first commit

文档润色流和知识库构建流/claude-scholar/.github/ISSUE_TEMPLATE/bug_report.yml

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+name: Bug report
+description: Report an installation, runtime, compatibility, or behavior bug in Claude Scholar.
+title: "[Bug]: "
+labels:
+  - bug
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Thanks for reporting a bug.
+
+        Please keep this report concrete. The fastest bug reports for Claude Scholar include:
+        - the client and branch,
+        - the exact command or prompt,
+        - the full warning or traceback,
+        - and a short reproduction path.
+
+  - type: checkboxes
+    id: preflight
+    attributes:
+      label: Before submitting
+      options:
+        - label: I checked the README / setup docs for the branch I am using.
+          required: true
+        - label: I included the exact error text instead of paraphrasing it.
+          required: true
+
+  - type: dropdown
+    id: client
+    attributes:
+      label: Client
+      options:
+        - Claude Code
+        - Codex
+        - OpenCode
+        - Other / unsure
+    validations:
+      required: true
+
+  - type: dropdown
+    id: branch
+    attributes:
+      label: Branch
+      options:
+        - main
+        - codex
+        - opencode
+        - unsure
+    validations:
+      required: true
+
+  - type: textarea
+    id: environment
+    attributes:
+      label: Environment
+      description: Include only the details that matter for reproducing the issue.
+      placeholder: |
+        OS: macOS 15.4
+        Shell: zsh
+        Install mode: scripts/setup.sh
+        Client version: Claude Code 2.1.42
+    validations:
+      required: true
+
+  - type: textarea
+    id: exact_action
+    attributes:
+      label: Exact command or exact prompt
+      placeholder: |
+        bash scripts/setup.sh
+
+        or
+
+        Review my Zotero collection on brain foundation models.
+    validations:
+      required: true
+
+  - type: textarea
+    id: actual_behavior
+    attributes:
+      label: Actual behavior
+      description: Describe what happened, then paste the full error or terminal output below.
+    validations:
+      required: true
+
+  - type: textarea
+    id: error_output
+    attributes:
+      label: Full error / terminal output
+      render: shell
+    validations:
+      required: true
+
+  - type: textarea
+    id: reproduction_steps
+    attributes:
+      label: Reproduction steps
+      placeholder: |
+        1. Clone branch ...
+        2. Run ...
+        3. Start client ...
+        4. Observe ...
+    validations:
+      required: true

文档润色流和知识库构建流/claude-scholar/.github/ISSUE_TEMPLATE/config.yml

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+blank_issues_enabled: false
+contact_links:
+  - name: Claude Scholar setup docs
+    url: https://github.com/Galaxy-Dawn/claude-scholar#quick-start
+    about: Please check the Quick Start section before opening an installation issue.
+  - name: Claude Scholar branch guide
+    url: https://github.com/Galaxy-Dawn/claude-scholar#why-claude-scholar
+    about: Confirm that you are using the correct branch for Claude Code, Codex, or OpenCode.

文档润色流和知识库构建流/claude-scholar/.github/ISSUE_TEMPLATE/docs_problem.yml

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+name: Documentation problem
+description: Report outdated, inconsistent, unclear, or incorrect documentation.
+title: "[Docs]: "
+labels:
+  - documentation
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Use this template for documentation issues such as:
+        - wrong commands or paths,
+        - branch-specific instructions that drifted,
+        - unclear wording,
+        - or setup docs that no longer match actual behavior.
+
+  - type: dropdown
+    id: doc_surface
+    attributes:
+      label: Affected document
+      options:
+        - README
+        - MCP_SETUP
+        - OBSIDIAN_SETUP
+        - CLAUDE / AGENTS docs
+        - Skill documentation
+        - Installer instructions
+        - Other
+    validations:
+      required: true
+
+  - type: dropdown
+    id: branch
+    attributes:
+      label: Affected branch
+      options:
+        - main
+        - codex
+        - opencode
+        - multiple branches
+        - unsure
+    validations:
+      required: true
+
+  - type: textarea
+    id: location
+    attributes:
+      label: Problematic location
+      description: Quote the current text, command, path, or section title.
+    validations:
+      required: true
+
+  - type: textarea
+    id: issue
+    attributes:
+      label: What is wrong
+    validations:
+      required: true
+
+  - type: textarea
+    id: suggested_fix
+    attributes:
+      label: Suggested fix
+      description: If you already know the corrected wording or command, propose it here.
+    validations:
+      required: false

文档润色流和知识库构建流/claude-scholar/.github/ISSUE_TEMPLATE/workflow_gap.yml

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+name: Workflow gap
+description: Report a missing, weak, or awkward handoff in a research workflow, even if nothing is technically broken.
+title: "[Workflow gap]: "
+labels:
+  - workflow
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Use this template when Claude Scholar technically works, but the workflow is still incomplete.
+
+        Examples:
+        - the workflow stops too early,
+        - a handoff between stages is weak,
+        - the current output is not enough for real research use,
+        - or an expected research step is missing.
+
+  - type: dropdown
+    id: stage
+    attributes:
+      label: Workflow stage
+      options:
+        - Ideation
+        - Literature review
+        - Zotero / paper intake
+        - Obsidian / project memory
+        - Experiment tracking
+        - Results analysis
+        - Publication artifacts (figures / tables)
+        - Results reporting
+        - Paper writing
+        - Rebuttal / review response
+        - Post-acceptance
+        - Cross-stage handoff
+    validations:
+      required: true
+
+  - type: textarea
+    id: gap
+    attributes:
+      label: Current gap
+      description: What is missing, awkward, or incomplete in the current workflow?
+    validations:
+      required: true
+
+  - type: textarea
+    id: desired_outcome
+    attributes:
+      label: Desired outcome
+      description: What should Claude Scholar help you produce, decide, or hand off here?
+    validations:
+      required: true
+
+  - type: textarea
+    id: example
+    attributes:
+      label: Concrete example
+      description: Provide a representative prompt, artifact path, or research situation.
+    validations:
+      required: true

