Fix operator session recovery: timeout, attempt persistence, interrupt logging

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,123 @@
+name: Bug Report
+description: Report a workflow, validation, operator, or terminal UI bug in AutoR.
+title: "[Bug] "
+labels:
+  - bug
+  - needs-triage
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for filing a bug report. Please keep it concrete and reproducible.
+
+        If possible, include:
+        - the exact command you ran
+        - whether this was `--fake-operator` or a real Claude run
+        - the run id and any relevant files under `runs/<run_id>/`
+
+  - type: dropdown
+    id: area
+    attributes:
+      label: Area
+      description: Which part of AutoR looks broken?
+      multiple: true
+      options:
+        - workflow / manager
+        - operator / Claude CLI integration
+        - validation / artifact gating
+        - terminal UI
+        - writing / venue packaging
+        - documentation
+    validations:
+      required: true
+
+  - type: dropdown
+    id: stage
+    attributes:
+      label: Relevant Stage
+      description: Pick the most relevant stage if this is stage-specific.
+      options:
+        - not stage-specific
+        - 01_literature_survey
+        - 02_hypothesis_generation
+        - 03_study_design
+        - 04_implementation
+        - 05_experimentation
+        - 06_analysis
+        - 07_writing
+        - 08_dissemination
+    validations:
+      required: true
+
+  - type: input
+    id: command
+    attributes:
+      label: Command
+      description: The exact command you ran.
+      placeholder: python main.py --goal "..."
+    validations:
+      required: true
+
+  - type: input
+    id: environment
+    attributes:
+      label: Environment
+      description: OS, Python version, model, and venue if relevant.
+      placeholder: Ubuntu 24.04, Python 3.11, sonnet, neurips_2025
+    validations:
+      required: true
+
+  - type: input
+    id: run_id
+    attributes:
+      label: Run ID
+      description: Optional, but very helpful for debugging.
+      placeholder: 20260402_101222
+
+  - type: textarea
+    id: reproduce
+    attributes:
+      label: Steps To Reproduce
+      description: List the smallest sequence that reproduces the problem.
+      placeholder: |
+        1. Run ...
+        2. Approve stage ...
+        3. Observe ...
+    validations:
+      required: true
+
+  - type: textarea
+    id: expected
+    attributes:
+      label: Expected Behavior
+    validations:
+      required: true
+
+  - type: textarea
+    id: actual
+    attributes:
+      label: Actual Behavior
+    validations:
+      required: true
+
+  - type: textarea
+    id: logs
+    attributes:
+      label: Relevant Logs Or File Paths
+      description: Paste a short excerpt or point to files under the run directory.
+      render: shell
+      placeholder: |
+        runs/<run_id>/logs.txt
+        runs/<run_id>/logs_raw.jsonl
+        runs/<run_id>/stages/07_writing.tmp.md
+
+  - type: checkboxes
+    id: checks
+    attributes:
+      label: Checklist
+      options:
+        - label: I searched existing issues first.
+          required: true
+        - label: I included the exact command and enough detail to reproduce the bug.
+          required: true
+

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,6 @@
+blank_issues_enabled: false
+contact_links:
+  - name: README and Quick Start
+    url: https://github.com/AutoX-AI-Labs/AutoR#quick-start
+    about: Check the README first for setup, workflow, and example-run details.
+

.github/ISSUE_TEMPLATE/docs_issue.yml

@@ -0,0 +1,52 @@
+name: Documentation Issue
+description: Report missing, unclear, outdated, or misleading docs.
+title: "[Docs] "
+labels:
+  - documentation
+  - needs-triage
+body:
+  - type: dropdown
+    id: doc_area
+    attributes:
+      label: Documentation Area
+      options:
+        - README
+        - quick start / setup
+        - example run / artifacts
+        - CLI usage
+        - writing / venue behavior
+        - contribution workflow
+        - other
+    validations:
+      required: true
+
+  - type: input
+    id: location
+    attributes:
+      label: Page Or File
+      description: Which doc page, section, or file is affected?
+      placeholder: README.md#quick-start
+    validations:
+      required: true
+
+  - type: textarea
+    id: issue
+    attributes:
+      label: What Is Wrong Or Missing
+    validations:
+      required: true
+
+  - type: textarea
+    id: suggestion
+    attributes:
+      label: Suggested Fix
+      description: If you already know the better wording or structure, put it here.
+
+  - type: checkboxes
+    id: checks
+    attributes:
+      label: Checklist
+      options:
+        - label: I checked the latest README and existing issues first.
+          required: true
+

