papilot 0.1.1 → 0.3.0

package/src/server/skills.ts

@@ -0,0 +1,57 @@
+import fs from 'node:fs';
+import path from 'node:path';
+import { DATA, ROOT } from './paths.ts';
+import type { Skill } from '../shared.ts';
+
+// Skills are Markdown instructions an author runs with "/" in the composer.
+// Papilot ships some in skills/; the data folder's skills/ adds the author's
+// own for every paper, and a paper's .papilot/skills/ its own. A later source
+// replaces an earlier skill with the same name. Each skill is <name>.md, or a
+// folder with a SKILL.md (the Agent Skills layout) whose other files the
+// agent may read. Front matter gives its name, description, composer hint
+// and order.
+export interface SkillFile extends Skill { body: string; folder?: string; order: number }
+const NAME = /^[a-z0-9][a-z0-9-]{0,47}$/;
+
+export function parseSkill(text: string, id: string, source: Skill['source'], folder?: string): SkillFile | null {
+  text = text.replace(/^\uFEFF/, '').replace(/\r\n?/g, '\n');
+  const header = /^---\n([\s\S]*?)\n---(?:\n|$)/.exec(text), fields: Record<string, string> = {};
+  for (const line of header?.[1].split('\n') || []) {
+    const field = /^([A-Za-z-]+):\s*(.*)$/.exec(line);
+    if (field) fields[field[1].toLowerCase()] = field[2].trim().replace(/^(['"])(.*)\1$/, '$2');
+  }
+  const body = text.slice(header ? header[0].length : 0).trim().slice(0, 20000);
+  if (!body) return null;
+  return { id, name: (fields.name || id).slice(0, 60), description: (fields.description || '').slice(0, 300), hint: (fields.hint || '').slice(0, 200), source, body, ...(folder ? { folder } : {}), order: fields.order && Number.isFinite(Number(fields.order)) ? Number(fields.order) : 1000 };
+}
+
+function read(dir: string, source: Skill['source']): SkillFile[] {
+  let entries: fs.Dirent[];
+  try { entries = fs.readdirSync(dir, { withFileTypes: true }); } catch { return []; }
+  const found: SkillFile[] = [];
+  for (const entry of entries) {
+    const id = entry.name.replace(/\.md$/i, '').toLowerCase();
+    if (!NAME.test(id)) continue;
+    try {
+      const skill = entry.isDirectory() ? parseSkill(fs.readFileSync(path.join(dir, entry.name, 'SKILL.md'), 'utf8'), id, source, path.join(dir, entry.name))
+        : entry.isFile() && /\.md$/i.test(entry.name) ? parseSkill(fs.readFileSync(path.join(dir, entry.name), 'utf8'), id, source) : null;
+      if (skill) found.push(skill);
+    } catch { /* A folder without a readable SKILL.md is not a skill. */ }
+  }
+  return found;
+}
+
+export function loadSkills(paper?: string, roots = { builtin: path.join(ROOT, 'skills'), user: path.join(DATA, 'skills') }): SkillFile[] {
+  const skills = new Map<string, SkillFile>();
+  const sources: [string, Skill['source']][] = [[roots.builtin, 'builtin'], [roots.user, 'user'], ...(paper ? [[path.join(paper, '.papilot', 'skills'), 'paper'] as [string, Skill['source']]] : [])];
+  for (const [dir, source] of sources) for (const skill of read(dir, source)) skills.set(skill.id, skill);
+  return [...skills.values()].sort((a, b) => a.order - b.order || a.name.localeCompare(b.name));
+}
+
+export function findSkill(paper: string, id: string) {
+  const skill = loadSkills(paper).find(item => item.id === id);
+  if (!skill) throw new Error(`The skill "${id}" is not available for this paper.`);
+  return skill;
+}
+
+export const listedSkill = ({ id, name, description, hint, source }: SkillFile): Skill => ({ id, name, description, hint, source });

package/src/server/workspace.ts

@@ -9,7 +9,11 @@ import { Codex, RpcResponseError } from './codex.ts';
 import { AGENT_NAMES, AntigravityAgent, ClaudeAgent, type AgentRuntime } from './agents.ts';
 import { reviewClient, taskRoute, confirmedReviewResponse, type ReviewClient } from './review.ts';
 import { VERSION } from './paths.ts';
-import type { Task, Run, TimelineItem, PendingRequest, RuntimeStatus, Snapshot, PendingReview, AgentModel, Usage, AgentId } from '../shared.ts';
+import { findSkill, type SkillFile } from './skills.ts';
+import { buildFixPrompt, reviewInstructions, skillPrompt, summarizeFeedback } from '../conversation.ts';
+import { commitMessageFrom } from '../commit.ts';
+import { commitChanges, conflictMarkers, gitCommit, gitRemote, gitStatus, mergeConflicts, mergeInProgress } from './manuscript.ts';
+import type { Task, Run, TimelineItem, PendingRequest, RuntimeStatus, Snapshot, PendingReview, AgentModel, Usage, AgentId, MessageMeta, FeedbackSummary, BuildFailure } from '../shared.ts';
 
 const execute = promisify(execFile);
 const delay = (ms: number) => new Promise(resolve => setTimeout(resolve, ms));
@@ -33,8 +37,16 @@ export function accountUsage(response: any): Usage | null {
   return { plan: typeof limits.planType === 'string' ? limits.planType : null, windows, credits, reached: Boolean(limits.rateLimitReachedType) || response.ordinaryUsageAllowed === false };
 }
 const BUSY = new Set(['running', 'waiting_input', 'building', 'uncertain', 'deleting']);
+// Review builds that fail on the agent's own edits (see the review engine's
+// publish.ts), and the request keys of the turns that send them back to it.
