skills: github-project-status auto-detect, pr-feedback-review companion auth, new introduce-reuse-compliance

README.md

@@ -7,9 +7,11 @@ software project maintenance, triage, and automation.
 
 | Skill | Description |
 |-------|-------------|
+| [analyze-duplicates](analyze-duplicates/) | Detect code and documentation duplication using jscpd, generate a Markdown report with collapsible `<details>` sections (suitable for GitHub/Gitea issues), and propose a mediation plan with refactoring strategies. |
 | [github-project-status](github-project-status/) | Assess whether a GitHub project is healthy, in maintenance mode, stagnant, or abandoned. Checks commits, releases, issues, PRs, forks, and package registries to produce a structured status report. |
 | [introduce-codespell](introduce-codespell/) | Add [codespell](https://github.com/codespell-project/codespell) spell-checking to a project end-to-end: config, GitHub Actions workflow, pre-commit hook, exclusion tuning, ambiguous-typo review, and automated fixes via `datalad run`. |
 | [introduce-git-bug](introduce-git-bug/) | Set up [git-bug](https://github.com/git-bug/git-bug) distributed issue tracking: configure GitHub bridge, sync issues, push `refs/bugs/*`, and document the workflow in DEVELOPMENT.md / CLAUDE.md. |
+| [introduce-reuse-compliance](introduce-reuse-compliance/) | Introduce [REUSE](https://reuse.software/) licensing compliance to a project: `LICENSES/`, `REUSE.toml`, SPDX headers, and integration with tox / pre-commit / Makefile / GitHub Actions. Handles BIDS dataset data-vs-code separation, [DUO](https://github.com/EBISPOT/DUO) data-use ontology codes, and DEP-3 patch tagging for vendoring repos. |
 | [issue-triage](issue-triage/) | Triage open GitHub issues by cross-referencing the codebase and git history. Detects duplicates, drafts proposed comments, and serves results in a local web dashboard. Includes Python helper scripts for gathering and serving data. |
 | [pr-feedback-review](pr-feedback-review/) | Load a PR's review feedback (human + bot), classify each comment by type and actionability, and recommend what to address vs dismiss — with draft code changes and responses. Works from a local repo or a PR URL. |
 | [pr-review-update](pr-review-update/) | Scan an [improveit-dashboard](https://github.com/yarikoptic/improveit-dashboard) for PRs awaiting your response, assess confidence, auto-rebase codespell PRs, and produce copy-paste-ready push commands. |

