Merge develop into main

.claude-plugin/plugin.json

@@ -0,0 +1,10 @@
+{
+  "name": "deeppapernote",
+  "description": "Academic paper reading and Obsidian note generation skills for building a research WIKI.",
+  "version": "0.1.0",
+  "author": {
+    "name": "917Dhj"
+  },
+  "repository": "https://github.com/917Dhj/DeepPaperNote",
+  "license": "MIT"
+}

.codex-plugin/plugin.json

@@ -0,0 +1,38 @@
+{
+  "name": "deeppapernote",
+  "version": "0.1.0",
+  "description": "Academic paper reading and Obsidian note generation skills for building a research WIKI.",
+  "author": {
+    "name": "917Dhj",
+    "url": "https://github.com/917Dhj"
+  },
+  "homepage": "https://github.com/917Dhj/DeepPaperNote",
+  "repository": "https://github.com/917Dhj/DeepPaperNote",
+  "license": "MIT",
+  "keywords": [
+    "academic-research",
+    "obsidian",
+    "paper-reading",
+    "research-paper",
+    "deep-reading"
+  ],
+  "skills": "./skills/",
+  "interface": {
+    "displayName": "DeepPaperNote",
+    "shortDescription": "Generate deep-reading notes for research papers.",
+    "longDescription": "Turn one paper at a time into an evidence-first, Obsidian-oriented deep-reading note with metadata, figures, tables, formulas, limitations, and final quality checks.",
+    "developerName": "917Dhj",
+    "category": "Productivity",
+    "capabilities": [
+      "Interactive",
+      "Write"
+    ],
+    "websiteURL": "https://github.com/917Dhj/DeepPaperNote",
+    "defaultPrompt": [
+      "Generate a deep-reading note for this paper.",
+      "Turn this DOI or arXiv paper into an Obsidian note.",
+      "Read this local PDF and write a research note."
+    ],
+    "brandColor": "#7C3AED"
+  }
+}

.github/workflows/ci.yml

@@ -10,7 +10,15 @@ permissions:
 
 jobs:
   test:
-    runs-on: macos-latest
+    name: Tests (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    env:
+      PYTHONUTF8: "1"
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-latest, windows-latest]
 
     steps:
       - name: Checkout repository
@@ -30,7 +38,7 @@ jobs:
 
       - name: Run syntax check
         run: |
-          python -m py_compile scripts/*.py
+          python -m compileall -q skills/deeppapernote/scripts
 
       - name: Run tests
         run: |

.gitignore

@@ -13,8 +13,11 @@ htmlcov/
 venv/
 dist/
 build/
+site/
 *.egg-info/
 .agent-work/
 tmp/
 DESIGN.md
+CONTEXT.md
 .claude/
+docs/

AGENTS.md

@@ -4,7 +4,7 @@
 
 DeepPaperNote is:
 
-- a single-skill repository
+- a dual-stack Claude Code and Codex plugin repository
 - designed for deep reading of one paper at a time
 - intended to support both Claude Code and Codex
 - focused on producing a high-quality Obsidian-oriented paper note
@@ -18,10 +18,11 @@ DeepPaperNote is not:
 
 Use the following source-of-truth hierarchy when working in this repository:
 
-- root `SKILL.md` is the canonical workflow definition
-- `scripts/` and `references/` are part of the reusable core
+- `skills/deeppapernote/SKILL.md` is the canonical workflow definition
+- `skills/deeppapernote/scripts/` and `skills/deeppapernote/references/` are part of the reusable core
 - `README.md` and `README.zh-CN.md` are user-facing documentation, not the canonical workflow
-- `agents/openai.yaml` is the Codex adapter layer; the root `SKILL.md` is the Claude Code skill entrypoint
+- `skills/deeppapernote/agents/openai.yaml` is the Codex adapter layer
+- `.claude-plugin/plugin.json` and `.codex-plugin/plugin.json` are host manifests and should stay thin
 
 Adapter layers should stay thin and should not redefine the workflow independently.
 