文档润色流和知识库构建流/claude-scholar/.github/PULL_REQUEST_TEMPLATE.md

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+## Summary
+- What changed?
+- Why did it change?
+
+## Affected surfaces
+- [ ] main
+- [ ] codex
+- [ ] opencode
+- [ ] README / docs
+- [ ] installer
+- [ ] skills
+- [ ] agents
+- [ ] hooks
+- [ ] MCP / Obsidian docs
+
+## Validation
+- [ ] Relevant docs were updated if behavior changed
+- [ ] No machine-specific private paths were introduced
+- [ ] No branch-specific path or config leaked into the wrong branch
+- [ ] Basic validation or smoke test was run
+
+## Behavior change note
+If this PR changes user-facing behavior, briefly describe:
+- previous behavior
+- new behavior
+- any migration or manual merge note
+
+## Evidence
+Include screenshots, terminal output, example artifacts, or acceptance notes when useful.

文档润色流和知识库构建流/claude-scholar/.github/workflows/installer_smoke.yml

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+name: installer-smoke
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+      - codex
+      - opencode
+
+jobs:
+  installer-smoke:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Verify installer entrypoints exist
+        run: |
+          set -euo pipefail
+          test -f scripts/setup.sh
+          test -f scripts/uninstall.sh
+          test -f scripts/test_install_uninstall.sh
+          test -f README.md
+          test -f README.zh-CN.md
+          test -f README.ja-JP.md
+
+      - name: Syntax check installer scripts
+        run: bash -n scripts/setup.sh
+
+      - name: Run install/uninstall smoke tests
+        run: bash scripts/test_install_uninstall.sh
+
+      - name: Verify branch-specific top-level docs exist
+        run: |
+          set -euo pipefail
+          if [ -f CLAUDE.md ]; then
+            test -f CLAUDE.zh-CN.md
+            test -f CLAUDE.ja-JP.md
+          fi
+          if [ -f AGENTS.md ]; then
+            test -f AGENTS.md
+          fi
+          test -f MCP_SETUP.md
+          test -f MCP_SETUP.zh-CN.md
+          test -f MCP_SETUP.ja-JP.md
+          test -f OBSIDIAN_SETUP.md
+          test -f OBSIDIAN_SETUP.zh-CN.md
+          test -f OBSIDIAN_SETUP.ja-JP.md
+
+      - name: Verify key skills still exist
+        run: |
+          set -euo pipefail
+          test -f skills/research-ideation/SKILL.md
+          test -f skills/results-analysis/SKILL.md
+          test -f skills/results-report/SKILL.md
+          test -f skills/ml-paper-writing/SKILL.md
+          test -f skills/publication-chart-skill/SKILL.md

文档润色流和知识库构建流/claude-scholar/.github/workflows/repo_sanity.yml

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+name: repo-sanity
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+      - codex
+      - opencode
+
+jobs:
+  repo-sanity:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Check tracked top-level docs for obvious machine-specific paths
+        run: |
+          set -euo pipefail
+          python3 - <<'PY'
+          import re
+          import subprocess
+          import sys
+          from pathlib import Path
+
+          tracked = subprocess.check_output(['git', 'ls-files'], text=True).splitlines()
+          allowed = {
+              'README.md', 'README.zh-CN.md', 'README.ja-JP.md',
+              'CLAUDE.md', 'CLAUDE.zh-CN.md', 'CLAUDE.ja-JP.md',
+              'AGENTS.md',
+              'MCP_SETUP.md', 'MCP_SETUP.zh-CN.md', 'MCP_SETUP.ja-JP.md',
+              'OBSIDIAN_SETUP.md', 'OBSIDIAN_SETUP.zh-CN.md', 'OBSIDIAN_SETUP.ja-JP.md',
+              'settings.json.template',
+              '.github/PULL_REQUEST_TEMPLATE.md',
+              '.github/ISSUE_TEMPLATE/bug_report.yml',
+              '.github/ISSUE_TEMPLATE/workflow_gap.yml',
+              '.github/ISSUE_TEMPLATE/docs_problem.yml',
+              '.github/ISSUE_TEMPLATE/config.yml',
+          }
+          pattern = re.compile(r'/Users/[A-Za-z0-9_.-]+|/home/[A-Za-z0-9_.-]+|[A-Za-z]:\\Users\\[A-Za-z0-9_. -]+')
+          bad = []
+          for rel in tracked:
+              if rel not in allowed:
+                  continue
+              try:
+                  text = Path(rel).read_text(encoding='utf-8')
+              except Exception:
+                  continue
+              if pattern.search(text):
+                  bad.append(rel)
+          if bad:
+              print('Found machine-specific paths in:')
+              for rel in bad:
+                  print(rel)
+              sys.exit(1)
+          PY
+
+      - name: Check tracked junk files
+        run: |
+          set -euo pipefail
+          if git ls-files | rg '(^|/)(\.DS_Store|Thumbs\.db|desktop\.ini)$'; then
+            echo "Tracked junk files detected."
+            exit 1
+          fi