analyze-duplicates/SKILL.md

@@ -0,0 +1,216 @@
+---
+name: analyze-duplicates
+description: Analyze codebase or documentation for code/text duplication using jscpd. Generates a Markdown report with collapsible sections (suitable for GitHub/Gitea issues) showing duplicate clusters, statistics, and a mediation plan proposing refactoring strategies.
+allowed-tools: Bash, Read, Write, Glob, Grep, Agent
+user-invocable: true
+---
+
+# Analyze Duplicates
+
+Detect code and documentation duplication in one or more paths, produce a
+Markdown report with `<details>` sections for posting as a GitHub/Gitea issue,
+and propose a concrete mediation plan.
+
+## When to Use
+
+- User wants to find duplicated code or documentation in a project
+- User asks to "check for duplicates", "find copy-paste code", "DRY audit"
+- User mentions "jscpd", "duplicate detection", or "code clones"
+- User runs `/analyze-duplicates`
+
+## Configuration
+
+| Variable | Default | Description |
+|----------|---------|-------------|
+| `MIN_LINES` | `6` | Minimum duplicate block size in lines |
+| `MIN_TOKENS` | `50` | Minimum duplicate block size in tokens |
+| `THRESHOLD` | `5` | Duplication percentage that flags a warning |
+| `FORMATS` | (auto-detect) | Comma-separated jscpd format list (e.g., `python,markdown`) |
+
+## Arguments
+
+The skill accepts one or more paths to scan. If none are provided, scan the
+current working directory.
+
+Optional flags (passed as part of the argument string):
+- `--formats python,markdown` — override auto-detected formats
+- `--min-lines N` — override MIN_LINES
+- `--min-tokens N` — override MIN_TOKENS
+- `--threshold N` — override warning threshold percentage
+- `--output PATH` — where to write the report (default: `.jscpd-report.md` in first scanned path)
+- `--cross-project` — when multiple paths given, also run a combined scan to find cross-project duplicates
+- `--no-html` — skip generating the HTML report (default: generate it)
+- `--badge` — also generate an SVG badge and embed it in the report (default: off)
+
+## Execution Steps
+
+### Step 0: Parse Arguments
+
+Parse the argument string. Extract paths (any arg not starting with `--`),
+and optional flags. Apply defaults from Configuration for anything not specified.
+
+If no paths provided, use the current working directory.
+
+Create the `.tmp/` directory in the current working directory for intermediate
+output. If `.tmp` is not already in `.gitignore`, add it (or warn the user).
+
+### Step 1: Ensure jscpd is Available
+
+Check if jscpd is available:
+
+```bash
+command -v jscpd || npx --yes jscpd@latest --version
+```
+
+If neither works, report the error and stop:
+> jscpd not found. Install via `npm install -g jscpd` or ensure `npx` is available.
+
+### Step 2: Detect Project Context
+
+For each scan path:
+1. Check if it is a git repository (`git -C PATH rev-parse --is-inside-work-tree`)
+2. Detect primary languages by file extension counts (`.py` -> python, `.js/.ts` -> javascript/typescript, `.md` -> markdown, etc.)
+3. If `--formats` was specified, use that instead of auto-detection
+4. Note the project name from the directory basename (or git remote if available)
+
+### Step 3: Run jscpd
+
+For each scan path, run jscpd with JSON, HTML, and badge reporters:
+
+```bash
+npx --yes jscpd@latest \
+    --min-lines MIN_LINES \
+    --min-tokens MIN_TOKENS \
+    --reporters "json,html" \
+    --output .tmp/jscpd-PROJECTNAME \
+    --ignore "IGNORE_PATTERNS" \
+    PATH
+```
+
+If `--no-html` is set, omit `html` from reporters. If `--badge` is set, add `badge` to reporters.
+If `--formats` is set, add `--format FORMATS`.
+
+**Building the ignore list** — start with these safe defaults:
+`**/.tox/**,**/venv*/**,**/.venv/**,**/node_modules/**,**/__pycache__/**,**/.eggs/**,**/.git/**,**/.npm/**,**/.tmp/**`
+
+Then for each of `build/`, `dist/`, `.eggs/`:
+- Check if the directory is **tracked by git** (`git ls-files --error-unmatch DIR/ 2>/dev/null`)
+- If tracked: do NOT ignore it (it's intentionally committed content)
+- If untracked: add it to the ignore list
+
+Additionally, find all **symlinks** in the scan path (`find PATH -type l`) and
+add ignore patterns for them (e.g., `**/symlinked-dir/**`). Symlinked content
+is intentionally shared — duplicates from symlinks are noise, not bugs.
+
+This produces:
+- `.tmp/jscpd-PROJECTNAME/jscpd-report.json` — structured data for the markdown report
+- `.tmp/jscpd-PROJECTNAME/html/index.html` — interactive HTML report with syntax highlighting
+- `.tmp/jscpd-PROJECTNAME/jscpd-badge.svg` — shields.io-style badge showing duplication % (only with `--badge`)
+
+If `--cross-project` and multiple paths: after individual scans, create a
+temporary parent directory with symlinks to all paths and run one combined scan.
+
+### Step 4: Parse Results and Generate Report
+
+Read each `.tmp/jscpd-PROJECTNAME/jscpd-report.json` and generate the report
+using the helper script:
+
+```bash
+python3 SKILL_DIR/generate-report.py \
+    --threshold THRESHOLD \
+    --output REPORT_PATH \
+    --jscpd-version "$(npx --yes jscpd@latest --version 2>/dev/null)" \
+    --scan-path PATH \
+    [--cross-project .tmp/jscpd-combined/jscpd-report.json] \
+    .tmp/jscpd-PROJECT1/jscpd-report.json \
+    [.tmp/jscpd-PROJECT2/jscpd-report.json ...]
+```
+
+Where `SKILL_DIR` is the directory containing this SKILL.md file. Resolve it
+by searching for `generate-report.py` in `~/.claude/skills/analyze-duplicates/`.
+
+If `--badge` was requested and a badge was generated, pass `--badge-path` with
+a relative path to the SVG. Copy the badge SVG to the output directory so both
+files are co-located.
+
+### Step 5: Review and Enhance Mediation Plan
+
+The `generate-report.py` script already produces a `## Mediation Plan` section
+with heuristic classifications (trivial/easy/moderate/hard) and strategies
+for each cluster. After the report is generated:
+
+1. Read the generated report and the duplicated fragments
+2. For each cluster, **verify** the heuristic recommendation makes sense in
+   context — read the actual source files around the duplicated lines if needed
+3. For **easy/trivial** clusters: add a concrete diff or pseudo-diff showing
+   the proposed refactoring (extract function, parametrize test, etc.)
+4. For **moderate/hard** clusters: enhance the description with specifics
+   about what the shared abstraction should look like
+5. Adjust difficulty ratings if the heuristic got it wrong (e.g., what looks
+   like a simple extract may actually involve different signatures)
+
+### Step 6: Present Results
+
+1. Print a brief summary to the console:
+   - Total duplication percentage per project
+   - Number of clone clusters found
+   - Whether threshold was exceeded
+2. Print paths to all generated artifacts:
+   - Markdown report (the primary deliverable, suitable for GitHub issues)
+   - HTML report directory (interactive browser view with syntax highlighting)
+   - Badge SVG path (only if `--badge` was used)
+3. If duplication exceeds the threshold, note this prominently
+
+## Report Format
+
+The report MUST be a Markdown file using `<details><summary>` blocks so it
+renders well when posted as a GitHub/Gitea issue. Structure:
+
+```markdown
+# Duplication Analysis Report
+
+> Generated: YYYY-MM-DD | Tool: jscpd VERSION | Threshold: N%
+
+## Summary
+
+| Project    | Files | Lines | Clones | Duplicated Lines | Percentage |
+|------------|------:|------:|-------:|-----------------:|-----------:|
+| my-project |    42 | 12000 |      5 |               83 |      0.69% |
+
+> Duplication is within the 5% threshold for all projects.
+
+## Duplicate Clusters
+
+| C | Lines | Difficulty | Strategy                      | Files   |
+|---|-------|------------|-------------------------------|---------|
+| 1 | 8     | Trivial    | Extract local helper function | file.py |
+
+<details>
+<summary><b>Cluster 1</b>: [Trivial] `file.py` lines 10-18
+&harr; `file.py` lines 30-38 (8 lines)</summary>
+
+**Files involved:**
+- [`file.py` (lines 10-18)](https://github.com/owner/repo/blob/main/file.py#L10-L18)
+- [`file.py` (lines 30-38)](https://github.com/owner/repo/blob/main/file.py#L30-L38)
+
+**Duplicated fragment:**
+~~~python
+<the duplicated code here>
+~~~
+
+**Mediation** (Trivial): Extract local helper function
+
+> Duplicated logic within `file.py`. Extract into a private function
+> in the same module.
+
+</details>
+```
+
+## Commit Co-Authorship
+
+All commits created during this workflow MUST include a `Co-Authored-By` trailer.
+Get the version via `claude --version`. Format:
+
+```
+Co-Authored-By: Claude Code <VERSION> / Claude <MODEL> <noreply@anthropic.com>
+```