lines", async () => {
     const result = await runSupervisorFixture({

packages/server/src/server/agent/activity-curator.test.ts

@@ -39,6 +39,45 @@ function row(seq: number, item: AgentTimelineItem): AgentTimelineRow {
 }
 
 describe("curateAgentActivity", () => {
+  it("keeps reasoning before the assistant text that followed it", () => {
+    const timeline: AgentTimelineItem[] = [
+      { type: "reasoning", text: "Check the commands first." },
+      { type: "assistant_message", text: "I will list the commands." },
+      toolCallItem({
+        callId: "shell-order",
+        name: "Bash",
+        detail: {
+          type: "shell",
+          command: "ls packages/cli/src/commands/agent/",
+          output: "",
+          exitCode: 0,
+        },
+      }),
+    ];
+
+    expect(curateAgentActivity(timeline)).toBe(
+      "[Thought] Check the commands first.\nI will list the commands.\n[Shell] ls packages/cli/src/commands/agent/",
+    );
+  });
+
+  it("preserves alternating text kinds, labels, and fragment concatenation", () => {
+    const timeline: AgentTimelineItem[] = [
+      { type: "assistant_message", text: "First message." },
+      { type: "reasoning", text: "First " },
+      { type: "reasoning", text: "thought." },
+      { type: "assistant_message", text: "Second " },
+      { type: "assistant_message", text: "message." },
+      { type: "reasoning", text: "Second thought." },
+    ];
+
+    expect(curateAgentActivity(timeline, { labelAssistantMessages: true })).toBe(
+      "[Assistant] First message.\n[Thought] First thought.\n[Assistant] Second message.\n[Thought] Second thought.",
+    );
+    expect(curateAgentActivity(timeline, { maxItems: 2 })).toBe(
+      "Second message.\n[Thought] Second thought.",
+    );
+  });
+
   it("renders user/assistant/reasoning entries", () => {
     const timeline: AgentTimelineItem[] = [
       { type: "user_message", text: "Hello" },

packages/server/src/server/agent/activity-curator.ts

@@ -25,36 +25,20 @@ interface ActivityEntry {
 
 type TextAgentAttachment = Extract<AgentAttachment, { type: "text" }>;
 
-function appendText(buffer: string, text: string): string {
-  const normalized = text.trim();
-  if (!normalized) {
-    return buffer;
-  }
-  if (!buffer) {
-    return normalized;
-  }
-  return `${buffer}\n${normalized}`;
-}
-
 function activityEntry(text: string): ActivityEntry {
   return { text };
 }
 
-function flushBuffers(
+function appendTextEntry(
   entries: ActivityEntry[],
-  buffers: { message: string; thought: string },
+  item: Extract<AgentTimelineItem, { type: "assistant_message" | "reasoning" }>,
   options?: ActivityCuratorOptions,
 ) {
-  if (buffers.message.trim()) {
-    const text = buffers.message.trim();
-    entries.push(activityEntry(options?.labelAssistantMessages ? `[Assistant] ${text}` : text));
-  }
-  if (buffers.thought.trim()) {
-    const text = buffers.thought.trim();
-    entries.push(activityEntry(`[Thought] ${text}`));
-  }
-  buffers.message = "";
-  buffers.thought = "";
+  const text = item.text.trim();
+  if (!text) return;
+  let prefix = options?.labelAssistantMessages ? "[Assistant] " : "";
+  if (item.type === "reasoning") prefix = "[Thought] ";
+  entries.push(activityEntry(`${prefix}${text}`));
 }
 
 function formatToolInputJson(input: unknown): string | null {
@@ -147,7 +131,6 @@ function curateProjectedActivityEntries(
   const recentItems = maxItems > 0 && items.length > maxItems ? items.slice(-maxItems) : items;
 
   const entries: ActivityEntry[] = [];
-  const buffers = { message: "", thought: "" };
 
   for (const item of recentItems) {
     if (!shouldIncludeItem(item, options)) {
@@ -156,17 +139,13 @@ function curateProjectedActivityEntries(
 
     switch (item.type) {
       case "user_message":
-        flushBuffers(entries, buffers, options);
         entries.push(activityEntry(`[User] ${item.text.trim()}`));
         break;
       case "assistant_message":
-        buffers.message = appendText(buffers.message, item.text);
-        break;
       case "reasoning":
-        buffers.thought = appendText(buffers.thought, item.text);
+        appendTextEntry(entries, item, options);
         break;
       case "tool_call": {
-        flushBuffers(entries, buffers, options);
         entries.push(formatToolCallEntry(item, options));
         if (item.detail.type === "sub_agent" && item.detail.log.trim()) {
           entries.push(activityEntry(item.detail.log.trim()));
@@ -174,7 +153,6 @@ function curateProjectedActivityEntries(
         break;
       }
       case "todo":
-        flushBuffers(entries, buffers, options);
         entries.push(activityEntry("[Tasks]"));
         for (const entry of item.items) {
           const checkbox = entry.completed ? "[x]" : "[ ]";
@@ -183,18 +161,14 @@ function curateProjectedActivityEntries(
         }
         break;
       case "error":
-        flushBuffers(entries, buffers, options);
         entries.push(activityEntry(`[Error] ${item.message}`));
         break;
       case "compaction":
-        flushBuffers(entries, buffers, options);
         entries.push(activityEntry("[Compacted]"));
         break;
     }
   }
 
-  flushBuffers(entries, buffers, options);
-
   return entries;
 }
 

packages/server/src/server/agent/agent-prompt.test.ts

@@ -222,6 +222,11 @@ function createFinishNotificationScenario(
         type: "agent_state",
         agent: childAgent,
       });
+      subscriber?.({
+        type: "agent_stream",
+        agentId: "child-agent",
+        event: { type: "turn_completed", provider: "codex" },
+      });
     },
     async finishChildAndReadParentPrompt() {
       const parentPrompt = new Promise<string>((resolve) => {
@@ -540,6 +545,11 @@ it("does not notify archived callers", async () => {
     type: "agent_state",
     agent: childAgent,
   });
+  subscriber?.({
+    type: "agent_stream",
+    agentId: "child-agent",
+    event: { type: "turn_completed", provider: "codex" },
+  });
 
   await vi.waitFor(() => {
     expect(agentStorageGetSpy).toHaveBeenCalledWith("caller-agent");

packages/server/src/server/agent/agent-prompt.ts

@@ -407,13 +407,20 @@ export interface SetupFinishNotificationParams {
   logger: Logger;
 }
 
-type FinishNotificationReason = "finished" | "errored" | "needs permission" | "was closed";
+type FinishNotificationReason =
+  | "finished"
+  | "errored"
+  | "needs permission"
+  | "was closed"
+  | "was canceled";
 
 const finishNotificationEvents = {
   finished: "finished",
   errored: "errored",
   "needs permission": "permission-required",
   "was closed": "closed",
+  // Use the existing failure event so older clients still parse agent-message metadata.
+  "was canceled": "errored",
 } as const;
 
 const FINISH_NOTIFICATION_MESSAGE_LIMIT = 4000;
@@ -568,10 +575,8 @@ export function setupFinishNotification(params: SetupFinishNotificationParams):
       notifySafely("errored");
       return;
     }
-    if (agent.lifecycle === "idle" && hasSeenRunning) {
-      notifySafely("finished");
-      return;
-    }
+    // Idle is published before the terminal stream event for both completion
+    // and cancellation. Let that event identify the outcome instead.
     if (agent.lifecycle === "closed") {
       notifySafely("was closed");
       return;
@@ -600,6 +605,18 @@ export function setupFinishNotification(params: SetupFinishNotificationParams):
         return;
       }
 
+      if (event.event.type === "turn_completed" || event.event.type === "turn_canceled") {
+        // Replacing a turn keeps the child running through the displaced turn's
+        // cancellation. The task settles only when the child becomes idle.
+        if (agentManager.getAgent(childAgentId)?.lifecycle !== "idle") return;
+        if (event.event.type === "turn_completed" && hasSeenRunning) {
+          notifySafely("finished");
+        } else if (event.event.type === "turn_canceled" && hasSeenTurn) {
+          notifySafely("was canceled");
+        }
+        return;
+      }
+
       if (event.event.type === "permission_requested") {
         // A permission pause is an intermediate checkpoint. Forget the run
         // observed before it so an idle state during follow-up startup cannot

packages/server/src/server/agent/mcp-parity.e2e.test.ts

@@ -12,6 +12,8 @@ import { createTestPaseoDaemon, type TestPaseoDaemon } from "../test-utils/paseo
 import { createTestAgentClients } from "../test-utils/fake-agent-client.js";
 import type { AgentClient, AgentProvider, AgentSessionConfig } from "./agent-sdk-types.js";
 import { PARENT_AGENT_ID_LABEL } from "@getpaseo/protocol/agent-labels";
+import { DaemonClient } from "../test-utils/daemon-client.js";
+import { parseAgentMessage } from "./agent-messages/index.js";
 
 interface StructuredContent {
   [key: string]: unknown;
@@ -311,6 +313,167 @@ afterAll(async () => {
 });
 
 describe("Suite A: Core Fixes", () => {
+  test.each([
+    ["Stop", "cancelAgent"],
+    ["Reload", "refreshAgent"],
+  ] as const)(
+    "%s tells the parent that a watched child was canceled",
+    async (_action, method) => {
+      let releaseChild!: () => void;
+      let childReachedGate!: () => void;
+      const heldTurn = new Promise<void>((resolve) => {
+        releaseChild = resolve;
+      });
+      const childAtGate = new Promise<void>((resolve) => {
+        childReachedGate = resolve;
+      });
+      const parentPrompts: string[] = [];
+      const daemon = await createTestPaseoDaemon({
+        agentClients: createTestAgentClients({
+          onStartTurn(prompt, config) {
+            if (config.title === "Watching parent" && typeof prompt === "string")
+              parentPrompts.push(prompt);
+          },
+          async beforeTurnComplete(prompt) {
+            if (
+              typeof prompt === "string" &&
+              parseAgentMessage(prompt).text === "Hold this child turn"
+            ) {
+              childReachedGate();
+              await heldTurn;
+            }
+          },
+        }),
+      });
+      const client = new DaemonClient({
+        url: `ws://127.0.0.1:${daemon.port}/ws`,
+        appVersion: "0.11.2",
+      });
+      let mcp: McpClient | undefined;
+      let unsubscribe: (() => void) | undefined;
+      try {
+        await client.connect();
+        await client.fetchAgents({ subscribe: {} });
+        const parent = await client.createAgent({
+          provider: "claude",
+          cwd: daemon.paseoHome,
+          title: "Watching parent",
+          modeId: "bypassPermissions",
+        });
+        mcp = await createMcpClient(
+          buildExpectedAgentMcpUrl({ host: "127.0.0.1", port: daemon.port, agentId: parent.id }),
+        );
+        const created = await callToolStructured(mcp, "create_agent", {
+          relationship: { kind: "subagent" },
+          workspace: { kind: "current" },
+          title: "Watched child",
+          provider: "codex/gpt-5.4",
+          initialPrompt: "Hold this child turn",
+          notifyOnFinish: true,
+          settings: { modeId: "full-access" },
+        });
+        const childId = str(created.agentId);
+        await childAtGate;
+        expect(daemon.daemon.agentManager.getAgent(childId)?.lifecycle).toBe("running");
+        const terminalEvents: string[] = [];
+        unsubscribe = daemon.daemon.agentManager.subscribe(
+          (event) => {
+            if (
+              event.type === "agent_stream" &&
+              event.agentId === childId &&
+              (event.event.type === "turn_completed" || event.event.type === "turn_canceled")
+            )
+              terminalEvents.push(event.event.type);
+          },
+          { agentId: childId, replayState: false },
+        );
+
+        await client[method](childId);
+        await waitFor({
+          timeoutMs: 10000,
+          label: "parent cancellation notification",
+          check: () => (parentPrompts.length === 1 ? true : null),
+        });
+        const notification = parseAgentMessage(parentPrompts[0]);
+        expect(terminalEvents).toEqual(["turn_canceled"]);
+        expect(notification.source).toEqual({
+          kind: "agent-notification",
+          agentId: childId,
+          title: "Watched child",
+          event: "errored",
+        });
+        expect(notification.text).toContain(`Agent ${childId} (Watched child) was canceled.`);
+        expect(notification.text).not.toContain("finished.");
+        await waitFor({
+          timeoutMs: 10000,
+          label: "parent notification turn drained",
+          check: () =>
+            daemon.daemon.agentManager.getAgent(parent.id)?.lifecycle === "idle" ? true : null,
+        });
+        expect(parentPrompts).toHaveLength(1);
+      } finally {
+        releaseChild();
+        unsubscribe?.();
+        await mcp?.close();
+        await client.close();
+        await daemon.close();
+      }
+    },
+    30000,
+  );
+
+  test.each([
+    { outcome: "finished", prompt: "say done and stop", status: "idle" },
+    { outcome: "errored", prompt: "Emit a turn failure", status: "error" },
+  ])(
+    "a watched child still reports $outcome after send_agent_prompt",
+    async ({ outcome, prompt, status }) => {
+      const childId = await createChildAgent({
+        title: "Follow-up child",
+        settings: { modeId: "bypassPermissions" },
+      });
+      try {
+        await waitFor({
+          timeoutMs: 10000,
+          label: "initial child turn completed",
+          check: () =>
+            daemonHandle.daemon.agentManager.getAgent(childId)?.lifecycle === "idle" ? true : null,
+        });
+        await callToolStructured(agentScopedClient, "send_agent_prompt", {
+          agentId: childId,
+          prompt,
+          notifyOnFinish: true,
+        });
+        const notifications = await waitFor({
+          timeoutMs: 10000,
+          label: `${outcome} notification`,
+          check: () => {
+            const items = daemonHandle.daemon.agentManager
+              .getTimeline(parentAgentId)
+              .filter(
+                (item) => item.type === "tool_call" && item.agentMessage?.sender.id === childId,
+              );
+            return items.length > 0 ? items : null;
+          },
+        });
+        expect(notifications).toEqual([
+          expect.objectContaining({
+            type: "tool_call",
+            agentMessage: {
+              event: outcome,
+              sender: { id: childId, title: "Follow-up child" },
+              text: expect.stringContaining(`(Follow-up child) ${outcome}.`),
+            },
+          }),
+        ]);
+        expect(daemonHandle.daemon.agentManager.getAgent(childId)?.lifecycle).toBe(status);
+      } finally {
+        await archiveAgentIfPresent(childId);
+      }
+    },
+    30000,
+  );
+
   test("AGENT_WAIT_TIMEOUT_MS is 30000", () => {
     expect(AGENT_WAIT_TIMEOUT_MS).toBe(30_000);
   });