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,79 @@
+name: Feature Request
+description: Suggest a focused improvement that fits AutoR's research workflow scope.
+title: "[Feature] "
+labels:
+  - enhancement
+  - needs-triage
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Please keep requests aligned with AutoR's current product shape:
+        terminal-first, file-based, human-in-the-loop, and oriented around real research artifacts.
+
+  - type: dropdown
+    id: area
+    attributes:
+      label: Area
+      multiple: true
+      options:
+        - workflow / manager
+        - operator / Claude CLI integration
+        - validation / artifact gating
+        - terminal UI
+        - writing / venue packaging
+        - developer experience / testing
+        - documentation
+    validations:
+      required: true
+
+  - type: textarea
+    id: problem
+    attributes:
+      label: Problem Statement
+      description: What concrete limitation are you hitting today?
+    validations:
+      required: true
+
+  - type: textarea
+    id: proposal
+    attributes:
+      label: Proposed Change
+      description: Describe the smallest useful version of the change.
+    validations:
+      required: true
+
+  - type: textarea
+    id: fit
+    attributes:
+      label: Why This Fits AutoR
+      description: Explain why this improves the current workflow instead of turning AutoR into a generic platform.
+    validations:
+      required: true
+
+  - type: textarea
+    id: artifacts
+    attributes:
+      label: Expected User-Or Artifact-Level Outcome
+      description: What should be materially better after this is implemented?
+      placeholder: |
+        - clearer stage approval loop
+        - stronger stage 07 validation
+        - less stale artifact leakage on redo-stage
+
+  - type: textarea
+    id: alternatives
+    attributes:
+      label: Alternatives Considered
+      description: Optional, but useful if you evaluated other approaches.
+
+  - type: checkboxes
+    id: checks
+    attributes:
+      label: Checklist
+      options:
+        - label: I searched existing issues first.
+          required: true
+        - label: This request is scoped as a concrete improvement, not a vague wishlist item.
+          required: true
+

.github/ISSUE_TEMPLATE/question.yml

@@ -0,0 +1,52 @@
+name: Usage Question
+description: Ask a concrete setup, workflow, or behavior question about using AutoR.
+title: "[Question] "
+labels:
+  - question
+  - needs-triage
+body:
+  - type: markdown
+    attributes:
+      value: |
+        For faster answers, please keep the question concrete and include the command or run state you are asking about.
+
+  - type: dropdown
+    id: topic
+    attributes:
+      label: Topic
+      options:
+        - setup / installation
+        - CLI usage
+        - resume / redo-stage behavior
+        - stage outputs / artifacts
+        - writing / venue packaging
+        - terminal UI
+        - other
+    validations:
+      required: true
+
+  - type: input
+    id: command
+    attributes:
+      label: Command Or Action
+      description: Optional, but helpful if your question is about a specific run.
+      placeholder: python main.py --resume-run latest --redo-stage 03
+
+  - type: textarea
+    id: question
+    attributes:
+      label: Question
+    validations:
+      required: true
+
+  - type: textarea
+    id: context
+    attributes:
+      label: Relevant Context
+      description: Add any details that would help someone answer correctly.
+      placeholder: |
+        - fake operator or real Claude run
+        - run id
+        - stage number
+        - what you already tried
+

.github/labels.yml

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+- name: needs-triage
+  color: d4c5f9
+  description: New issue that still needs maintainer triage.
+- name: area:workflow
+  color: 0e8a16
+  description: ResearchManager flow, stage loop, approval, resume, or redo-stage behavior.
+- name: area:operator
+  color: 1d76db
+  description: Claude CLI execution, sessions, prompt cache, streaming, or repair flow.
+- name: area:validation
+  color: b60205
+  description: Stage summary validation, artifact gating, freshness checks, or file contracts.
+- name: area:terminal-ui
+  color: fbca04
+  description: Terminal rendering, menus, banners, stream formatting, or TTY fallback behavior.
+- name: area:writing
+  color: 5319e7
+  description: Stage 07 writing flow, venue packaging, LaTeX, PDF, or review artifacts.

.github/workflows/ci.yml

@@ -0,0 +1,28 @@
+name: tests
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Compile Python sources
+        run: python -m py_compile main.py src/*.py tests/*.py
+
+      - name: Run unit tests
+        run: python -m unittest discover -s tests -p "test_*.py" -v

.gitignore

@@ -3,3 +3,6 @@ __pycache__/
 runs/
 .tmp/
 AGENTS.md
+.codex
+docs/
+examples/