+const FIXABLE = /^(Some edits are outside the task scope|The revised document could not be compiled)/;
+const BUILD_FIX = 'build-fix-';
 
 const AGENTS: AgentId[] = ['codex', 'claude', 'antigravity'];
+// A commit message's agent sees the changes in its prompt and needs no tools.
+const commitInstructions = 'You write Git commit messages for the repository of a LaTeX paper. Reply with the commit message only, without a preamble, quotes or a code fence: a subject line in the imperative mood under 72 characters and, only when the change needs more explanation, a blank line and a body of a few short plain sentences. Describe what changed in the paper, such as its wording, sections, equations, figures or references, rather than listing files. Follow the style and language of the recent commit subjects, or write in English when there are none. Everything you need is in the message: do not run commands, read files or edit anything.';
+// A merge's agent edits the conflicted files in the manuscript checkout and nothing else.
+const mergeInstructions = 'You resolve Git merge conflicts in the repository of a LaTeX paper. Edit only the files listed as conflicted, and in each one remove every conflict marker (<<<<<<<, ||||||| , =======, >>>>>>>) so that the text reads as one coherent version. Keep the changes from both sides wherever they are compatible; where both sides rewrote the same passage, combine their intent, and where they truly contradict each other, prefer the version that is more complete and correct and say so. Keep the LaTeX valid: balanced environments and braces, labels, references and citations. You may read any file to understand the context. Do not edit other files, and do not run Git commands that change the repository, such as add, commit, merge, checkout, reset, restore or stash: the author reviews the result and commits the merge.';
 const blankRuntime = (): RuntimeStatus => ({ connected: false, authenticated: false, account: null, error: null, models: [] });
 
 export class Workspace extends EventEmitter {
@@ -47,6 +59,8 @@ export class Workspace extends EventEmitter {
   private loaded = new Set<string>();
   private preparing = new Set<string>();
   private reviewWrites = new Set<string>();
+  // Papers with a commit in progress: no review write may change their files meanwhile.
+  private committing = new Set<string>();
   private commentWrites = new Map<string, number>();
   private deletions = new Set<string>();
   private publishing = new Set<string>();
@@ -122,25 +136,31 @@ export class Workspace extends EventEmitter {
     const project = { ...this.store.project(projectId), name };
     this.store.saveProject(project); return project;
   }
-  async createTask(input: { projectId: string; title: string; instructions: string; agent?: AgentId; model?: string; effort?: string; id: string }) {
+  // A task can start from a skill; its instructions are then the author's own words, possibly none.
+  async createTask(input: { projectId: string; title: string; instructions: string; skill?: string; agent?: AgentId; model?: string; effort?: string; id: string }) {
     if (!/^[\w-]{16,64}$/.test(input.id)) throw new Error('Invalid task ID.');
     if (this.store.taskDeleted(input.id)) throw new Error('This task was deleted. Create a new task instead.');
     const existing = this.store.tasks().find(t => t.id === input.id); if (existing) return existing;
     if (this.preparing.has(input.id)) throw new Error('This task is being created. Refresh in a moment.');
     this.preparing.add(input.id);
     try {
-      const project = this.store.project(input.projectId), client = await this.connectReview(project.path);
+      const project = this.store.project(input.projectId), skill = input.skill ? findSkill(project.path, input.skill) : undefined;
+      if (!skill && !input.instructions.trim()) throw new Error('Describe the revision, or choose a skill.');
+      const client = await this.connectReview(project.path);
       const name = 'p-' + input.id.toLowerCase().replace(/[^a-z0-9-]/g, '').slice(0, 48);
       const info = await client.post('/api/tasks', { name, title: input.title });
-      const task: Task = { id: input.id, projectId: project.id, name, title: input.title, instructions: input.instructions,
+      const task: Task = { id: input.id, projectId: project.id, name, title: input.title, instructions: skill ? skillPrompt(skill, input.instructions) : input.instructions,
         worktree: info.worktree, threadId: null, turnId: null, agent: input.agent || 'codex', model: input.model || null, effort: input.effort || null, status: 'idle',
         createdAt: Date.now(), updatedAt: Date.now(), feedbackCursor: 0, error: null, review: null };
       this.store.saveTask(task);
-      await this.enqueue(task.id, input.instructions, 'initial-' + task.id, false);
+      await this.enqueue(task.id, input.instructions, 'initial-' + task.id, false, { skill });
       return this.store.task(task.id);
     } finally { this.preparing.delete(input.id); }
   }
-  async enqueue(taskId: string, text: string, requestKey: string, includeFeedback = true) {
+  // The author's message, a skill run with or without one, the review
+  // feedback alone, or a build the agent broke. The chat keeps what happened;
+  // the agent gets the prompt.
