5 added, 4 removed. Audit A to A.
# sci-paper plugin — project working directory instructions
## What this project is
A standalone Claude Code plugin for scientific paper writing, rewriting,
review, figure review, adversarial critique, narrative analysis, and research
ideation. `docs/SCIPAPER_STANDARD.md` is the single normative writing standard.
Corpus profiles, structural measurements, UID evidence, and learned
field-similarity models are descriptive or calibrational evidence; they do not
create an authorship verdict or a separate paper gate.
## Working principles for THIS project
1. **One normative contract.** Writing and review skills must implement
`docs/SCIPAPER_STANDARD.md` and `sci-paper.feedback.v1`. Do not introduce a
competing consequence vocabulary, universal prose PASS/FAIL gate, or
authorship claim. Field-specific scientific guidance may remain explicitly
marked `[WGL]`; do not silently generalize domain facts while changing the
shared writing contract.
2. **Corpus evidence is read-only input.** The corpus is user-supplied and
copyright-sensitive; never commit PDFs from `style-corpus/` (`.gitignore`
excludes them). Treat `style-corpus/<field>/tier-*` as read-only inputs;
generated evidence belongs under `style-profile/<field>/`. Corpus statistics
cannot redefine consequence classes or prove authorship.
**Field-aware layout.** Never assume a specific field exists. Tools/skills
auto-detect only when exactly one field is present; multi-field corpora
require explicit `--field <name>`. Add new sources under
`style-corpus/<new-field>/{tier-1-top,tier-2-mentor,tier-3-reference}/` and
run `python tools/extract_style.py --field <new-field>`.
3. **Honest measurement states.** Missing calibration, optional dependencies,
complete-document corpora, or human labels remain `unmeasured` or
`degraded`. Never convert unavailable evidence into zero findings. Current
metrics and limitations belong in `EVALUATION.md`, not the normative standard.
4. **Plugin manifest format is verified.** `.claude-plugin/plugin.json` per
the official Claude Code plugins reference; skills live at
`skills/<name>/SKILL.md` (NOT inside `.claude-plugin/`). When invoked
from another project via `--plugin-dir`, skills are namespaced as
`/sci-paper:paper`, etc.
## Cross-project references
- - **Source project:** the sibling `weak-gravitational-lensing` project
- (sci-paper was extracted from its `.claude/skills/{paper, paper-review,
- figure-review}`). Those existing skills are the v0 inputs to this plugin.
- Record your local clone path in `CLAUDE.local.md` (gitignored) if you
+ - **Source project:** `wgl-suite`, the weak-gravitational-lensing research hub
+ (sci-paper was extracted from the `paper`, `paper-review` and `figure-review`
+ skills of its predecessor repo, which was folded into wgl-suite on 2026-05-18).
+ wgl-suite remains the primary consumer and the source of the `wgl` style
+ corpus. Record your local clone path in `CLAUDE.local.md` (gitignored) if you
want an absolute reference handy.
- **User's global writing-quality memory** lives in the user-level
`~/.claude/CLAUDE.md` (Linux/macOS) or `%USERPROFILE%\.claude\CLAUDE.md`
(Windows). The rule that matters here, verbatim:
> **Paper writing: never quote from memory.** Every number, date,
> coefficient, figure caption, and citation in a manuscript edit must
> be re-read from its source in the same turn it's pasted.
## Toolchain
Python ≥ 3.11 on PATH (developed against 3.13; nothing in `tools/` uses
3.12-only syntax).
Optional capabilities are listed in `requirements.txt`:
- `pymupdf` — PDF corpus extraction and compiled-page inspection
- `sentence-transformers` — exemplar retrieval and embedding features
- `scikit-learn` + `joblib` — legacy and learned field-similarity models
- `transformers` + `torch` — optional token-surprisal / UID measurement
- `numpy` — learned feature, cache, and rewrite-score utilities
The shared schema, deterministic L0 linter, model-free L1/L2 axes, and validator
remain standard-library paths. Missing optional dependencies must stay visible as
`unmeasured` or `degraded`.
## Personal / machine-specific notes
Put paths, virtualenv locations, or anything else that shouldn't go to
the public repo in `CLAUDE.local.md` next to this file. That filename
is gitignored on purpose — Claude Code reads both, but only this file
is shared.