packages/server/src/server/agent/mcp-server.test.ts

@@ -4359,6 +4359,10 @@ describe("send_agent_prompt MCP tool", () => {
       await vi.waitFor(() => expect(finishNotifications()).not.toHaveLength(0));
       await new Promise((resolve) => setTimeout(resolve, 100));
       expect(finishNotifications()).toHaveLength(1);
+      expect(parentClient.sessions[0]!.prompts).toHaveLength(1);
+      expect(parseAgentMessage(parentClient.sessions[0]!.prompts[0])).toMatchObject({
+        source: { kind: "agent-notification", agentId: childId, event: "finished" },
+      });
     } finally {
       await removeAgentStateDir(agentManager, storage, workdir);
     }

packages/server/src/server/bootstrap-web-ui.test.ts

@@ -134,6 +134,44 @@ describe("daemon web UI bootstrap", () => {
     });
   });
 
+  test("spells out the scheme default port when the Host header omits it", async () => {
+    const distDir = await createWebUiDist();
+
+    daemonHandle = await createTestPaseoDaemon({
+      mcpEnabled: false,
+      webUi: {
+        enabled: true,
+        distDir,
+      },
+    });
+
+    // A browser reaching a proxy that terminates TLS on 443 sends a Host header
+    // with no port at all. The app rejects a portless `listen`, so the daemon
+    // has to supply the default itself.
+    const httpsHint = readInjectedConnectionHint(
+      await fetchDaemonWebUi({
+        port: daemonHandle.port,
+        headers: { host: "paseo.example.test", "x-forwarded-proto": "https" },
+      }),
+    );
+    const httpHint = readInjectedConnectionHint(
+      await fetchDaemonWebUi({
+        port: daemonHandle.port,
+        headers: { host: "paseo.example.test" },
+      }),
+    );
+    const ipv6Hint = readInjectedConnectionHint(
+      await fetchDaemonWebUi({
+        port: daemonHandle.port,
+        headers: { host: "[::1]", "x-forwarded-proto": "https" },
+      }),
+    );
+
+    expect(httpsHint.listen).toBe("paseo.example.test:443");
+    expect(httpHint.listen).toBe("paseo.example.test:80");
+    expect(ipv6Hint.listen).toBe("[::1]:443");
+  });
+
   test("ignores forwarded HTTPS when proxy trust is disabled", async () => {
     const distDir = await createWebUiDist();
 

packages/server/src/server/bootstrap.ts

@@ -832,6 +832,9 @@ export async function createPaseoDaemon(
     try {
       fileHandle = await open(entry.absolutePath, DOWNLOAD_OPEN_FLAGS);
       const fileStats = await fileHandle.stat();
+      if (res.destroyed) {
+        return;
+      }
       if (!fileStats.isFile()) {
         res.status(404).json({ error: "File not found" });
         return;
@@ -843,6 +846,7 @@ export async function createPaseoDaemon(
 
       const stream = fileHandle.createReadStream();
       fileHandle = null;
+      res.once("close", () => stream.destroy());
       stream.on("error", (err) => {
         logger.error({ err }, "Failed to stream download");
         if (!res.headersSent) {

packages/server/src/server/daemon-e2e/checkout-diff-content.e2e.test.ts

@@ -0,0 +1,87 @@
+import { execFileSync } from "node:child_process";
+import { mkdtempSync, rmSync, writeFileSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { expect, test } from "vitest";
+import { createDaemonTestContext } from "../test-utils/index.js";
+
+function git(cwd: string, ...args: string[]): string {
+  return execFileSync("git", args, { cwd, encoding: "utf8" });
+}
+
+test.each(["uncommitted", "base", "commit"] as const)(
+  "%s diff preserves removed SQL comments and their deletion counts",
+  async (mode) => {
+    const ctx = await createDaemonTestContext();
+    const cwd = mkdtempSync(join(tmpdir(), "checkout-diff-content-"));
+
+    try {
+      git(cwd, "init", "-b", "main");
+      git(cwd, "config", "user.name", "Test");
+      git(cwd, "config", "user.email", "test@example.com");
+      writeFileSync(join(cwd, "query.sql"), "-- old comment\nSELECT 1;\n");
+      writeFileSync(join(cwd, "control.sql"), "SELECT 1;\n");
+      git(cwd, "add", ".");
+      git(cwd, "-c", "commit.gpgsign=false", "commit", "-m", "initial");
+      writeFileSync(join(cwd, "query.sql"), "-- new comment\nSELECT 1;\n");
+      writeFileSync(join(cwd, "control.sql"), "SELECT 2;\n");
+
+      expect(git(cwd, "diff", "--numstat", "HEAD", "--", "query.sql").trim()).toBe(
+        "1\t1\tquery.sql",
+      );
+
+      if (mode !== "uncommitted") {
+        git(cwd, "checkout", "-b", "feature");
+        git(cwd, "add", ".");
+        git(cwd, "-c", "commit.gpgsign=false", "commit", "-m", "edit");
+      }
+
+      const files =
+        mode === "commit"
+          ? [
+              (
+                await ctx.client.getCommitFileDiff(
+                  cwd,
+                  git(cwd, "rev-parse", "HEAD").trim(),
+                  "query.sql",
+                )
+              ).file,
+              (
+                await ctx.client.getCommitFileDiff(
+                  cwd,
+                  git(cwd, "rev-parse", "HEAD").trim(),
+                  "control.sql",
+                )
+              ).file,
+            ]
+          : (await ctx.client.getCheckoutDiff(cwd, { mode, baseRef: "main" })).files;
+
+      const control = files.find((file) => file?.path === "control.sql");
+      expect(control).toMatchObject({ additions: 1, deletions: 1 });
+      expect(control?.hunks.flatMap((hunk) => hunk.lines)).toEqual(
+        expect.arrayContaining([
+          expect.objectContaining({ type: "remove", content: "SELECT 1;" }),
+          expect.objectContaining({ type: "add", content: "SELECT 2;" }),
+        ]),
+      );
+
+      const query = files.find((file) => file?.path === "query.sql");
+      expect
+        .soft(query)
+        .toMatchObject({ additions: 1, deletions: 1, isNew: false, isDeleted: false });
+      expect
+        .soft(query?.hunks.flatMap((hunk) => hunk.lines))
+        .toEqual(
+          expect.arrayContaining([
+            expect.objectContaining({ type: "remove", content: "-- old comment" }),
+            expect.objectContaining({ type: "add", content: "-- new comment" }),
+            expect.objectContaining({ type: "context", content: "SELECT 1;" }),
+          ]),
+        );
+    } finally {
+      await ctx.cleanup();
+      rmSync(cwd, { recursive: true, force: true });
+    }
+  },
+  60_000,
+);

packages/server/src/server/daemon-e2e/file-download.e2e.test.ts

@@ -1,5 +1,15 @@
 import { describe, test, expect, beforeEach, afterEach } from "vitest";
-import { mkdtempSync, writeFileSync, rmSync } from "fs";
+import {
+  mkdtempSync,
+  writeFileSync,
+  rmSync,
+  readdirSync,
+  readlinkSync,
+  realpathSync,
+  symlinkSync,
+} from "fs";
+import { once } from "node:events";
+import { get } from "node:http";
 import { tmpdir } from "os";
 import path from "path";
 import { createDaemonTestContext, type DaemonTestContext } from "../test-utils/index.js";
@@ -8,6 +18,41 @@ function tmpCwd(): string {
   return mkdtempSync(path.join(tmpdir(), "daemon-e2e-"));
 }
 
