chore: public-release cleanup (internal docs, 26-source reconcile, OSS files)#54
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… add OSS files) Brings the repo to a state fit to be seen publicly, from the release-readiness audit (verdict CLOSE, 5 P0 blockers — all addressed here). No engine behavior changes. Removed internal scaffolding from the tracked tree (kept in git history; the strategy docs are archived locally): - deleted the obsolete process/handoff docs: RESUME, WORK_DESIGNATION, RECONCILIATION, FOUNDER_ACTIONS, Operon_PRD, Operon_Build_Handoff. - removed DECISIONS, BUILD_ROADMAP, ARXIV, REHOSTING from the tree. - untracked the two .planning handoff files and tightened .gitignore so .planning never ships. Fixed public-facing defects: - README: dropped the "license is a placeholder" caveat (LICENSE is a finalized Apache-2.0); reconciled the source count to the true 26 and pointed at `pinakes catalog` as the live list; fixed the uniprot organism_taxon_id example (operator eq -> in); added a Versioning & stability section and Contributing/Security/Changelog pointers. - schema/manifest.schema.json: $id and description -> pinakes.sh + the pinakes.sh/pinakes module path (the only wrong-domain string in any contract artifact; a pre-1.0 correction, no ManifestSchemaVersion bump — the schema is not yet publicly shipped and no test pins it). - skill docs: rebuilt the source tables from `pinakes catalog` ground truth (14 -> 26, accurate SPDX/posture/attribution per source). - CONTRACTS.md / RELEASING.md: made them stand alone (removed citations to the deleted docs). - removed internal-process attribution from Go comments. Added OSS table-stakes: CONTRIBUTING.md, CODE_OF_CONDUCT.md, CHANGELOG.md, a PR template, and bug/feature issue templates. cmd/pinakes: version now falls back to runtime/debug.ReadBuildInfo so `go install ...@vX` binaries self-identify instead of reporting "dev". Touches the frozen surface (schema/manifest.schema.json, engine/resolver test comments) -> carries the spine-change label. make ci green; govulncheck clean. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Public-release cleanup
Brings the repo to a state fit to be public, addressing all 5 P0 blockers from the
release-readiness audit (verdict was CLOSE — engine A-grade, surroundings C-grade). No engine
behavior changes;
make cigreen, govulncheck clean.Removed internal scaffolding
RESUME.md,WORK_DESIGNATION.md,RECONCILIATION.md,FOUNDER_ACTIONS.md,Operon_PRD.md,Operon_Build_Handoff.md.DECISIONS.md,BUILD_ROADMAP.md,ARXIV.md,REHOSTING.mdfrom the tree (archivedlocally for reference; git history retains everything).
.planninghandoff files; tightened.gitignoreso.planning/never ships.Fixed public-facing defects
LICENSEis finalized Apache-2.0);reconciled the source count
10/14 → 26and madepinakes catalogthe authoritative list;fixed the broken
uniprotorganism_taxon_idexample (eq → in, verified against the binary);added a Versioning & stability section and Contributing/Security/Changelog pointers.
$id+ description →pinakes.shand thepinakes.sh/pinakesmodule path (the only wrong-domain string in any contract artifact). Pre-1.0 correction — no
ManifestSchemaVersionbump (schema not yet publicly shipped; no test pins it).pinakes catalogground truth (14 → 26 rows,accurate SPDX / posture / attribution per source).
Added OSS table-stakes
CONTRIBUTING.md,CODE_OF_CONDUCT.md,CHANGELOG.md, a PR template, and bug/feature issuetemplates.
Tooling
cmd/pinakesversion now falls back toruntime/debug.ReadBuildInfo, sogo install …@vXbinaries self-identify instead of reporting
dev.Touches the frozen surface (
schema/manifest.schema.json,engine/resolvertest comments) →carries the spine-change label.
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