+  async enqueue(taskId: string, text: string, requestKey: string, includeFeedback = true, options: { skill?: SkillFile; feedback?: boolean; build?: BuildFailure } = {}) {
     const task = this.store.task(taskId);
     if (task.status === 'deleting') throw new Error('This task is being deleted.');
     const existing = this.store.runByKey(requestKey);
@@ -148,15 +168,18 @@ export class Workspace extends EventEmitter {
     if (task.status === 'uncertain') throw new Error('Check the task status before sending more instructions.');
     const pauseVersion = task.pauseVersion || 0;
     if (this.store.runs().some(r => r.taskId === taskId && r.status === 'queued')) throw new Error('This task already has queued instructions. Wait or pause it first.');
-    let prompt = text.trim(), cursor = task.feedbackCursor;
+    let prompt = options.build ? buildFixPrompt(options.build) : options.feedback ? reviewInstructions : options.skill ? skillPrompt(options.skill, text) : text.trim(), cursor = task.feedbackCursor;
+    let summary: FeedbackSummary | undefined;
     if (includeFeedback) {
       const client = await this.connectReview(this.store.project(task.projectId).path);
       const feedback = await client.get(`${taskRoute(task.name)}/feedback?after=${task.feedbackCursor}`);
-      cursor = feedback.cursor;
+      cursor = feedback.cursor; summary = summarizeFeedback(feedback);
+      if (options.feedback && !summary) throw new Error('There is no new review feedback to send.');
       if (feedback.feedback?.length || feedback.build_error) prompt += '\n\nPapilot review feedback (bound to the specified review round and source changes):\n' + JSON.stringify(feedback, null, 2);
       if (task.error) prompt += '\n\nLatest task/review error:\n' + task.error + '\nThe latest accepted manuscript is at ' + this.store.project(task.projectId).path + '. You may read it to understand accepted changes, but must only edit your isolated task worktree. Prepare a revised proposal for another review; never write to or accept changes in the manuscript checkout.';
     }
     const run: Run = { id: randomUUID(), taskId, requestKey, prompt, feedbackCursor: cursor, status: 'queued', createdAt: Date.now(), finishedAt: null };
+    const meta: MessageMeta = { ...(options.skill ? { skill: { id: options.skill.id, name: options.skill.name } } : {}), ...(summary ? { feedback: summary } : {}), ...(options.feedback ? { sendsFeedback: true } : {}), ...(options.build ? { build: options.build } : {}) };
     const saved = this.store.transaction(() => {
       // Feedback loading yields to other requests. Recheck identity, queue, and
       // task status together before committing; none of the earlier reads own a lock.
@@ -172,7 +195,7 @@ export class Workspace extends EventEmitter {
       if (current.status === 'uncertain') throw new Error('Check the task status before sending more instructions.');
       this.store.saveRun(run);
       if (!BUSY.has(current.status)) this.store.updateTask(taskId, { status: 'queued', error: null });
-      this.store.saveItem({ id: run.id, taskId, type: 'user', text: text.trim(), createdAt: run.createdAt });
+      this.store.saveItem({ id: run.id, taskId, type: 'user', text: options.feedback || options.build ? '' : text.trim(), createdAt: run.createdAt, ...(Object.keys(meta).length ? { meta } : {}) });
       return run;
     });
     this.schedule();
@@ -195,12 +218,20 @@ export class Workspace extends EventEmitter {
       void this.startRun(run).catch(e => this.failRun(run, e));
     }
   }
-  private instructions(task: Task) {
+  // The paths a task's review covers, or none when it covers the whole worktree.
+  private async reviewScope(task: Task): Promise<string[]> {
+    try {
+      const client = await this.connectReview(this.store.project(task.projectId).path);
+      const files: string[] = (await client.get(taskRoute(task.name))).scope?.files || [];
+      return files.some(file => file === '' || file === '.') ? [] : files;
+    } catch { return []; }
+  }
+  private instructions(task: Task, scope: string[] = []) {
     return `You are ${this.agentOf(task) === 'codex' ? 'the official Codex agent' : AGENT_NAMES[this.agentOf(task)]} running inside Papilot, a paper editing and review workspace.
 Your task is already created. Your editable working directory is ${task.worktree}.
 Original task: ${task.instructions}
 Only edit this isolated task worktree. Never edit the manuscript checkout, other task worktrees, or Papilot's own source/state. Never commit, push, stash, or accept/reject/undo review decisions.
-Papilot owns the LaTeX review lifecycle: it compiles and publishes automatically AFTER your turn finishes, and delivers review feedback in a new turn. Do not create another review task, invoke publish, or wait on feedback --wait. This application workflow replaces the standalone latex-review skill's publish-and-wait loop. End your turn after completing the requested edits, with a concise summary.