+// Linux exposes the real open descriptors without replacing file or HTTP methods.
+function openDownloadDescriptors(filePath: string): string[] {
+  const realFilePath = realpathSync(filePath);
+  return readdirSync("/proc/self/fd").filter((fd) => {
+    try {
+      return readlinkSync(`/proc/self/fd/${fd}`) === realFilePath;
+    } catch (error) {
+      // A descriptor can close between listing it and reading its link.
+      if ((error as NodeJS.ErrnoException).code === "ENOENT") return false;
+      throw error;
+    }
+  });
+}
+
+async function expectDownloadClosed(filePath: string): Promise<void> {
+  await expect.poll(() => openDownloadDescriptors(filePath)).toEqual([]);
+}
+
+async function cancelDownloadAfterFirstChunk(url: string): Promise<void> {
+  const request = get(url);
+  try {
+    const [response] = await once(request, "response");
+    expect(response.statusCode).toBe(200);
+    const [chunk] = await once(response, "data");
+    expect(chunk.length).toBeGreaterThan(0);
+    expect(chunk.length).toBeLessThan(64 * 1024 * 1024);
+    const closed = once(response, "close");
+    response.destroy();
+    request.destroy();
+    await closed;
+  } finally {
+    request.destroy();
+  }
+}
+
 // Use gpt-5.4-mini with low thinking preset for faster test execution
 const CODEX_TEST_MODEL = "gpt-5.4-mini";
 const CODEX_TEST_THINKING_OPTION_ID = "low";
@@ -24,6 +69,39 @@ describe("daemon E2E", () => {
   }, 60000);
 
   describe("file download tokens", () => {
+    test.skipIf(process.platform !== "linux")(
+      "releases file descriptors after repeated HTTP download cancellations",
+      async () => {
+        const directory = tmpCwd();
+        const cwd = path.join(directory, "linked-files");
+        symlinkSync(mkdtempSync(path.join(directory, "files-")), cwd, "dir");
+        const filePath = path.join(cwd, "large.bin");
+        const fileSize = 64 * 1024 * 1024;
+        writeFileSync(filePath, Buffer.alloc(fileSize));
+        try {
+          const completedToken = await ctx.client.requestDownloadToken(cwd, "large.bin");
+          expect(completedToken.error).toBeNull();
+          const completed = await fetch(
+            `http://127.0.0.1:${ctx.daemon.port}/api/files/download?token=${completedToken.token}`,
+          );
+          expect(completed.status).toBe(200);
+          expect((await completed.arrayBuffer()).byteLength).toBe(fileSize);
+          await expectDownloadClosed(filePath);
+
+          for (let attempt = 0; attempt < 3; attempt++) {
+            const token = await ctx.client.requestDownloadToken(cwd, "large.bin");
+            expect(token.error).toBeNull();
+            await cancelDownloadAfterFirstChunk(
+              `http://127.0.0.1:${ctx.daemon.port}/api/files/download?token=${token.token}`,
+            );
+            await expectDownloadClosed(filePath);
+          }
+        } finally {
+          rmSync(directory, { recursive: true, force: true });
+        }
+      },
+    );
+
     test.each([
       { fileName: "download.txt", disposition: 'attachment; filename="download.txt"' },
       {

packages/server/src/server/daemon-e2e/filesystem.e2e.test.ts

@@ -1,5 +1,5 @@
 import { describe, test, expect, beforeEach, afterEach } from "vitest";
-import { mkdtempSync, writeFileSync, rmSync, mkdirSync } from "fs";
+import { mkdtempSync, writeFileSync, rmSync, mkdirSync, symlinkSync, readdirSync } from "fs";
 import { tmpdir } from "os";
 import path from "path";
 import { createDaemonTestContext, type DaemonTestContext } from "../test-utils/index.js";
@@ -23,6 +23,287 @@ afterEach(async () => {
 }, 60000);
 
 describe("file explorer", () => {
+  test.each([
+    { description: "a long ASCII name", fileName: `${"a".repeat(236)}.txt` },
+    { description: "an ordinary name", fileName: "notes.txt" },
+    { description: "a long Unicode name", fileName: `${"文".repeat(76)}.txt` },
+  ])("saves text files with $description", async ({ fileName }) => {
+    const cwd = tmpCwd();
+    try {
+      const created = await ctx.client.createFileEntry({
+        cwd,
+        parentPath: ".",
+        name: fileName,
+        kind: "file",
+      });
+      expect(created).toMatchObject({ path: fileName, success: true, error: null });
+      writeFileSync(path.join(cwd, fileName), "original payload\n");
+      const initial = await ctx.client.readFile(cwd, fileName);
+
+      const saved = await ctx.client.writeFile({
+        cwd,
+        path: fileName,
+        content: "saved payload\n",
+        expectedModifiedAt: initial.modifiedAt,
+        expectedRevision: initial.revision,
+      });
+      expect(saved).toMatchObject({ status: "written", size: 14 });
+      const after = await ctx.client.readFile(cwd, fileName);
+      expect(after.path).toBe(fileName);
+      expect(new TextDecoder().decode(after.bytes)).toBe("saved payload\n");
+
+      const staleSave = await ctx.client.writeFile({
+        cwd,
+        path: fileName,
+        content: "stale payload\n",
+        expectedModifiedAt: initial.modifiedAt,
+        expectedRevision: initial.revision,
+      });
+      expect(staleSave).toMatchObject({
+        status: "conflict",
+        version: {
+          status: "ready",
+          path: fileName,
+          size: after.size,
+          modifiedAt: after.modifiedAt,
+          revision: after.revision,
+        },
+      });
+      const afterConflict = await ctx.client.readFile(cwd, fileName);
+      expect(new TextDecoder().decode(afterConflict.bytes)).toBe("saved payload\n");
+
+      const secondSave = await ctx.client.writeFile({
+        cwd,
+        path: fileName,
+        content: "second payload\n",
+        expectedModifiedAt: afterConflict.modifiedAt,
+        expectedRevision: afterConflict.revision,
+      });
+      expect(secondSave).toMatchObject({ status: "written", size: 15 });
+      const final = await ctx.client.readFile(cwd, fileName);
+      expect(new TextDecoder().decode(final.bytes)).toBe("second payload\n");
+      expect(readdirSync(cwd)).toEqual([fileName]);
+    } finally {
+      rmSync(cwd, { recursive: true, force: true });
+    }
+  });
+
+  test.each([
+    {
+      query: "implementation",
+      expectedPaths: [
+        ".cursor/plans/implementation-plan.md",
+        ".codex/plans/implementation-plan.md",
+        ".claude/plans/implementation-plan.md",
+      ],
+    },
+    {
+      query: ".cursor/plans/implementation",
+      expectedPaths: [".cursor/plans/implementation-plan.md"],
+    },
+  ])(
+    "workspace suggestions find hidden agent plans for '$query'",
+    async ({ query, expectedPaths }) => {
+      const cwd = tmpCwd();
+      try {
+        for (const directory of [".cursor", ".codex", ".claude", ".hidden"]) {
+          mkdirSync(path.join(cwd, directory, "plans"), { recursive: true });
+          writeFileSync(path.join(cwd, directory, "plans", "implementation-plan.md"), "plan\n");
+        }
+
+        const response = await ctx.client.getDirectorySuggestions({
+          cwd,
+          query,
+          limit: 50,
+          includeFiles: true,
+          includeDirectories: true,
+        });
+        expect(response.error).toBeNull();
+        expect(response.entries).toHaveLength(expectedPaths.length);
+        expect(response.entries).toEqual(
+          expect.arrayContaining(
+            expectedPaths.map((entryPath) => ({ path: entryPath, kind: "file" })),
+          ),
+        );
+      } finally {
+        rmSync(cwd, { recursive: true, force: true });
+      }
+    },
+  );
+
+  test.each(["..", "..."])("supports file operations on names starting with %s", async (prefix) => {
+    const cwd = tmpCwd();
+    const fileName = `${prefix}notes.txt`;
+    const directoryName = `${prefix}drafts`;
+    try {
+      const createdFile = await ctx.client.createFileEntry({
+        cwd,
+        parentPath: ".",
+        name: fileName,
+        kind: "file",
+      });
+      expect(createdFile).toMatchObject({ path: fileName, success: true, error: null });
+      writeFileSync(path.join(cwd, fileName), "notes payload\n");
+      writeFileSync(path.join(cwd, ".notes.txt"), "dotfile control\n");
+      writeFileSync(path.join(cwd, "notes.txt"), "ordinary control\n");
+
+      const createdDirectory = await ctx.client.createFileEntry({
+        cwd,
+        parentPath: ".",
+        name: directoryName,
+        kind: "directory",
+      });
+      expect(createdDirectory).toMatchObject({ path: directoryName, success: true, error: null });
+      const createdChild = await ctx.client.createFileEntry({
+        cwd,
+        parentPath: directoryName,
+        name: "inside.txt",
+        kind: "file",
+      });
+      expect(createdChild).toMatchObject({
+        path: `${directoryName}/inside.txt`,
+        success: true,
+        error: null,
+      });
+      writeFileSync(path.join(cwd, directoryName, "inside.txt"), "nested payload\n");
+
+      const directory = await ctx.client.listDirectory(cwd, ".");
+      expect(
+        Object.fromEntries(directory.entries.map((entry) => [entry.path, entry.kind])),
+      ).toEqual({
+        [directoryName]: "directory",
+        [fileName]: "file",
+        ".notes.txt": "file",
+        "notes.txt": "file",
+      });
+      const children = await ctx.client.listDirectory(cwd, directoryName);
+      expect(children.entries.map((entry) => entry.path)).toEqual([`${directoryName}/inside.txt`]);
+      const file = await ctx.client.readFile(cwd, fileName);
+      expect(file.path).toBe(fileName);
+      expect(new TextDecoder().decode(file.bytes)).toBe("notes payload\n");
+      const nestedFile = await ctx.client.readFile(cwd, `${directoryName}/inside.txt`);
+      expect(nestedFile.path).toBe(`${directoryName}/inside.txt`);
+      expect(new TextDecoder().decode(nestedFile.bytes)).toBe("nested payload\n");
+
+      const dotfile = await ctx.client.readFile(cwd, ".notes.txt");
+      expect(new TextDecoder().decode(dotfile.bytes)).toBe("dotfile control\n");
+      const ordinaryFile = await ctx.client.readFile(cwd, "notes.txt");
+      expect(new TextDecoder().decode(ordinaryFile.bytes)).toBe("ordinary control\n");
+
+      const download = await ctx.client.requestDownloadToken(cwd, fileName);
+      expect(download.error).toBeNull();
+      expect(download.fileName).toBe(fileName);
+      const response = await fetch(
+        `http://127.0.0.1:${ctx.daemon.port}/api/files/download?token=${download.token}`,
+      );
+      expect(response.status).toBe(200);
+      expect(await response.text()).toBe("notes payload\n");
+
+      const renamedFileName = `${prefix}renamed.txt`;
+      const renamed = await ctx.client.renameFileEntry({
+        cwd,
+        path: fileName,
+        name: renamedFileName,
+      });
+      expect(renamed).toMatchObject({ renamedPath: renamedFileName, success: true, error: null });
+      const renamedFile = await ctx.client.readFile(cwd, renamedFileName);
+      expect(new TextDecoder().decode(renamedFile.bytes)).toBe("notes payload\n");
+
+      const copiedDirectoryName = `${directoryName} copy`;
+      const duplicated = await ctx.client.duplicateFileEntry({ cwd, path: directoryName });
+      expect(duplicated).toMatchObject({
+        duplicatedPath: copiedDirectoryName,
+        success: true,
+        error: null,
+      });
+      const copiedFile = await ctx.client.readFile(cwd, `${copiedDirectoryName}/inside.txt`);
+      expect(new TextDecoder().decode(copiedFile.bytes)).toBe("nested payload\n");
+
+      const deletedDirectory = await ctx.client.deleteFileEntry({ cwd, path: directoryName });
+      expect(deletedDirectory).toMatchObject({ success: true, error: null });
+      const deletedFile = await ctx.client.deleteFileEntry({ cwd, path: renamedFileName });
+      expect(deletedFile).toMatchObject({ success: true, error: null });
+      const remaining = await ctx.client.listDirectory(cwd, ".");
+      expect(remaining.entries.map((entry) => entry.path).sort()).toEqual(
+        [".notes.txt", "notes.txt", copiedDirectoryName].sort(),
+      );
+    } finally {
+      rmSync(cwd, { recursive: true, force: true });
+    }
+  });
+
+  test("rejects parent traversal and absolute paths to a sibling workspace", async () => {
+    const directory = tmpCwd();
+    const cwd = path.join(directory, "workspace");
+    const outside = path.join(directory, "workspace-sibling");
+    try {
+      mkdirSync(cwd);
+      mkdirSync(outside);
+      writeFileSync(path.join(outside, "secret.txt"), "outside payload\n");
+      for (const requestedPath of ["..", "../workspace-sibling", outside]) {
+        await expect(ctx.client.listDirectory(cwd, requestedPath)).rejects.toThrow(
+          "Access outside of workspace is not allowed",
+        );
+      }
+      for (const requestedPath of [
+        "../workspace-sibling/secret.txt",
+        path.join(outside, "secret.txt"),
+      ]) {
+        await expect(ctx.client.readFile(cwd, requestedPath)).rejects.toThrow(
+          "Access outside of workspace is not allowed",
+        );
+        const download = await ctx.client.requestDownloadToken(cwd, requestedPath);
+        expect(download).toMatchObject({
+          token: null,
+          error: "Access outside of workspace is not allowed",
+        });
+        const deleted = await ctx.client.deleteFileEntry({ cwd, path: requestedPath });
+        expect(deleted).toMatchObject({
+          success: false,
+          error: "Access outside of workspace is not allowed",
+        });
+      }
+      expect(readdirSync(outside)).toEqual(["secret.txt"]);
+    } finally {
+      rmSync(directory, { recursive: true, force: true });
+    }
+  });
+
+  test("accepts symlinks to double-dot names inside the workspace and rejects outside targets", async () => {
+    const directory = tmpCwd();
+    const cwd = path.join(directory, "workspace");
+    const outside = path.join(directory, "workspace-sibling");
+    try {
+      mkdirSync(path.join(cwd, "..drafts"), { recursive: true });
+      mkdirSync(outside);
+      writeFileSync(path.join(cwd, "..drafts", "notes.txt"), "inside payload\n");
+      writeFileSync(path.join(outside, "secret.txt"), "outside payload\n");
+      // Junctions also work on Windows without requiring symlink privileges.
+      symlinkSync(path.join(cwd, "..drafts"), path.join(cwd, "inside-link"), "junction");
+      symlinkSync(outside, path.join(cwd, "outside-link"), "junction");
+
+      const listing = await ctx.client.listDirectory(cwd, ".");
+      expect(listing.entries.map((entry) => entry.path).sort()).toEqual([
+        "..drafts",
+        "inside-link",
+      ]);
+      const file = await ctx.client.readFile(cwd, "inside-link/notes.txt");
+      expect(file.path).toBe("inside-link/notes.txt");
+      expect(new TextDecoder().decode(file.bytes)).toBe("inside payload\n");
+      await expect(ctx.client.readFile(cwd, "outside-link/secret.txt")).rejects.toThrow(
+        "Access outside of workspace is not allowed",
+      );
+      const download = await ctx.client.requestDownloadToken(cwd, "outside-link/secret.txt");
+      expect(download).toMatchObject({
+        token: null,
+        error: "Access outside of workspace is not allowed",
+      });
+      expect(readdirSync(outside)).toEqual(["secret.txt"]);
+    } finally {
+      rmSync(directory, { recursive: true, force: true });
+    }
+  });
+
   test("lists directory contents", async () => {
     const cwd = tmpCwd();
 