@@ -43,17 +44,19 @@ Future changes should preserve these product invariants:
 
 The repository is layered as follows:
 
-- `SKILL.md` is the canonical workflow definition and the skill entrypoint for both Claude Code and other agents
+- `skills/deeppapernote/SKILL.md` is the canonical workflow definition and the skill entrypoint for both Claude Code and other agents
 - `CLAUDE.md` provides Claude Code project-level guidance and includes `AGENTS.md` via `@AGENTS.md`
-- `references/` stores durable workflow and writing guidance
-- `scripts/` implements the deterministic pipeline and support utilities
-- `agents/openai.yaml` is the Codex adapter
+- `.claude-plugin/plugin.json` identifies the Claude Code plugin
+- `.codex-plugin/plugin.json` identifies the Codex plugin
+- `skills/deeppapernote/references/` stores durable workflow and writing guidance
+- `skills/deeppapernote/scripts/` implements the deterministic pipeline and support utilities
+- `skills/deeppapernote/agents/openai.yaml` is the Codex adapter
 - `README.md` and `README.zh-CN.md` are user-facing documentation
 
 ## Environment and Onboarding Boundary
 
 - user installation, configuration, and onboarding belong primarily in `README.md` and `README.zh-CN.md`
-- `scripts/check_environment.py` is a maintenance and troubleshooting utility
+- `skills/deeppapernote/scripts/check_environment.py` is a maintenance and troubleshooting utility
 - DeepPaperNote should not reintroduce a separate public `doctor`, `setup`, or `start` skill surface
 
 ## Working Commands
@@ -63,14 +66,14 @@ Common commands for local validation and maintenance:
 - install the core runtime dependency with `python3 -m pip install PyMuPDF`
 - install the local development environment with `python3 -m pip install -e '.[dev]'`
 - run the test suite with `python3 -m pytest -q`
-- when checking environment-related problems, use `python3 scripts/check_environment.py`
+- when checking environment-related problems, use `python3 skills/deeppapernote/scripts/check_environment.py`
 
 ## Verification Expectations
 
 When making meaningful changes:
 
 - run `python3 -m pytest -q`
-- confirm adapters remain aligned with the root `SKILL.md`
+- confirm adapters remain aligned with `skills/deeppapernote/SKILL.md`
 - confirm no wrapper introduces a second conflicting workflow
 - confirm legacy public pseudo-commands are not reintroduced
 - if packaging files are touched, keep them syntactically valid

CHANGELOG.md

@@ -12,7 +12,20 @@ Add an entry here when the project meaningfully changes for users, for example:
 
 ## Unreleased
 
-No unreleased user-facing changes yet.
+### Changed
+
+- Converted the repository to a dual-stack Claude Code and Codex plugin layout with the canonical skill under `skills/deeppapernote/`.
+- Updated the recommended install command to select the `deeppapernote` skill from the plugin repository.
+
+### Fixed
+
+- Fixed Windows-style Obsidian subdirectories so `Research/Papers` is not duplicated in saved note paths.
+- Cross-platform (Windows) path and encoding robustness: read files with `utf-8-sig` so a UTF-8 BOM (as written by PowerShell/Notepad) no longer crashes JSON loading or corrupts saved notes; tolerate CRLF line endings in note linting; and compare/emit paths without assuming `/` so the vault folder and Markdown image links resolve correctly on Windows. No behavior change on Linux/macOS.
+
+### Contributors
+
+- Incorporated the Windows Obsidian path normalization fix from PR #4 by KumamuKuma.
+- Incorporated the Windows path/encoding robustness fix from PR #5 by jiang4wqy.
 
 ## v2.0.0
 

CLAUDE.md

@@ -2,11 +2,11 @@
 
 ## Claude Code Integration
 
-The root `SKILL.md` is both the canonical workflow definition and the Claude Code skill entrypoint.
-There is no separate Claude Code wrapper — `SKILL.md` is loaded directly when the skill is invoked.
+`skills/deeppapernote/SKILL.md` is both the canonical workflow definition and the Claude Code skill entrypoint.
+`.claude-plugin/plugin.json` identifies the plugin, but it must not restate the workflow.
 
 - Do not fork or restate the DeepPaperNote workflow in any Claude-only file.
-- All workflow logic stays in the root `SKILL.md`.
+- All workflow logic stays in `skills/deeppapernote/SKILL.md`.
 
 ### Skill Invocation