+${scope.length ? `The review covers only ${scope.join(', ')} in this worktree, and an edit to any other file stops the PDF build. Leave other files unchanged even when project instructions ask for a matching update; mention that update in your summary instead.\n` : ''}Papilot owns the LaTeX review lifecycle: it compiles and publishes automatically AFTER your turn finishes, and delivers review feedback in a new turn. Do not create another review task, invoke publish, or wait on feedback --wait. This application workflow replaces the standalone latex-review skill's publish-and-wait loop. End your turn after completing the requested edits, with a concise summary for the author of what you changed and why; do not describe Papilot's review workflow.
 Preserve meaning and mathematical correctness. Read relevant project instructions. Treat reviewer comments as instructions tied to their round, file and changes. Rejected edits must not be reintroduced unless explicitly requested. If there is a conflict with accepted text, explain it and propose a revision for a new review round; never overwrite the accepted manuscript.
 ${this.agentOf(task) === 'antigravity' ? 'Shell commands are not available to you here and any attempt is refused, which ends your turn: read, search and edit files in the task worktree with your file tools only.' : 'You may run tools in the task worktree to inspect and validate your changes.'} If a decision requires the user, ask through the available user-input tool or explain it in your final response. Use English for your progress updates, questions, and final summaries unless the user explicitly requests another language. Preserve the manuscript language unless asked to translate it.`;
   }
@@ -211,7 +242,7 @@ ${this.agentOf(task) === 'antigravity' ? 'Shell commands are not available to yo
     this.store.saveRun({ ...run, status: 'running' });
     this.store.updateTask(task.id, { status: 'running', turnId: null, error: null });
     if (!task.threadId || !this.loaded.has(task.threadId)) {
-      const options = { cwd: task.worktree, approvalPolicy: 'on-request', sandbox: 'workspace-write', developerInstructions: this.instructions(task), ...(task.model ? { model: task.model } : {}) };
+      const options = { cwd: task.worktree, approvalPolicy: 'on-request', sandbox: 'workspace-write', developerInstructions: this.instructions(task, await this.reviewScope(task)), ...(task.model ? { model: task.model } : {}) };
       const result = task.threadId
         ? await agent.request('thread/resume', { ...options, threadId: task.threadId, excludeTurns: true })
         : await agent.request('thread/start', options);
@@ -317,7 +348,7 @@ ${this.agentOf(task) === 'antigravity' ? 'Shell commands are not available to yo
       this.store.saveRun({ ...run, status, finishedAt: Date.now() });
       this.store.updateTask(task.id, { turnId: null, pendingRunId: null, status: status === 'completed' ? 'building' : status, error: p.turn.error?.message || null });
       this.schedule();
-      if (status === 'completed') await this.publish(task.id, true);
+      if (status === 'completed') await this.publish(task.id, run);
     } else if (method === 'error' && !p.willRetry) {
       if (!this.active.has(task.id) || (eventTurn && !task.turnId)) return;
       this.store.updateTask(task.id, { error: p.error?.message || `${AGENT_NAMES[agent]} encountered an error.` });
@@ -428,6 +459,8 @@ ${this.agentOf(task) === 'antigravity' ? 'Shell commands are not available to yo
       }
     }
     if (this.active.has(taskId) || this.publishing.has(taskId) || BUSY.has(task.status) || task.status === 'queued') throw new Error('Pause the task before accepting, rejecting, or undoing changes. Wait for any PDF build to finish.');
+    if (this.committing.has(task.projectId)) throw new Error('A commit is in progress. Try again when it finishes.');
+    if (mergeInProgress(this.store.project(task.projectId).path)) throw new Error('Finish or abort the merge in the Git panel before accepting, rejecting, or undoing changes.');
     if (this.reviewWrites.has(taskId)) throw new Error('A review action is already in progress. Wait for it to finish.');
     this.reviewWrites.add(taskId);
     if (pending) this.store.updateTask(taskId, { pendingReview: { ...pending, previousStatus: task.status } });
@@ -441,17 +474,19 @@ ${this.agentOf(task) === 'antigravity' ? 'Shell commands are not available to yo
     }
     finally { this.reviewWrites.delete(taskId); this.schedule(); }
   }
-  publish(taskId: string, automatic = false): Promise<void> {
-    const task = this.store.task(taskId);
+  // A build is automatic after the agent's run `after` completes. When its
+  // edits break the build, the agent gets the error in a new turn, once.