packages/server/src/server/daemon-e2e/git-operations.e2e.test.ts

@@ -1,5 +1,14 @@
 import { test, expect, beforeEach, afterEach } from "vitest";
-import { mkdtempSync, writeFileSync, existsSync, rmSync, readFileSync, realpathSync } from "fs";
+import {
+  mkdtempSync,
+  writeFileSync,
+  existsSync,
+  rmSync,
+  readFileSync,
+  realpathSync,
+  mkdirSync,
+} from "fs";
+import { execFileSync } from "node:child_process";
 import { tmpdir } from "os";
 import path from "path";
 import { createDaemonTestContext, type DaemonTestContext } from "../test-utils/index.js";
@@ -152,6 +161,78 @@ afterEach(async () => {
   await ctx.cleanup();
 }, 60000);
 
+interface GitCommandOptions {
+  cwd: string;
+  args: string[];
+}
+
+async function mergeFeatureIntoBaseWorktree(baseName: string): Promise<void> {
+  const directory = realpathSync(tmpCwd());
+  const base = path.join(directory, baseName);
+  const feature = path.join(directory, "feature");
+  function git({ cwd, args }: GitCommandOptions): string {
+    return execFileSync("git", args, { cwd, encoding: "utf8", stdio: "pipe" });
+  }
+  try {
+    mkdirSync(base);
+    git({ cwd: base, args: ["init", "-b", "main"] });
+    git({ cwd: base, args: ["config", "user.name", "Paseo Test"] });
+    git({ cwd: base, args: ["config", "user.email", "test@paseo.local"] });
+    git({ cwd: base, args: ["config", "commit.gpgsign", "false"] });
+    git({ cwd: base, args: ["config", "core.autocrlf", "false"] });
+    git({ cwd: base, args: ["commit", "--allow-empty", "-m", "base"] });
+    git({ cwd: base, args: ["worktree", "add", "-b", "feature", feature] });
+    writeFileSync(path.join(feature, "feature.txt"), "feature payload\n");
+    git({ cwd: feature, args: ["add", "feature.txt"] });
+    git({ cwd: feature, args: ["commit", "-m", "feature"] });
+    const featureCommit = git({ cwd: feature, args: ["rev-parse", "HEAD"] }).trim();
+
+    const merged = await ctx.client.checkoutMerge(feature, { baseRef: "main" });
+    expect(merged).toMatchObject({ success: true, error: null });
+    expect(git({ cwd: base, args: ["rev-parse", "HEAD"] }).trim()).toBe(featureCommit);
+    expect(readFileSync(path.join(base, "feature.txt"), "utf8")).toBe("feature payload\n");
+    expect(git({ cwd: feature, args: ["symbolic-ref", "--short", "HEAD"] }).trim()).toBe("feature");
+  } finally {
+    rmSync(directory, { recursive: true, force: true });
+  }
+}
+
+test.skipIf(isPlatform("win32")).each(["base\ncheckout", "base "])(
+  "merges into a base worktree whose path preserves %j",
+  mergeFeatureIntoBaseWorktree,
+);
+
+test.each(["base checkout", "中文 checkout"])(
+  "merges into a base worktree named %j",
+  mergeFeatureIntoBaseWorktree,
+);
+
+test("merges into a local base branch without another worktree", async () => {
+  const cwd = realpathSync(tmpCwd());
+  function git(args: string[]): string {
+    return execFileSync("git", args, { cwd, encoding: "utf8", stdio: "pipe" });
+  }
+  try {
+    git(["init", "-b", "main"]);
+    git(["config", "user.name", "Paseo Test"]);
+    git(["config", "user.email", "test@paseo.local"]);
+    git(["config", "commit.gpgsign", "false"]);
+    git(["commit", "--allow-empty", "-m", "base"]);
+    git(["checkout", "-b", "feature"]);
+    writeFileSync(path.join(cwd, "feature.txt"), "feature payload\n");
+    git(["add", "feature.txt"]);
+    git(["commit", "-m", "feature"]);
+    const featureCommit = git(["rev-parse", "HEAD"]).trim();
+
+    const merged = await ctx.client.checkoutMerge(cwd, { baseRef: "main" });
+    expect(merged).toMatchObject({ success: true, error: null });
+    expect(git(["rev-parse", "main"]).trim()).toBe(featureCommit);
+    expect(git(["symbolic-ref", "--short", "HEAD"]).trim()).toBe("feature");
+  } finally {
+    rmSync(cwd, { recursive: true, force: true });
+  }
+});
+
 test("returns diff for modified file in git repo", async () => {
   const cwd = tmpCwd();
 

packages/server/src/server/daemon-e2e/terminal-workspace-sdk.e2e.test.ts

@@ -6,6 +6,7 @@ import { afterEach, beforeEach, expect, test } from "vitest";
 import { createPaseoClient, type PaseoClient } from "@getpaseo/client";
 import { DaemonClient } from "../test-utils/daemon-client.js";
 import { createTestPaseoDaemon, type TestPaseoDaemon } from "../test-utils/paseo-daemon.js";
+import { runPaseoCli } from "../test-utils/cli.js";
 
 let daemon: TestPaseoDaemon;
 let client: DaemonClient;
@@ -28,6 +29,75 @@ afterEach(async () => {
   await rm(cwd, { recursive: true, force: true, maxRetries: 3, retryDelay: 100 });
 });
 
+async function createQuietTerminal() {
+  const workspaceId = await createWorkspace("CLI capture");
+  return sdk.terminals.create({
+    workspaceId,
+    command: process.execPath,
+    args: ["-e", "process.stdin.resume()"],
+    size: { rows: 10, cols: 40 },
+  });
+}
+
+test.each([
+  ["--end", "4503599627370496.5"],
+  ["--start", "1.0000000000000001"],
+  ["--end", "4.5035996273704965e15"],
+  ["--end", "1e-324"],
+  ["--start", "1.5"],
+  ["--end", "1.5"],
+  ["--start", "1abc"],
+  ["--end", "1abc"],
+  ["--start", ""],
+  ["--end", ""],
+  ["--start", "9007199254740993"],
+  ["--end", "9007199254740993"],
+])("CLI terminal capture rejects %s %j", async (flag, value) => {
+  const terminal = await createQuietTerminal();
+  try {
+    const result = await runPaseoCli({
+      daemon,
+      args: ["terminal", "capture", terminal.id, flag, value, "--json"],
+    });
+    expect(result.exitCode, result.stdout + result.stderr).toBe(1);
+    expect(JSON.parse(result.stderr)).toEqual({
+      error: {
+        code: "INVALID_LINE_NUMBER",
+        message: `Invalid ${flag} value: ${value}`,
+        details: "Use an integer line number.",
+      },
+    });
+  } finally {
+    await terminal.kill();
+  }
+});
+
+test.each([
+  { args: [], lineCount: 10 },
+  { args: ["--start", "0", "--end", "1"], lineCount: 2 },
+  { args: ["--end", "1.0"], lineCount: 2 },
+  { args: ["--end", "10e-1"], lineCount: 2 },
+  { args: ["--end", ".1e1"], lineCount: 2 },
+  { args: ["--start", "-2", "--end", "-1"], lineCount: 2 },
+  { args: ["--scrollback", "--start", "7", "--end", "1"], lineCount: 2 },
+])("CLI terminal capture preserves valid ranges $args", async ({ args, lineCount }) => {
+  const terminal = await createQuietTerminal();
+  try {
+    const result = await runPaseoCli({
+      daemon,
+      args: ["terminal", "capture", terminal.id, ...args, "--json"],
+    });
+    expect(result.exitCode, result.stderr).toBe(0);
+    expect(JSON.parse(result.stdout)).toEqual({
+      terminalId: terminal.id,
+      lines: Array.from({ length: lineCount }, () => ""),
+      totalLines: 10,
+    });
+  } finally {
+    await terminal.kill();
+  }
+});
+
 test("SDK and workspace handles preserve ownership and actual process directories", async () => {
   const first = await createWorkspace("main");
   const second = await createWorkspace("feature-work");

packages/server/src/server/file-explorer/service.test.ts

@@ -12,8 +12,8 @@ import {
 } from "node:fs/promises";
 import os from "node:os";
 import path from "node:path";
-import { describe, expect, it } from "vitest";
-import { runGitCommand } from "../../utils/run-git-command.js";
+import { describe, expect, it, vi } from "vitest";
+import { runGitCommand, snapshotGitCommandRuntimeMetrics } from "../../utils/run-git-command.js";
 import {
   createExplorerEntry,
   deleteExplorerEntry,
@@ -517,6 +517,129 @@ describe("file explorer service", () => {
     }
   });
 
