feat: minted keys, VRF seeds, RFC 9162 proofs, history roots, tag URIs and a transparency log

Keys (spec/02 §2.4), the rule paperstack settled on:
- A work key is a Scholar-style citation key, a hyphen and the first four
  Crockford base32 characters of SHA-256("scienting-key/1:" + identity),
  where the identity is the first of doi, arxiv, isbn, pmid, pmcid and
  openalex in same_as, else the folded title, year and family name. A
  collision lengthens the later key by two characters; a key is minted
  once and never recomputed. A document key adds .si, .v<seq> or .<type>
  for versions other than the version of record.
- Every fixture key is now minted (hale2026harmonic-damb,
  okafor2025solvent-acth, writer2027fixed-ynr7.v3, tiny2026tiny-j4qm), so
  every node and record ID was re-minted and the docs rewritten to match.
  The validator checks the document key against the work key and version
  (doc.key.work) and the hash part against the identifier (doc.key.suffix).
  vectors/keys.jsonl pins the cases paperstack's tests pin.

Review:
- Spot-check seeds are ECVRF-EDWARDS25519-SHA512-TAI proofs (RFC 9381),
  implemented in tools/oracle/vrf.py in plain Python and reproduced
  against the RFC's Example 16; the sample ranks by the VRF output. The
  earlier Ed25519 seed could be ground by a dishonest checker.
- RFC 9162 inclusion and consistency proofs (crypto.inclusion_path,
  verify_inclusion, consistency_proof, verify_consistency) with
  scienting-proof/1, vectors/proofs.jsonl and two fixture records.
- document.json carries `history`, the root over the corrections, with
  the empty-tree hash for none (spec/11 §11.5, rule doc.history).
- A provisional transparency log (spec/23): log entries, signed-note
  checkpoints with key hashes as transparency logs share them, the rule
  that a logged revocation beats a self-asserted time, and vectors.
- Reserved signature schemes cose and ml-dsa-65 (spec/08 §8.4).

Identifiers and text:
- urn:scienting: becomes tag:scient.ing,2026: (RFC 4151), since the URN
  namespace was never registered.
- Unicode 16.0 is pinned for normalization and categories (spec/01 §1.4);
  the checker refuses another version.

Checking:
- check.py: keys, proofs, VRF and checkpoint vectors; the proof and
  checkpoint records; a check that every ID and hash the prose quotes
  exists in the fixtures or vectors; three more broken packages
  (history-wrong, key-suffix, key-work).
- stress.py: key, VRF, proof and checkpoint properties.
- Docs: a keys section in the concepts and FAQ, rationale entries for
  keys, VRF, proofs, tag URIs and the Unicode pin, a "Looking ahead"
  section, media-type registration and OCI distribution notes.

Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
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alexmandClaude committed 2026-10-14 23:21:57 -04:00
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@@ -1,14 +1,14 @@
[workspace]
name = "manuspec"
name = "paperspec"
version = "0.1.0"
description = "The scienting data formats: specification, JSON Schemas, SQL, test vectors and fixtures"
authors = ["Scientific Computing Studio <maintainer@scient.ing>"]
license = "CC-BY-4.0 AND CC0-1.0 AND Apache-2.0"
license-file = "LICENSE.md"
readme = "README.md"
homepage = "https://scient.ing"
repository = "https://git.scient.ing/infra/manuspec"
documentation = "https://git.scient.ing/infra/manuspec/src/branch/main/docs/README.md"
homepage = "https://paperspec.scient.ing"
repository = "https://git.scient.ing/infra/paperspec"
documentation = "https://paperspec.scient.ing/docs/"
channels = ["conda-forge"]
platforms = ["linux-64", "linux-aarch64", "osx-64", "osx-arm64"]
requires-pixi = ">=0.40"
@@ -29,3 +29,4 @@ lint = { cmd = "markdownlint-cli2", description = "Lint every Markdown file with
load = { cmd = "python tools/load.py", description = "Load packages into SQLite: pixi run load --sqlite lab.db PACKAGE..." }
validate = { cmd = "python tools/validate.py", description = "Validate packages, or run proposed corrections through the gate" }
stress = { cmd = "python tools/stress.py", description = "Stress the oracle with random inputs: pixi run stress -- --seed N" }
site = { cmd = "python tools/site.py", description = "Build the website into _site/" }