+  publish(taskId: string, after?: Run): Promise<void> {
+    const task = this.store.task(taskId), automatic = Boolean(after);
     if (task.status === 'deleting') throw new Error('This task is being deleted.');
     if (this.active.has(taskId)) throw new Error('Pause Codex before building a review.');
     if (this.reviewWrites.has(taskId)) throw new Error('Wait for the current review action before building a review.');
     if (this.publishing.has(taskId) || (!automatic && (BUSY.has(task.status) || task.status === 'queued'))) throw new Error('This task is busy. Wait for it to finish or pause it first.');
     this.publishing.add(taskId);
     this.store.updateTask(taskId, { status: 'building', error: null });
-    return this.buildReview(task).finally(() => { this.publishing.delete(taskId); this.schedule(); });
+    return this.buildReview(task, Boolean(after && !after.requestKey.startsWith(BUILD_FIX))).finally(() => { this.publishing.delete(taskId); this.schedule(); });
   }
-  private async buildReview(task: Task) {
+  private async buildReview(task: Task, sendBack: boolean) {
     const taskId = task.id;
     try {
       const client = await this.connectReview(this.store.project(task.projectId).path);
@@ -460,9 +495,17 @@ ${this.agentOf(task) === 'antigravity' ? 'Shell commands are not available to yo
         if (this.closing) return;
         const current = await client.get(`/api/jobs/${job.job}`);
         const summary = await client.get(taskRoute(task.name));
-        this.store.updateTask(taskId, { review: { state: summary.state, round: summary.round, counts: summary.counts, job: current, unsent: this.store.task(taskId).review?.unsent } });
+        this.store.updateTask(taskId, { review: { ...this.store.task(taskId).review, state: summary.state, round: summary.round, counts: summary.counts, job: current } });
         if (current.status === 'done' || current.status === 'completed' || current.status === 'succeeded') break;
-        if (current.status === 'failed') throw new Error([current.error, ...(current.details || [])].filter(Boolean).join('\n') || 'PDF build failed.');
+        if (current.status === 'failed') {
+          const failure: BuildFailure = { error: current.error || 'PDF build failed.', details: current.details || [], ...(current.log ? { log: current.log } : {}) };
+          // Instructions the author queued meanwhile go first; the build after them sends any error that remains.
+          if (sendBack && FIXABLE.test(failure.error) && await this.enqueue(taskId, '', BUILD_FIX + job.job, false, { build: failure }).then(() => true, () => false)) {
+            this.store.updateTask(taskId, { status: 'queued', error: null });
+            return;
+          }
+          throw new Error([failure.error, ...failure.details].join('\n'));
+        }
         await delay(1500);
       }
       this.store.updateTask(taskId, { status: this.store.runs().some(r => r.taskId === taskId && r.status === 'queued') ? 'queued' : 'reviewing', error: null });
@@ -473,19 +516,121 @@ ${this.agentOf(task) === 'antigravity' ? 'Shell commands are not available to yo
     try {
       const task = this.store.task(taskId);
       if (task.status === 'deleting') return;
-      const client = await this.connectReview(this.store.project(task.projectId).path);
+      const project = this.store.project(task.projectId), client = await this.connectReview(project.path);
       const summary = await client.get(taskRoute(task.name));
-      const unsent = await this.unsentComments(client, this.store.task(taskId));
+      const { unsent, comments } = await this.unsentReviewFeedback(client, this.store.task(taskId));
+      const files = await acceptedFiles(project.path, task.name, task.committed?.accepted);
       const current = this.store.task(taskId);
-      if (current.status !== 'deleting') this.store.updateTask(taskId, { review: { state: summary.state, round: summary.round, counts: summary.counts, job: current.review?.job, unsent } });
+      if (current.status !== 'deleting') this.store.updateTask(taskId, { review: { state: summary.state, round: summary.round, counts: summary.counts, job: current.review?.job, unsent, comments, files } });
     } catch { /* The task remains visible even if its project is temporarily unavailable. */ }
   }
-  // Review comments Codex has not received yet. A queued or in-flight message
-  // already carries the feedback up to its own cursor.
-  private async unsentComments(client: ReviewClient, task: Task) {
+  // Review decisions, comments and undo updates the agent has not received yet.
+  // The engine excludes decisions undone before delivery. A queued or in-flight message
+  // already carries the feedback up to its own cursor. Comments and notes ask for a revision.
+  private async unsentReviewFeedback(client: ReviewClient, task: Task) {
     const after = Math.max(task.feedbackCursor, ...this.store.runs().filter(r => r.taskId === task.id && ['queued', 'running', 'uncertain'].includes(r.status)).map(r => r.feedbackCursor || 0));
     const feedback = await client.get<{ feedback?: { kind?: string }[] }>(`${taskRoute(task.name)}/feedback?after=${after}`);
-    return (feedback.feedback || []).filter(item => item.kind === 'comment').length;
+    const items = feedback.feedback || [];
+    return { unsent: items.length, comments: items.filter(item => item.kind === 'comment' || item.kind === 'note').length };
+  }
+  // The agent that writes a commit message or resolves a merge: the one the
+  // author chose, or else the first that is signed in, with the chosen model
+  // or the default one.
+  private helper(choice: { agent?: AgentId; model?: string }, task: string) {
+    const usable = (id: AgentId) => this.agents[id].ready && this.runtimes[id].authenticated;
+    const id = choice.agent && usable(choice.agent) ? choice.agent : AGENTS.find(usable);
+    if (!id) throw new Error(`Sign in to Codex, Claude or Antigravity to ${task}.`);
+    const models = this.runtimes[id].models;
+    return { id, model: models.find(item => item.id === choice.model) || models.find(item => item.isDefault) };
+  }
+  // One turn on a thread the agent does not keep, outside any task: its
+  // reply is returned and no chat shows it.