+  it("renames an untracked bracketed filename without matching a tracked sibling", async () => {
+    const root = await createTempDir("paseo-entry-literal-rename-");
+    try {
+      await runGitCommand(["init"], { cwd: root });
+      await writeFile(path.join(root, "i.tsx"), "tracked\n", "utf8");
+      await runGitCommand(["add", "i.tsx"], { cwd: root });
+      await writeFile(path.join(root, "[id].tsx"), "untracked\n", "utf8");
+
+      snapshotGitCommandRuntimeMetrics();
+      const result = await renameExplorerEntry({
+        root,
+        relativePath: "[id].tsx",
+        name: "renamed.tsx",
+      });
+
+      expect(result).toEqual({ status: "ok", path: "renamed.tsx" });
+      expect(snapshotGitCommandRuntimeMetrics().operationsTop).toEqual([
+        ["ls-files", 1],
+        ["rev-parse", 1],
+      ]);
+      expect(await readFile(path.join(root, "renamed.tsx"), "utf8")).toBe("untracked\n");
+      await expect(stat(path.join(root, "[id].tsx"))).rejects.toMatchObject({ code: "ENOENT" });
+      expect(await readFile(path.join(root, "i.tsx"), "utf8")).toBe("tracked\n");
+      expect((await runGitCommand(["ls-files", "-z"], { cwd: root })).stdout).toBe("i.tsx\0");
+    } finally {
+      await rm(root, { recursive: true, force: true });
+    }
+  });
+
+  it("renames an untracked bracketed folder without matching a tracked sibling", async () => {
+    const root = await createTempDir("paseo-folder-literal-rename-");
+    try {
+      await runGitCommand(["init"], { cwd: root });
+      await mkdir(path.join(root, "i"));
+      await writeFile(path.join(root, "i", "route.tsx"), "tracked\n", "utf8");
+      await runGitCommand(["add", "i"], { cwd: root });
+      await mkdir(path.join(root, "[id]"));
+      await writeFile(path.join(root, "[id]", "route.tsx"), "untracked\n", "utf8");
+
+      const result = await renameExplorerEntry({ root, relativePath: "[id]", name: "route" });
+
+      expect(result).toEqual({ status: "ok", path: "route" });
+      expect(await readFile(path.join(root, "route", "route.tsx"), "utf8")).toBe("untracked\n");
+      await expect(stat(path.join(root, "[id]"))).rejects.toMatchObject({ code: "ENOENT" });
+      expect(await readFile(path.join(root, "i", "route.tsx"), "utf8")).toBe("tracked\n");
+      expect((await runGitCommand(["ls-files", "-z"], { cwd: root })).stdout).toBe("i/route.tsx\0");
+    } finally {
+      await rm(root, { recursive: true, force: true });
+    }
+  });
+
+  it("uses Git to rename a tracked bracketed filename and preserves its tracked sibling", async () => {
+    const root = await createTempDir("paseo-tracked-literal-rename-");
+    try {
+      await runGitCommand(["init"], { cwd: root });
+      await writeFile(path.join(root, "[id].tsx"), "tracked route\n", "utf8");
+      await writeFile(path.join(root, "i.tsx"), "tracked sibling\n", "utf8");
+      await runGitCommand(["add", "--", "[id].tsx", "i.tsx"], { cwd: root });
+
+      const result = await renameExplorerEntry({
+        root,
+        relativePath: "[id].tsx",
+        name: "renamed.tsx",
+      });
+
+      expect(result).toEqual({ status: "ok", path: "renamed.tsx" });
+      expect(await readFile(path.join(root, "renamed.tsx"), "utf8")).toBe("tracked route\n");
+      await expect(stat(path.join(root, "[id].tsx"))).rejects.toMatchObject({ code: "ENOENT" });
+      expect(await readFile(path.join(root, "i.tsx"), "utf8")).toBe("tracked sibling\n");
+      expect((await runGitCommand(["ls-files", "-z"], { cwd: root })).stdout).toBe(
+        "i.tsx\0renamed.tsx\0",
+      );
+    } finally {
+      await rm(root, { recursive: true, force: true });
+    }
+  });
+
+  it.each([
+    {
+      sourcePath: "[id].tsx",
+      sourceFile: "[id].tsx",
+      targetName: "renamed.tsx",
+      targetFile: "renamed.tsx",
+    },
+    {
+      sourcePath: "[id]",
+      sourceFile: "[id]/route.tsx",
+      targetName: "route",
+      targetFile: "route/route.tsx",
+    },
+  ])(
+    "keeps tracked renames in the index with inherited literal pathspecs ($sourcePath)",
+    async ({ sourcePath, sourceFile, targetName, targetFile }) => {
+      const root = await createTempDir("paseo-inherited-literal-rename-");
+      try {
+        vi.stubEnv("GIT_LITERAL_PATHSPECS", "1");
+        await runGitCommand(["init"], { cwd: root });
+        await mkdir(path.dirname(path.join(root, sourceFile)), { recursive: true });
+        await writeFile(path.join(root, sourceFile), "tracked route\n", "utf8");
+        await writeFile(path.join(root, "i.tsx"), "tracked sibling\n", "utf8");
+        await runGitCommand(["add", "."], { cwd: root });
+
+        const result = await renameExplorerEntry({
+          root,
+          relativePath: sourcePath,
+          name: targetName,
+        });
+
+        expect(result).toEqual({ status: "ok", path: targetName });
+        expect(await readFile(path.join(root, targetFile), "utf8")).toBe("tracked route\n");
+        await expect(stat(path.join(root, sourcePath))).rejects.toMatchObject({ code: "ENOENT" });
+        expect(await readFile(path.join(root, "i.tsx"), "utf8")).toBe("tracked sibling\n");
+        expect((await runGitCommand(["ls-files", "-z"], { cwd: root })).stdout).toBe(
+          `i.tsx\0${targetFile}\0`,
+        );
+        expect(process.env.GIT_LITERAL_PATHSPECS).toBe("1");
+      } finally {
+        vi.unstubAllEnvs();
+        await rm(root, { recursive: true, force: true });
+      }
+    },
+  );
+
   it("supports case-only renames for tracked and untracked files", async () => {
     const root = await createTempDir("paseo-entry-case-rename-");
     try {

packages/server/src/server/file-explorer/service.ts

@@ -489,7 +489,7 @@ export async function writeExplorerFile({
 
   const temporaryPath = path.join(
     path.dirname(filePath.resolvedPath),
-    `.${path.basename(filePath.resolvedPath)}.paseo-${randomUUID()}.tmp`,
+    `.paseo-${randomUUID()}.tmp`,
   );
   let temporaryHandle: FileHandle | null = null;
   try {
@@ -724,7 +724,11 @@ export async function renameExplorerEntry({
     });
     const tracked =
       repository.exitCode === 0
-        ? await runGitCommand(["ls-files", "-z", "--", sourcePath], { cwd: realRoot })
+        ? await runGitCommand(["ls-files", "-z", "--", `:(literal)${sourcePath}`], {
+            cwd: realRoot,
+            // Inherited literal mode disables the :(literal) pathspec magic.
+            envOverlay: { GIT_LITERAL_PATHSPECS: undefined },
+          })
         : null;
     if (tracked?.stdout) {
       await runGitCommand(["mv", "--", sourcePath, renamedPath], { cwd: realRoot });
@@ -820,8 +824,9 @@ async function resolveScopedPath({
 
 function assertWithinWorkspace(root: string, candidate: string): void {
   const relative = path.relative(root, candidate);
-  if (relative === "" || (!relative.startsWith("..") && !path.isAbsolute(relative))) return;
-  throw new Error(ACCESS_OUTSIDE_WORKSPACE_MESSAGE);
+  const isOutsideWorkspace =
+    relative === ".." || relative.startsWith(`..${path.sep}`) || path.isAbsolute(relative);
+  if (isOutsideWorkspace) throw new Error(ACCESS_OUTSIDE_WORKSPACE_MESSAGE);
 }
 
 async function openFileForRead(filePath: string): Promise<FileHandle> {

packages/server/src/server/persisted-config-json-schema.test.ts

@@ -0,0 +1,78 @@
+import { readFileSync } from "node:fs";
+import Ajv from "ajv";
+import { expect, test } from "vitest";
+import { z } from "zod";
+
+import { PersistedConfigSchema } from "./persisted-config.js";
+
+const publishedSchema = JSON.parse(
+  readFileSync(
+    new URL("../../../website/public/schemas/paseo.config.v1.json", import.meta.url),
+    "utf8",
+  ),
+);
+
+test("editors accept the daemon's browser, profile, plugin and metadata configuration", () => {
+  const config = {
+    $schema: "https://paseo.sh/schemas/paseo.config.v1.json",
+    version: 1,
+    daemon: {
+      browserTools: { enabled: true },
+      terminalProfiles: [],
+      agentProfiles: [],
+    },
+    pluginsEnabled: true,
+    plugins: {},
+    agents: {
+      metadataGeneration: { providers: [{ provider: "claude", model: "claude-opus-5" }] },
+    },
+  };
+  expect(PersistedConfigSchema.parse(config)).toEqual(config);
+  const validate = new Ajv({ allErrors: true, strict: false }).compile(publishedSchema);
+  const valid = validate(config);
+  expect(validate.errors).toBeNull();
+  expect(valid).toBe(true);
+});
+
+test("the published schema stays current with the daemon's configuration schema", () => {
+  const generated = z.toJSONSchema(PersistedConfigSchema, {
+    target: "draft-07",
+    unrepresentable: "any",
+    io: "input",
+  });
+  generated.title = "PaseoConfigV1";
+  expect(
+    publishedSchema,
+    "Run npm run generate:config-schema --workspace=@getpaseo/server",
+  ).toEqual(generated);
+});
+
+test("editors retain the existing proxy configuration help", () => {
+  const daemon = publishedSchema.properties.daemon.properties;
+  expect(daemon.trustedProxies.description).toBe(
+    'Express trusted proxy setting for X-Forwarded-* headers. Defaults to ["loopback"]. Use true only when the final trusted proxy overwrites client-supplied forwarded headers.',
+  );
+  expect(daemon.serviceProxy.properties.enabled.description).toBe(
+    "Compatibility shim. false suppresses optional service proxy listen/public layers only; localhost proxying remains enabled.",
+  );
+  expect(daemon.serviceProxy.properties.listen.description).toBe(
+    "Optional service-only listener address. Presence enables the standalone service proxy listener.",
+  );
+  expect(daemon.serviceProxy.properties.publicBaseUrl.description).toBe(
+    "Optional public base URL for service host aliases.",
+  );
+});
+
+test.each([
+  { daemon: { browserTools: { enabled: "yes" } } },
+  { daemon: { terminalProfiles: "default" } },
+  { daemon: { agentProfiles: "default" } },
+  { pluginsEnabled: "yes" },
+  { plugins: [] },
+  { agents: { metadataGeneration: { providers: [{ provider: "" }] } } },
+  { unknownSetting: true },
+])("editors still reject invalid configuration: %j", (config) => {
+  expect(PersistedConfigSchema.safeParse(config).success).toBe(false);
+  const validate = new Ajv({ allErrors: true, strict: false }).compile(publishedSchema);
+  expect(validate(config)).toBe(false);
+});

packages/server/src/server/persisted-config.ts

@@ -237,7 +237,12 @@ export const PersistedConfigSchema = z
         listen: z.string().optional(),
         hostnames: z.union([z.literal(true), z.array(z.string())]).optional(),
         allowedHosts: z.union([z.literal(true), z.array(z.string())]).optional(),
-        trustedProxies: z.union([z.literal(true), z.array(z.string())]).optional(),
+        trustedProxies: z
+          .union([z.literal(true), z.array(z.string())])
+          .optional()
+          .describe(
+            'Express trusted proxy setting for X-Forwarded-* headers. Defaults to ["loopback"]. Use true only when the final trusted proxy overwrites client-supplied forwarded headers.',
+          ),
         mcp: z
           .object({
             enabled: z.boolean().optional(),
@@ -284,9 +289,22 @@ export const PersistedConfigSchema = z
             // COMPAT(serviceProxyEnabled): added 2026-06-02, remove after 2026-12-02.
             // Parsed only to suppress optional public/listen layers for old configs;
             // localhost service proxying remains always enabled.
-            enabled: z.boolean().optional(),
-            listen: z.string().optional(),
-            publicBaseUrl: z.url().optional(),
+            enabled: z
+              .boolean()
+              .optional()
+              .describe(
+                "Compatibility shim. false suppresses optional service proxy listen/public layers only; localhost proxying remains enabled.",
+              ),
+            listen: z
+              .string()
+              .optional()
+              .describe(
+                "Optional service-only listener address. Presence enables the standalone service proxy listener.",
+              ),
+            publicBaseUrl: z
+              .url()
+              .optional()
+              .describe("Optional public base URL for service host aliases."),
           })
           .strict()
           .optional(),

packages/server/src/server/schedule-run-lifecycle.e2e.test.ts

@@ -13,6 +13,7 @@ import {
 } from "./test-utils/index.js";
 import type { SessionOutboundMessage } from "./messages.js";
 import { getPaseoWorktreesRoot } from "../utils/worktree.js";
+import { runPaseoCli } from "./test-utils/cli.js";
 
 type AgentUpdateMessage = Extract<SessionOutboundMessage, { type: "agent_update" }>;
 type WorkspaceUpdateMessage = Extract<SessionOutboundMessage, { type: "workspace_update" }>;
@@ -42,6 +43,137 @@ function makeTempDir(prefix: string): string {
   return dir;
 }
 