+  private async oneOff(id: AgentId, options: { cwd: string; sandbox: 'read-only' | 'workspace-write'; instructions: string; prompt: string; model?: AgentModel; effort?: string | null; timeout: number; what: string }) {
+    const agent = this.agents[id], name = AGENT_NAMES[id];
+    const thread = await agent.request('thread/start', { cwd: options.cwd, approvalPolicy: 'never', sandbox: options.sandbox, ephemeral: true, developerInstructions: options.instructions, ...(options.model ? { model: options.model.id } : {}) });
+    const threadId = thread.thread.id;
+    return new Promise<string>((resolve, reject) => {
+      let text = '', turnId = '';
+      const listen = (message: any) => {
+        const p = message.params || {};
+        if (p.threadId !== threadId) return;
+        if (message.method === 'item/completed' && p.item?.type === 'agentMessage') text = p.item.text || text;
+        else if (message.method === 'turn/completed') finish(p.turn?.status === 'completed' ? null : new Error(p.turn?.error?.message || `${name} stopped before it could ${options.what}.`));
+      };
+      const timer = setTimeout(() => {
+        if (turnId) agent.request('turn/interrupt', { threadId, turnId }).catch(() => undefined);
+        finish(new Error(`${name} did not ${options.what} in time. Try again.`));
+      }, options.timeout);
+      const finish = (error: Error | null) => { clearTimeout(timer); agent.off('notification', listen); if (error) reject(error); else resolve(text); };
+      agent.on('notification', listen);
+      agent.request('turn/start', { threadId, input: [{ type: 'text', text: options.prompt }], cwd: options.cwd, ...(options.effort ? { effort: options.effort } : {}) })
+        .then(result => { turnId = result?.turn?.id || ''; }, error => finish(error instanceof Error ? error : new Error(String(error))));
+    });
+  }
+  // Writes a commit message for the chosen manuscript files, like Cursor's
+  // generate button: one read-only turn with the lightest reasoning the model offers.
+  async commitMessage(projectId: string, paths: string[], choice: { agent?: AgentId; model?: string } = {}) {
+    const project = this.store.project(projectId), { id, model } = this.helper(choice, 'write a commit message');
+    const { files, patch, recent } = await commitChanges(project.path, paths);
+    const tasks = this.store.tasks().filter(task => task.projectId === projectId && task.review?.files?.some(file => paths.includes(file))).map(task => task.title);
+    const prompt = [
+      recent.length ? `Recent commit subjects in this repository:\n${recent.map(subject => `- ${subject}`).join('\n')}` : 'This repository has no commits yet.',
+      tasks.length ? `Papilot tasks whose accepted changes are in these files:\n${tasks.map(title => `- ${title}`).join('\n')}` : '',
+      `Changed files:\n${files.map(file => `${file.status === '?' ? 'A' : file.status} ${file.from ? `${file.from} -> ` : ''}${file.path}`).join('\n')}`,
+      `Diff:\n${patch}`,
+    ].filter(Boolean).join('\n\n');
+    const reply = await this.oneOff(id, { cwd: project.path, sandbox: 'read-only', instructions: commitInstructions, prompt, model, effort: model?.efforts[0], timeout: 120000, what: 'write a commit message' });
+    const message = commitMessageFrom(reply);
+    if (!message) throw new Error(`${AGENT_NAMES[id]} did not return a commit message. Try again.`);
+    return { message, agent: id };
+  }
+  // Resolves a merge's conflicts in the manuscript checkout itself: the agent
+  // edits only the conflicted files, at the model's default reasoning, and
+  // leaves committing the merge to the author once they have read the diffs.
+  async resolveConflicts(projectId: string, choice: { agent?: AgentId; model?: string } = {}) {
+    const project = this.store.project(projectId), { id, model } = this.helper(choice, 'resolve conflicts');
+    const { files, branch, upstream, ours, theirs } = await mergeConflicts(project.path);
+    if (!files.length) throw new Error('No file has conflict markers left. Commit the merge.');
+    const list = (items: string[]) => items.length ? items.map(item => `- ${item}`).join('\n') : '- (none listed)';
+    const prompt = [
+      `${branch} is being merged with ${upstream} in ${project.path}, and these files have conflicts:\n${list(files)}`,
+      `Commits on ${branch} since the two diverged:\n${list(ours)}`,
+      `Commits from ${upstream} being merged in:\n${list(theirs)}`,
+      'Resolve every conflict in those files, then reply with a short summary for the author: how you resolved each conflict, and any place where you had to choose one side.',
+    ].join('\n\n');
+    const summary = await this.oneOff(id, { cwd: project.path, sandbox: 'workspace-write', instructions: mergeInstructions, prompt, model, effort: model?.defaultEffort, timeout: 600000, what: 'resolve the conflicts' });
+    return { summary: summary.trim(), remaining: files.filter(file => conflictMarkers(project.path, file)), agent: id, git: await gitStatus(project.path) };
+  }
+  // Commits what the author accepted from this task since its last commit,
+  // with the message they confirmed, and pushes it if they asked. Other
+  // uncommitted files stay as they are; a file another task also changed is
+  // committed as it is on disk.
+  async commitTask(taskId: string, message: string, push = false) {
+    const task = this.store.task(taskId);
+    if (task.status === 'deleting') throw new Error('This task is being deleted.');
+    if (task.pendingReview) throw new Error('Wait for the current review action before committing.');
+    const project = this.store.project(task.projectId);
+    return this.exclusiveCommit(project.id, async () => {
+      const accepted = await acceptedCommit(project.path, task.name);
+      const files = accepted ? await acceptedFiles(project.path, task.name, this.store.task(taskId).committed?.accepted) : [];
+      const paths = (await gitStatus(project.path)).files.filter(file => files.includes(file.path)).map(file => file.path);
+      if (!paths.length) throw new Error('This task has no accepted changes left to commit.');
+      const hash = await gitCommit(project.path, message, paths);
+      this.store.updateTask(taskId, { committed: { hash, accepted: accepted!, at: Date.now() } });
+      void this.refresh(taskId);
+      // The commit stands even when the push fails; the author can push again.
+      let pushError: string | undefined;
+      if (push) try { await gitRemote(project.path, 'push'); } catch (error) { pushError = errorText(error); }
+      return { commit: hash, git: await gitStatus(project.path), ...(pushError ? { pushError } : {}) };
+    });
+  }
+  // A commit reads the working tree that accepting, rejecting and undoing
+  // write, so neither starts while the other runs on the same paper.
+  async exclusiveCommit<T>(projectId: string, work: () => Promise<T>): Promise<T> {
+    if (this.committing.has(projectId)) throw new Error('A commit is already in progress. Wait for it to finish.');
+    if ([...this.reviewWrites].some(id => this.store.task(id).projectId === projectId)) throw new Error('Wait for the current review action before committing.');
+    this.committing.add(projectId);
+    try { return await work(); } finally { this.committing.delete(projectId); }
   }
   renameTask(taskId: string, title: string) {
     if (this.store.task(taskId).status === 'deleting') throw new Error('This task is being deleted.');
@@ -528,3 +673,18 @@ ${this.agentOf(task) === 'antigravity' ? 'Shell commands are not available to yo
   }
   close() { this.closing = true; for (const timer of this.usageTimers.values()) clearTimeout(timer); this.flush(); for (const id of AGENTS) this.agents[id].close(); }
 }
+
+// The review engine records each task's accepted text as a commit beside the
+// one it started from; their difference is what the task put in the
+// manuscript, and the difference from the accepted text at the task's last
+// commit is what it has added since. A rename counts as both of its paths.
+export async function acceptedFiles(root: string, name: string, since?: string) {
+  try {
+    const { stdout } = await execute('git', ['-C', root, 'diff', '--name-only', '--no-renames', '-z', since || `refs/latex-review/${name}/base`, `refs/latex-review/${name}/accepted`, '--']);
+    return stdout.split('\0').filter(Boolean);
+  } catch { return []; }
+}
+export async function acceptedCommit(root: string, name: string) {
+  try { return (await execute('git', ['-C', root, 'rev-parse', '--verify', '-q', `refs/latex-review/${name}/accepted^{commit}`])).stdout.trim() || undefined; }
+  catch { return undefined; }
+}

package/src/shared.ts

@@ -1,6 +1,9 @@
 export type TaskStatus = 'idle' | 'queued' | 'running' | 'waiting_input' | 'building' | 'reviewing' | 'interrupted' | 'failed' | 'uncertain' | 'deleting';
 export interface Project { id: string; name: string; path: string; createdAt: number }
-export interface ReviewSummary { state: string; round: number | null; counts: Record<string, number>; unsent?: number; next?: string; job?: { phase: string; status: string; error?: string; details?: string[] } | null }
+// unsent counts review updates the agent has not received; comments are the
+// ones that ask for a revision. files are the manuscript files this task's
+// accepted changes touched since its last commit, relative to the repository root.
+export interface ReviewSummary { state: string; round: number | null; counts: Record<string, number>; unsent?: number; comments?: number; files?: string[]; next?: string; job?: { phase: string; status: string; error?: string; details?: string[] } | null }
 export interface PendingReview { route: string; body: Record<string, unknown>; previousStatus: TaskStatus }
 export interface Task {
   id: string; projectId: string; name: string; title: string; instructions: string;
@@ -9,9 +12,19 @@ export interface Task {
   error: string | null; review: ReviewSummary | null;
   pauseVersion?: number; pendingRunId?: string | null;
   pendingReview?: PendingReview | null;
+  // The task's last commit from its review, and the accepted text it included.
+  committed?: { hash: string; accepted: string; at: number } | null;
 }
 export interface Run { id: string; taskId: string; requestKey: string; prompt: string; feedbackCursor?: number; status: 'queued' | 'running' | 'completed' | 'failed' | 'interrupted' | 'uncertain'; createdAt: number; finishedAt: number | null }
-export interface TimelineItem { id: string; taskId: string; type: string; text: string; detail?: string; status?: string; createdAt: number }
+export interface TimelineItem { id: string; taskId: string; type: string; text: string; detail?: string; status?: string; createdAt: number; meta?: MessageMeta }
+// A user message can run a skill or carry review feedback; the chat shows
+// those as what they are rather than as the prompt the agent receives.