+test.each([
+  "4503599627370496.5",
+  "1.0000000000000001",
+  "2.5",
+  "2runs",
+  "9007199254740993",
+  "0",
+  "-1",
+  "",
+])("CLI schedule create rejects max-runs %j without saving a schedule", async (maxRuns) => {
+  const cwd = makeTempDir("schedule-cli-integer-");
+  const result = await runPaseoCli({
+    daemon: ctx.daemon,
+    args: [
+      "schedule",
+      "create",
+      "Integer limit",
+      "--cron",
+      "0 0 1 1 *",
+      "--provider",
+      "claude",
+      "--cwd",
+      cwd,
+      "--max-runs",
+      maxRuns,
+      "--json",
+    ],
+  });
+  expect(result.exitCode, result.stdout + result.stderr).toBe(1);
+  expect(JSON.parse(result.stderr)).toEqual({
+    error: { code: "INVALID_INTEGER", message: "--max-runs must be a positive integer" },
+  });
+  expect((await ctx.client.scheduleList()).schedules).toEqual([]);
+});
+
+test.each(["2.5", "2runs", "4503599627370496.5"])(
+  "CLI schedule update rejects max-runs %j without changing the schedule",
+  async (maxRuns) => {
+    const cwd = makeTempDir("schedule-cli-update-integer-");
+    const schedule = await createNewAgentSchedule({
+      prompt: "Original prompt",
+      cadence: { type: "cron", expression: "0 0 1 1 *", timezone: "UTC" },
+      target: { type: "new-agent", config: { provider: "claude", cwd } },
+      maxRuns: 3,
+      runOnCreate: false,
+    });
+    const before = await ctx.client.scheduleInspect({ id: schedule.id });
+    const result = await runPaseoCli({
+      daemon: ctx.daemon,
+      args: [
+        "schedule",
+        "update",
+        schedule.id,
+        "--prompt",
+        "Should not apply",
+        "--max-runs",
+        maxRuns,
+        "--json",
+      ],
+    });
+    expect(result.exitCode, result.stdout + result.stderr).toBe(1);
+    expect(JSON.parse(result.stderr)).toEqual({
+      error: { code: "INVALID_INTEGER", message: "--max-runs must be a positive integer" },
+    });
+    const after = await ctx.client.scheduleInspect({ id: schedule.id });
+    expect(after.error).toBeNull();
+    expect(after.schedule).toEqual(before.schedule);
+  },
+);
+
+test.each([
+  { limitArgs: [], maxRuns: null },
+  { limitArgs: ["--max-runs", "3"], maxRuns: 3 },
+  { limitArgs: ["--max-runs", "3.0"], maxRuns: 3 },
+  { limitArgs: ["--max-runs", "1e2"], maxRuns: 100 },
+])(
+  "CLI schedule create stores max-runs $maxRuns from $limitArgs",
+  async ({ limitArgs, maxRuns }) => {
+    const cwd = makeTempDir("schedule-cli-valid-integer-");
+    const result = await runPaseoCli({
+      daemon: ctx.daemon,
+      args: [
+        "schedule",
+        "create",
+        "Integer limit",
+        "--cron",
+        "0 0 1 1 *",
+        "--provider",
+        "claude",
+        "--cwd",
+        cwd,
+        ...limitArgs,
+        "--json",
+      ],
+    });
+    expect(result.exitCode, result.stderr).toBe(0);
+    expect((await ctx.client.scheduleList()).schedules).toEqual([
+      expect.objectContaining({ maxRuns, prompt: "Integer limit" }),
+    ]);
+  },
+);
+
+test("CLI schedule update preserves, changes, and clears valid run limits", async () => {
+  const cwd = makeTempDir("schedule-cli-valid-update-");
+  const schedule = await createNewAgentSchedule({
+    prompt: "Original prompt",
+    cadence: { type: "cron", expression: "0 0 1 1 *", timezone: "UTC" },
+    target: { type: "new-agent", config: { provider: "claude", cwd } },
+    maxRuns: 3,
+    runOnCreate: false,
+  });
+  for (const { args, maxRuns } of [
+    { args: ["--name", "Renamed"], maxRuns: 3 },
+    { args: ["--max-runs", "5"], maxRuns: 5 },
+    { args: ["--no-max-runs"], maxRuns: null },
+  ]) {
+    const result = await runPaseoCli({
+      daemon: ctx.daemon,
+      args: ["schedule", "update", schedule.id, ...args, "--json"],
+    });
+    expect(result.exitCode, result.stderr).toBe(0);
+    expect((await ctx.client.scheduleInspect({ id: schedule.id })).schedule).toMatchObject({
+      maxRuns,
+      name: "Renamed",
+      prompt: schedule.prompt,
+      target: schedule.target,
+      cadence: schedule.cadence,
+    });
+  }
+}, 60_000);
+
 function createGitRepo(): string {
   const tempRoot = makeTempDir("schedule-run-worktree-");
   const repoDir = path.join(tempRoot, "repo");
@@ -60,7 +192,13 @@ function createGitRepo(): string {
     cwd: repoDir,
     stdio: "pipe",
   });
-  return repoDir;
+  // Use Git's canonical root, as worktree creation does, including Windows path aliases.
+  return realpathSync(
+    execFileSync("git", ["rev-parse", "--show-toplevel"], {
+      cwd: repoDir,
+      encoding: "utf8",
+    }).trim(),
+  );
 }
 
 async function createNewAgentSchedule(options: ScheduleCreateOptions): Promise<ScheduleSummary> {

packages/server/src/server/test-utils/cli.ts

@@ -0,0 +1,54 @@
+import { spawn } from "node:child_process";
+import { fileURLToPath } from "node:url";
+import type { TestPaseoDaemon } from "./paseo-daemon.js";
+
+interface CliOptions {
+  daemon: Pick<TestPaseoDaemon, "port" | "paseoHome">;
+  args: string[];
+}
+
+interface CliResult {
+  exitCode: number | null;
+  stdout: string;
+  stderr: string;
+}
+
+export function runPaseoCli({ daemon, args }: CliOptions): Promise<CliResult> {
+  return new Promise((resolve, reject) => {
+    const child = spawn(
+      process.execPath,
+      [
+        "--no-warnings",
+        "--conditions=source",
+        "--import",
+        "tsx",
+        fileURLToPath(new URL("../../../../cli/src/index.ts", import.meta.url)),
+        "--host",
+        `127.0.0.1:${daemon.port}`,
+        ...args,
+      ],
+      {
+        env: { ...process.env, PASEO_HOME: daemon.paseoHome },
+        stdio: ["ignore", "pipe", "pipe"],
+        timeout: 20_000,
+        killSignal: "SIGKILL",
+      },
+    );
+    let stdout = "";
+    let stderr = "";
+    child.stdout.on("data", (chunk: Buffer) => {
+      stdout += chunk.toString();
+    });
+    child.stderr.on("data", (chunk: Buffer) => {
+      stderr += chunk.toString();
+    });
+    child.once("error", reject);
+    child.once("close", (exitCode, signal) => {
+      if (signal) {
+        reject(new Error(`CLI exited on ${signal}:\n${stdout}\n${stderr}`));
+      } else {
+        resolve({ exitCode, stdout, stderr });
+      }
+    });
+  });
+}

packages/server/src/server/utils/diff-highlighter.test.ts

@@ -190,6 +190,34 @@ index 1234567..abcdefg 100644
 `;
 
 describe("parseDiff", () => {
+  it.each(["-- comment", "++ marker"])(
+    "preserves hunk content resembling patch headers: %s",
+    (content) => {
+      const files = parseDiff(`diff --git a/example.txt b/example.txt
+index 1234567..abcdefg 100644
+--- a/example.txt
++++ b/example.txt
+@@ -1 +1 @@
+-${content} before
++${content} after
+`);
+
+      expect(files).toHaveLength(1);
+      expect(files[0]).toMatchObject({
+        path: "example.txt",
+        isNew: false,
+        isDeleted: false,
+        additions: 1,
+        deletions: 1,
+      });
+      expect(files[0].hunks[0].lines).toEqual([
+        { type: "header", content: "@@ -1 +1 @@" },
+        { type: "remove", content: `${content} before` },
+        { type: "add", content: `${content} after` },
+      ]);
+    },
+  );
+
   it("parses a simple diff with one hunk", () => {
     const files = parseDiff(SIMPLE_DIFF);
 

packages/server/src/server/utils/diff-highlighter.ts

@@ -79,16 +79,6 @@ function extractPathFromDiffHeader(lines: string[]): string {
   return "unknown";
 }
 
-function isMetadataLine(line: string): boolean {
-  return (
-    line.startsWith("index ") ||
-    line.startsWith("--- ") ||
-    line.startsWith("+++ ") ||
-    line.startsWith("new file mode") ||
-    line.startsWith("deleted file mode")
-  );
-}
-
 function parseHunkHeader(line: string): DiffHunk | null {
   const hunkMatch = line.match(/^@@ -(\d+)(?:,(\d+))? \+(\d+)(?:,(\d+))? @@/);
   if (!hunkMatch) return null;
@@ -116,8 +106,6 @@ function parseSectionBody(lines: string[]): ParsedSectionBody {
   for (let i = 1; i < lines.length; i++) {
     const line = lines[i];
 
-    if (isMetadataLine(line)) continue;
-
     const newHunk = parseHunkHeader(line);
     if (newHunk) {
       if (currentHunk) hunks.push(currentHunk);

packages/server/src/server/web-ui.ts

@@ -250,6 +250,22 @@ function serializeInlineScriptJson(value: unknown): string {
     .replace(/&/g, "\\u0026");
 }
 
+/**
+ * A Host header carries no port when the client used the scheme's default one,
+ * which is what every browser sends to a proxy terminating TLS on 443. The app
+ * parses `listen` with parseHostPort, which requires an explicit port and
+ * rejects the value outright, so the hint has to spell the port out.
+ */
+function hasExplicitPort(host: string): boolean {
+  if (host.startsWith("[")) {
+    // IPv6 literals are bracketed: [::1] has no port, [::1]:443 does.
+    const end = host.indexOf("]");
+    return end !== -1 && /^:\d{1,5}$/.test(host.slice(end + 1));
+  }
+  const colon = host.indexOf(":");
+  return colon !== -1 && colon === host.lastIndexOf(":") && /^\d{1,5}$/.test(host.slice(colon + 1));
+}
+
 function injectConnectionHint(
   html: string,
   req: Parameters<RequestHandler>[0],
@@ -257,8 +273,16 @@ function injectConnectionHint(
 ): string {
   const host = typeof req.headers.host === "string" ? req.headers.host : "";
   const useTls = req.protocol === "https";
+  let listen = host;
+  if (host && !hasExplicitPort(host)) {
+    let defaultPort = 80;
+    if (useTls) {
+      defaultPort = 443;
+    }
+    listen = `${host}:${defaultPort}`;
+  }
   const hint = {
-    listen: host,
+    listen,
     useTls,
     label,
   };

packages/server/src/utils/checkout-git.commits.test.ts

@@ -25,7 +25,10 @@ function git(args: string[], cwd?: string): void {
 }
 
 function commit(repoDir: string, message: string): void {
-  git(["-c", "commit.gpgsign=false", "commit", "-m", message], repoDir);
+  git(
+    ["-c", "commit.gpgsign=false", "commit", "--author=Test User <test@test.com>", "-m", message],
+    repoDir,
+  );
 }
 
 function commitFile(repoDir: string, name: string, content: string, message: string): void {
@@ -92,6 +95,30 @@ function addBareRemote(repoDir: string, tempDir: string): string {
 }
 