+// Papilot itself sends the agent a build its own edits broke.
+export interface MessageMeta { skill?: { id: string; name: string }; feedback?: FeedbackSummary; sendsFeedback?: boolean; build?: BuildFailure }
+// A failed review build as the engine reports it; log is the compiler log's path.
+export interface BuildFailure { error: string; details: string[]; log?: string }
+export interface FeedbackSummary { round: number | null; accepted: number; rejected: number; undone: number; comments: { where: string; text: string }[]; buildError?: boolean }
+export interface Skill { id: string; name: string; description: string; hint: string; source: 'builtin' | 'user' | 'paper' }
 export interface PendingRequest { id: string; taskId: string; method: string; params: Record<string, any>; createdAt: number }
 export type AgentId = 'codex' | 'claude' | 'antigravity';
 export interface AgentModel { id: string; name: string; isDefault: boolean; efforts: string[]; defaultEffort: string | null }
@@ -21,7 +34,8 @@ export interface Usage { plan: string | null; windows: UsageWindow[]; credits: {
 export interface RuntimeStatus { connected: boolean; authenticated: boolean; account: string | null; error: string | null; models: AgentModel[]; usage?: Usage | null }
 export interface Snapshot { projects: Project[]; tasks: Task[]; requests: PendingRequest[]; runtime: RuntimeStatus; runtimes?: Partial<Record<AgentId, RuntimeStatus>>; version: string }
 export interface GitFile { path: string; status: string; staged: boolean; lines?: [number, number]; from?: string }
-export interface GitStatus { branch: string | null; upstream: string | null; ahead: number; behind: number; files: GitFile[]; head: { hash: string; subject: string; date: number } | null; remote?: boolean }
+// merging is a merge in progress, with the files whose conflict markers remain.
+export interface GitStatus { branch: string | null; upstream: string | null; ahead: number; behind: number; files: GitFile[]; head: { hash: string; subject: string; date: number } | null; remote?: boolean; merging?: { message: string; conflicts: string[] } | null }
 export interface GitDiff { path: string; diff: string; truncated: boolean }
 export interface ManuscriptBuild { status: 'building' | 'ready' | 'failed'; key?: string; pages?: [number, number][]; builtAt?: number; error?: string; current: boolean }
 export interface Annotation { id: string; projectId: string; key: string; page: number; rect: [number, number, number, number]; rects?: [number, number, number, number][]; comment: string; quote: string; source: { file: string; lines: [number, number]; excerpt?: string } | null; createdAt: number; taskId?: string }

package/vendor/latex-review/dist/web/assets/index-Bg-VqnPa.css

@@ -0,0 +1 @@
+@font-face{font-family:Review Serif;src:url(/assets/TeXGyrePagellaX-Regular-DQJjZE_L.otf)format("opentype");font-weight:400;font-display:swap}@font-face{font-family:Review Serif;src:url(/assets/TeXGyrePagellaX-Bold-CEtYdOXj.otf)format("opentype");font-weight:700;font-display:swap}:root{--lightningcss-light:initial;--lightningcss-dark: ;color-scheme:light;--serif:"Review Serif", Palatino, "Palatino Linotype", "Songti SC", Georgia, serif;--sans:-apple-system, BlinkMacSystemFont, "Segoe UI", "PingFang SC", "Noto Sans", sans-serif;--frame:#fff;--bar:#fff;--ink:#171717;--muted:#666;--line:#e5e5e5;--paper:#fff;--accent:#356aa0;--accept:#1d7448;--reject:#b0313b;--comment:#356aa0;--before:#fbeeee;--before-edge:#d17c82;--after:#eef8f1;--after-edge:#68ab82;--head:#fafafa;--shadow:0 1px 2px #0000000f, 0 4px 18px #0000000d;--paper-top:24px;font:14px/1.5 var(--sans);color:var(--ink);background:var(--frame)}*{box-sizing:border-box}body{background:var(--frame);text-rendering:optimizelegibility;grid-template-rows:auto 1fr;height:100dvh;margin:0;display:grid;overflow:hidden}button,input,select,textarea{font:inherit;color:inherit}button{cursor:pointer}button:disabled{cursor:default;opacity:.38}button:focus-visible,a:focus-visible,input:focus-visible,select:focus-visible{outline:2px solid var(--accent);outline-offset:3px}[hidden]{display:none!important}.muted{color:var(--muted)}a{color:var(--accent);text-underline-offset:.18em}h1,h2,.brand{font-family:var(--serif);font-weight:400;line-height:1.3}.brand{letter-spacing:.02em;color:var(--ink);font-size:20px;font-variant-caps:small-caps;text-decoration:none}kbd{border:1px solid var(--line);color:var(--muted);background:var(--frame);vertical-align:1px;border-radius:4px;margin-left:6px;padding:2px 4px;font:600 10px/1 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