 describe("listCheckoutCommits", () => {
+  it("keeps fixture authors independent of command-scoped Git configuration", async () => {
+    const overrides = {
+      GIT_CONFIG_COUNT: "1",
+      GIT_CONFIG_KEY_0: "user.name",
+      GIT_CONFIG_VALUE_0: "Other User",
+    };
+    const previous = Object.fromEntries(
+      Object.keys(overrides).map((key) => [key, process.env[key]]),
+    );
+    let repoDir: string;
+    try {
+      Object.assign(process.env, overrides);
+      ({ repoDir } = initRepoOnMain());
+    } finally {
+      for (const [key, value] of Object.entries(previous)) {
+        if (value === undefined) delete process.env[key];
+        else process.env[key] = value;
+      }
+    }
+
+    const { commits } = await listCheckoutCommits({ cwd: repoDir });
+    expect(commits[0]?.authorName).toBe("Test User");
+  });
+
   it("lists recent commits newest-first with on-remote flags and file stats", async () => {
     const { repoDir, tempDir } = initRepoOnMain();
     git(["checkout", "-b", "feature"], repoDir);

packages/server/src/utils/checkout-git.patch-format.test.ts

@@ -1,13 +1,14 @@
 import { execFileSync } from "node:child_process";
-import { mkdirSync, mkdtempSync, realpathSync, rmSync, writeFileSync } from "node:fs";
+import { existsSync, mkdirSync, mkdtempSync, realpathSync, rmSync, writeFileSync } from "node:fs";
 import { tmpdir } from "node:os";
 import { join } from "node:path";
-import { afterEach, describe, expect, it } from "vitest";
+import { afterEach, describe, expect, it, vi } from "vitest";
 import { getCheckoutDiff, getCommitFileDiff } from "./checkout-git.js";
 
 const repos: string[] = [];
 
 afterEach(() => {
+  vi.unstubAllEnvs();
   for (const repo of repos.splice(0)) rmSync(repo, { recursive: true, force: true });
 });
 
@@ -62,6 +63,95 @@ function createChangedRepo(config: string): string {
   return cwd;
 }
 
+function createExternalDiffCommand() {
+  const directory = realpathSync.native(mkdtempSync(join(tmpdir(), "checkout-external-diff-")));
+  repos.push(directory);
+  const script = join(directory, "external-diff.cjs");
+  const marker = join(directory, "invoked");
+  writeFileSync(
+    script,
+    'require("node:fs").writeFileSync(process.argv[2], "invoked");\n' +
+      'process.stdout.write("CUSTOM EXTERNAL DIFF\\n");\n',
+  );
+  const command = [process.execPath, script, marker]
+    .map((argument) => `'${argument.replaceAll("'", "'\\''")}'`)
+    .join(" ");
+  return { command, marker };
+}
+
+function createExternalDiffRepo() {
+  vi.stubEnv("GIT_EXTERNAL_DIFF", undefined);
+  const cwd = createChangedRepo("color.diff=always");
+  const { command, marker } = createExternalDiffCommand();
+  git(cwd, "config", "diff.external", command);
+  expect(git(cwd, "diff", "HEAD", "--", "file.txt")).toBe("CUSTOM EXTERNAL DIFF\n");
+  expect(existsSync(marker)).toBe(true);
+  rmSync(marker);
+  return { cwd, command, marker };
+}
+
+function expectStandardPatch(result: Awaited<ReturnType<typeof getCheckoutDiff>>) {
+  expect(result.structured).toMatchObject([
+    {
+      path: "file.txt",
+      additions: 1,
+      deletions: 1,
+      status: "ok",
+      hunks: [
+        {
+          lines: [
+            { type: "header", content: "@@ -1 +1 @@" },
+            { type: "remove", content: "before" },
+            { type: "add", content: "after" },
+          ],
+        },
+      ],
+    },
+  ]);
+}
+
+it("returns Git patch hunks when a repository configures an external diff command", async () => {
+  const { cwd, command, marker } = createExternalDiffRepo();
+
+  const result = await getCheckoutDiff(cwd, { mode: "uncommitted", includeStructured: true });
+
+  expectStandardPatch(result);
+  expect(existsSync(marker)).toBe(false);
+  expect(git(cwd, "config", "--get", "diff.external").trim()).toBe(command);
+});
+
+it("returns Git patch hunks against the base branch with an external diff command", async () => {
+  const { cwd, command, marker } = createExternalDiffRepo();
+  git(cwd, "checkout", "-b", "feature");
+  git(cwd, "add", ".");
+  git(cwd, "-c", "commit.gpgsign=false", "commit", "-m", "edit");
+
+  const result = await getCheckoutDiff(cwd, {
+    mode: "base",
+    baseRef: "main",
+    includeStructured: true,
+  });
+
+  expectStandardPatch(result);
+  expect(existsSync(marker)).toBe(false);
+  expect(git(cwd, "config", "--get", "diff.external").trim()).toBe(command);
+});
+
+it("returns Git patch hunks when GIT_EXTERNAL_DIFF configures the external command", async () => {
+  const cwd = createChangedRepo("color.diff=always");
+  const { command, marker } = createExternalDiffCommand();
+  vi.stubEnv("GIT_EXTERNAL_DIFF", command);
+  expect(git(cwd, "diff", "HEAD", "--", "file.txt")).toBe("CUSTOM EXTERNAL DIFF\n");
+  expect(existsSync(marker)).toBe(true);
+  rmSync(marker);
+
+  const result = await getCheckoutDiff(cwd, { mode: "uncommitted", includeStructured: true });
+
+  expectStandardPatch(result);
+  expect(existsSync(marker)).toBe(false);
+  expect(process.env.GIT_EXTERNAL_DIFF).toBe(command);
+});
+
 describe.each(["diff.mnemonicPrefix=true", "color.diff=always"])(
   "patch format with %s",
   (config) => {

packages/server/src/utils/checkout-git.test.ts

@@ -539,10 +539,129 @@ describe("checkout git utilities", () => {
     });
 
     expect(diff.structured).toContainEqual(
-      expect.objectContaining({ path: "renamed.txt", oldPath: "file.txt" }),
+      expect.objectContaining({
+        path: "renamed.txt",
+        oldPath: "file.txt",
+        additions: 0,
+        deletions: 0,
+        hunks: [],
+      }),
     );
   });
 
+  it.each([
+    { mode: "uncommitted", oldPath: "to-rename.txt", path: "renamed.txt" },
+    { mode: "base", oldPath: "to-rename.txt", path: "renamed.txt" },
+    { mode: "uncommitted", oldPath: "old [file].txt", path: "new [file].txt" },
+  ] as const)(
+    "shows only the edited line of a rename ($mode, $path)",
+    async ({ mode, oldPath, path }) => {
+      const original = Array.from({ length: 12 }, (_, index) => `line ${index + 1}`);
+      commitFile(repoDir, oldPath, original.join("\n") + "\n", "file to rename");
+      if (mode === "base") {
+        execFileSync("git", ["checkout", "-b", "feature/rename"], { cwd: repoDir });
+      }
+      execFileSync("git", ["mv", oldPath, path], { cwd: repoDir });
+      const edited = [...original];
+      edited[5] = "edited line 6";
+      writeFileSync(join(repoDir, path), edited.join("\n") + "\n");
+      execFileSync("git", ["add", path], { cwd: repoDir });
+
+      expect(
+        execFileSync("git", ["diff", "--name-status", "HEAD"], { cwd: repoDir }).toString(),
+      ).toMatch(/R\d+\t/);
+      if (mode === "base") {
+        execFileSync("git", ["-c", "commit.gpgsign=false", "commit", "-m", "rename and edit"], {
+          cwd: repoDir,
+        });
+      }
+
+      const diff = await getCheckoutDiff(repoDir, {
+        mode,
+        ...(mode === "base" ? { baseRef: "main" } : {}),
+        includeStructured: true,
+      });
+
+      expect(diff.structured).toEqual([
+        expect.objectContaining({
+          path,
+          oldPath,
+          isNew: false,
+          isDeleted: false,
+          additions: 1,
+          deletions: 1,
+          status: "ok",
+        }),
+      ]);
+      expect(diff.diff).toContain(`rename from ${oldPath}`);
+      expect(diff.diff).toContain(`rename to ${path}`);
+      expect(diff.diff).toContain("-line 6\n+edited line 6");
+      expect(diff.diff).not.toContain("new file mode");
+    },
+  );
+
+  it("includes a changed copy source only once in the diff", async () => {
+    const original =
+      Array.from({ length: 12 }, (_, index) => `line ${index + 1}`).join("\n") + "\n";
+    commitFile(repoDir, "source.txt", original, "copy source");
+    execFileSync("git", ["config", "diff.renames", "copies"], { cwd: repoDir });
+    writeFileSync(join(repoDir, "copy.txt"), original);
+    writeFileSync(join(repoDir, "source.txt"), original.replace("line 6", "edited line 6"));
+    execFileSync("git", ["add", "copy.txt", "source.txt"], { cwd: repoDir });
+    expect(
+      execFileSync("git", ["diff", "--name-status", "HEAD"], { cwd: repoDir }).toString(),
+    ).toContain("C100\tsource.txt\tcopy.txt");
+
+    const diff = await getCheckoutDiff(repoDir, {
+      mode: "uncommitted",
+      includeStructured: true,
+    });
+    expect(diff.structured).toEqual([
+      expect.objectContaining({
+        path: "copy.txt",
+        oldPath: "source.txt",
+        additions: 0,
+        deletions: 0,
+      }),
+      expect.objectContaining({ path: "source.txt", additions: 1, deletions: 1 }),
+    ]);
+    expect(diff.diff.match(/^diff --git a\/source.txt b\/source.txt$/gm)).toHaveLength(1);
+    expect(diff.diff).toContain("copy from source.txt");
+    expect(diff.diff).toContain("copy to copy.txt");
+  });
+
+  it("keeps a small copy patch when its edited source exceeds the patch limit", async () => {
+    const original =
+      Array.from({ length: 12 }, (_, index) => `line ${index + 1}`).join("\n") + "\n";
+    commitFile(repoDir, "source.txt", original, "copy source");
+    execFileSync("git", ["config", "diff.renames", "copies"], { cwd: repoDir });
+    writeFileSync(join(repoDir, "copy.txt"), original);
+    writeFileSync(join(repoDir, "source.txt"), original + "added source line\n".repeat(80_000));
+    execFileSync("git", ["add", "copy.txt", "source.txt"], { cwd: repoDir });
+    expect(
+      execFileSync("git", ["diff", "--name-status", "HEAD"], { cwd: repoDir }).toString(),
+    ).toContain("C100\tsource.txt\tcopy.txt");
+
+    const diff = await getCheckoutDiff(repoDir, {
+      mode: "uncommitted",
+      includeStructured: true,
+    });
+    expect(diff.structured).toEqual([
+      expect.objectContaining({
+        path: "copy.txt",
+        oldPath: "source.txt",
+        additions: 0,
+        deletions: 0,
+        hunks: [],
+        status: "ok",
+      }),
+      expect.objectContaining({ path: "source.txt", status: "too_large", hunks: [] }),
+    ]);
+    expect(diff.diff).toContain("copy from source.txt");
+    expect(diff.diff).toContain("copy to copy.txt");
+    expect(diff.diff).not.toContain("+added source line");
+  });
+
   it("reads the origin URL once when collecting facts for an origin-tracking branch", async () => {
     setupRemoteTrackingMain(repoDir, tempDir);
 
@@ -1508,9 +1627,11 @@ const x = 1;
     expect(diff.diff).toContain("# generated.js: diff too large omitted");
     expect(diff.diff).toContain(`-export const value = "old";`);
     expect(diff.diff).toContain(`+export const value = "new";`);
-    expect(commands).toContain("diff --no-color --src-prefix=a/ --dst-prefix=b/ --numstat HEAD");
     expect(commands).toContain(
-      "diff --no-color --src-prefix=a/ --dst-prefix=b/ HEAD -- :(literal)generated.js :(literal)small.ts",
+      "diff --no-ext-diff --no-color --src-prefix=a/ --dst-prefix=b/ --numstat HEAD",
+    );
+    expect(commands).toContain(
+      "diff --no-ext-diff --no-color --src-prefix=a/ --dst-prefix=b/ HEAD -- :(literal)generated.js :(literal)small.ts",
     );
     expect(metrics.maxConcurrent).toBeLessThanOrEqual(8);
   });

packages/server/src/utils/checkout-git.ts

@@ -637,7 +637,7 @@ function normalizeNumstatPath(pathField: string): string {
 }
 
 // Parsed patches need a stable wire format regardless of terminal presentation settings.
-const GIT_PATCH_FORMAT_ARGS = ["--no-color", "--src-prefix=a/", "--dst-prefix=b/"];
+const GIT_PATCH_FORMAT_ARGS = ["--no-ext-diff", "--no-color", "--src-prefix=a/", "--dst-prefix=b/"];
 
 function buildGitDiffArgs(args: { ignoreWhitespace?: boolean; extra: string[] }): string[] {
   return [
@@ -721,12 +721,19 @@ async function getTrackedDiffTextForPath(input: {
   cwd: string;
   refsForDiff: CheckoutDiffRefs;
   path: string;
+  oldPath?: string;
   ignoreWhitespace: boolean;
 }): Promise<{ path: string; text: string; truncated: boolean }> {
+  const paths = input.oldPath ? [input.oldPath, input.path] : [input.path];
   const result = await runGitCommand(
     buildGitDiffArgs({
       ignoreWhitespace: input.ignoreWhitespace,
-      extra: [...getCheckoutDiffRefArgs(input.refsForDiff), "--", `:(literal)${input.path}`],
+      extra: [
+        ...(input.oldPath ? ["--diff-filter=RC"] : []),
+        ...getCheckoutDiffRefArgs(input.refsForDiff),
+        "--",
+        ...paths.map((path) => `:(literal)${path}`),
+      ],
     }),
     {
       cwd: input.cwd,
@@ -735,9 +742,22 @@ async function getTrackedDiffTextForPath(input: {
     },
   );
 
+  // A source path can participate in another rename/copy in the same request.
+  // Return only the requested destination; the filter keeps source edits out of its budget.
+  let text = result.stdout;
+  if (input.oldPath && !result.truncated) {
+    text = result.stdout
+      .split(/(?=^diff --git )/m)
+      .filter((section) => {
+        const hunkStart = section.indexOf("\n@@ ");
+        const header = hunkStart < 0 ? section : section.slice(0, hunkStart);
+        return parseDiff(header)[0]?.path === input.path;
+      })
+      .join("");
+  }
   return {
     path: input.path,
-    text: result.stdout,
+    text,
     truncated: result.truncated,
   };
 }
@@ -1167,13 +1187,16 @@ export function parseWorktreeList(output: string): GitWorktreeEntry[] {
 
 async function getWorktreePathForBranch(cwd: string, branchName: string): Promise<string | null> {
   try {
-    const { stdout } = await runGitCommand(["worktree", "list", "--porcelain"], {
-      cwd,
-      envOverlay: READ_ONLY_GIT_ENV,
-    });
-    const entries = parseWorktreeList(stdout);
     const ref = branchName.startsWith("refs/heads/") ? branchName : `refs/heads/${branchName}`;
-    return entries.find((entry) => entry.branchRef === ref)?.path ?? null;
+    const { stdout } = await runGitCommand(
+      ["for-each-ref", "--format=%(refname)%00%(worktreepath)%00", ref],
+      { cwd, envOverlay: READ_ONLY_GIT_ENV },
+    );
+    for (const record of stdout.split("\0\n")) {
+      const [reference, worktreePath] = record.split("\0");
+      if (reference === ref) return worktreePath || null;
+    }
+    return null;
   } catch {
     return null;
   }
@@ -3314,26 +3337,29 @@ async function processTrackedChanges(
 
   let trackedDiffText = "";
   let trackedDiffBytes = 0;
-  const renamedPaths = new Set(
-    trackedChanges.filter((change) => change.oldPath).map((change) => change.path),
+  const oldPathByPath = new Map(
+    trackedChanges
+      .filter((change) => change.oldPath)
+      .map((change) => [change.path, change.oldPath]),
   );
   for (let start = 0; start < trackedDiffPaths.length; start += TRACKED_DIFF_BATCH_SIZE) {
     const paths = trackedDiffPaths.slice(start, start + TRACKED_DIFF_BATCH_SIZE);
-    // Keep rename/copy path filtering identical to the existing per-file command.
+    // Rename/copy detection needs both paths.
     const ordinary = await getTrackedDiffTexts({
       cwd,
       refsForDiff,
-      paths: paths.filter((path) => !renamedPaths.has(path)),
+      paths: paths.filter((path) => !oldPathByPath.has(path)),
       ignoreWhitespace,
     });
     const renamed = await Promise.all(
       paths
-        .filter((path) => renamedPaths.has(path))
+        .filter((path) => oldPathByPath.has(path))
         .map((path) =>
           getTrackedDiffTextForPath({
             cwd,
             refsForDiff,
             path,
+            oldPath: oldPathByPath.get(path),
             ignoreWhitespace,
           }),
         ),

packages/server/src/utils/directory-suggestions.ts

@@ -146,6 +146,7 @@ export const WORKSPACE_SEARCH_HIDDEN_DIRECTORIES = [
   ".agents",
   ".claude",
   ".codex",
+  ".cursor",
   ".github",
   ".opencode",
   ".paseo",

packages/server/src/utils/spawn.launch-regression.test.ts

@@ -126,10 +126,15 @@ async function runFixture(params: {
   command: string;
   args: string[];
   shell?: boolean;
+  env?: NodeJS.ProcessEnv;
 }): Promise<SpawnResult> {
   const child = spawnProcess(params.command, params.args, {
     env: {
       ...process.env,
+      ...params.env,
+      // Terminal color settings must not add Node warnings to the argv fixture's stderr.
+      NO_COLOR: undefined,
+      FORCE_COLOR: undefined,
       PASEO_EXPECTED_ARGV_JSON: JSON.stringify(["--config", JSON_ARG]),
     },
     stdio: ["ignore", "pipe", "pipe"],
@@ -216,6 +221,8 @@ async function findAndLaunch(fixture: LaunchFixture): Promise<{
     const child = spawnProcess(found, fixture.args, {
       env: {
         ...process.env,
+        NO_COLOR: undefined,
+        FORCE_COLOR: undefined,
         PASEO_EXPECTED_ARGV_JSON: fixture.expectedArgvJson,
         PASEO_ARGV_SLICE_FROM: String(fixture.sliceFrom),
       },
@@ -331,18 +338,25 @@ describe.runIf(isPlatform("win32"))("Windows spawn launch regression", () => {
 });
 
 describe.skipIf(isPlatform("win32"))("spawn launch regression smoke", () => {
-  test("direct launch with a space-containing executable works on this platform", async () => {
-    const fixture = makeFixture();
+  test.each([
+    { colors: "inherited", env: {} },
+    { colors: "conflicting", env: { NO_COLOR: "1", FORCE_COLOR: "1" } },
+  ])(
+    "direct launch with a space-containing executable works with $colors colors",
+    async ({ env }) => {
+      const fixture = makeFixture();
 
-    const result = await runFixture({
-      command: fixture.fakeDaemonNode,
-      args: [fixture.assertScript, ...fixture.expectedArgs],
-      shell: false,
-    });
+      const result = await runFixture({
+        command: fixture.fakeDaemonNode,
+        args: [fixture.assertScript, ...fixture.expectedArgs],
+        shell: false,
+        env,
+      });
 
-    expect(result.error).toBeNull();
-    expect(result.code).toBe(0);
-    expect(result.stderr).toBe("");
-    expect(result.stdout.trim()).toBe("ARGV_OK");
-  });
+      expect(result.error).toBeNull();
+      expect(result.code).toBe(0);
+      expect(result.stderr).toBe("");
+      expect(result.stdout.trim()).toBe("ARGV_OK");
+    },
+  );
 });

packages/server/src/utils/worktree.test.ts

@@ -10,6 +10,7 @@ import {
   type WorktreeConfig,
 } from "./worktree";
 import { execFileSync } from "child_process";
+import { rm } from "node:fs/promises";
 import {
   mkdtempSync,
   mkdirSync,
@@ -89,8 +90,8 @@ describe("paseo worktree manager", () => {
     });
   });
 
-  afterEach(() => {
-    rmSync(tempDir, { recursive: true, force: true });
+  afterEach(async () => {
+    await rm(tempDir, { recursive: true, force: true, maxRetries: 10, retryDelay: 100 });
   });
 
   it("treats a worktree as paseo-owned even when its .git admin is missing", async () => {

plugins/claude-usage-source/server/stores.test.ts

@@ -45,6 +45,8 @@ async function logins(options: Parameters<typeof discover>[1]) {
 async function database(path: string) {
   await mkdir((await import("node:path")).dirname(path), { recursive: true });
   const db = new DatabaseSync(path);
+  // Create the fixture with one durable commit instead of one per row.
+  db.exec("BEGIN");
   db.exec(
     "CREATE TABLE auth_credentials (id INTEGER PRIMARY KEY, provider TEXT, credential_type TEXT, data TEXT, disabled_cause TEXT)",
   );
@@ -78,6 +80,7 @@ async function database(path: string) {
     null,
   );
   insert.run(5, "anthropic", "oauth", "invalid", null);
+  db.exec("COMMIT");
   db.close();
 }
 

plugins/codex-usage-source/server/stores.test.ts

@@ -39,6 +39,8 @@ async function database(path: string) {
   await mkdir((await import("node:path")).dirname(path), { recursive: true });
   const { DatabaseSync } = await import("node:sqlite");
   const db = new DatabaseSync(path);
+  // Create the fixture with one durable commit instead of one per row.
+  db.exec("BEGIN");
   db.exec(
     "CREATE TABLE auth_credentials (id INTEGER PRIMARY KEY, provider TEXT, credential_type TEXT, data TEXT, disabled_cause TEXT)",
   );
@@ -72,6 +74,7 @@ async function database(path: string) {
     null,
   );
   insert.run(5, "openai-codex", "oauth", "invalid", null);
+  db.exec("COMMIT");
   db.close();
 }
 

plugins/muse-provider/test/provider.test.ts

@@ -73,7 +73,8 @@ async function harness(
     predicate: (event: ProviderEvent) => boolean,
     from = 0,
   ): Promise<ProviderEvent> {
-    for (let count = 0; count < 200; count++) {
+    const deadline = Date.now() + 5000;
+    while (Date.now() < deadline) {
       const event = events.slice(from).find(predicate);
       if (event) return event;
       await delay(10);
@@ -1219,6 +1220,18 @@ test("silent active turns page after two minutes and stop polling on recovered t
   await vi.advanceTimersByTimeAsync(240000);
   expect((await h.recorded()).filter((f) => f.method === "view/page")).toHaveLength(1);
 });
+test("session readiness accepts initialization beyond the old event polling window", async () => {
+  const h = await harness("text-reasoning", { MUSE_TEST_INITIALIZE_DELAY_MS: "3500" });
+  expect(await h.open()).toMatchObject({ type: "session.ready" });
+  expect((await h.recorded()).find((frame) => frame.event === "hostStarted").args).toEqual([
+    "serve",
+    "--sandbox-network",
+    "proxy-only",
+    "--disable-sandbox",
+    "--trust-workspace",
+  ]);
+}, 10000);
+
 test("default launch disables sandbox and trusts workspace", async () => {
   const h = await harness();
   await h.open();

vitest.config.ts

@@ -2,6 +2,9 @@ import fs from "node:fs";
 import path from "node:path";
 import { configDefaults, defineConfig } from "vitest/config";
 
+// React's test APIs require its development build, even in a production shell.
+process.env.NODE_ENV = "test";
+
 const appDir = path.resolve(__dirname, "packages/app");
 const appNodeModules = path.resolve(appDir, "node_modules");
 const rootNodeModules = path.resolve(__dirname, "node_modules");