Integration harness: profiles, merge hygiene, and granular re-anchor - #70
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The fork (hyperpolymath) and upstream (JoshuaJewell) share no git ancestor, so a naive merge three-way-merges nothing and conflicts on all 159 shared-but-different files (measured; see docs/integration/conflict-map-2026-09-25.md). This makes the maintainer's integration tractable and keeps both sides runnable with zero extra effort. - .gitattributes: stop git line-merging lockfiles/build output (merge: unset) so they resolve by regeneration, never by editing. - config/integration.toml + scripts/integrate.sh + `just integrate`: profiles (base -> transitional -> full) and per-component toggles, so the maintainer adopts work incrementally and learns to trust it. Default is `base` (pure upstream); nothing risk-bearing is active, so operations are never compromised. - Justfile: doctor (full toolchain report), heal (repair), merge-drivers (opt-in lockfile auto-resolve), renv-restore, and suspend/augment component toggles. bootstrap/setup-full now cover the whole toolchain + R lane, so a fresh clone always runs. - docs/integration/: the guide and the measured conflict map. All new paths are fork-only or brand new, so this aid introduces no conflicts of its own. Hygiene gates (spdx, format) green. Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>
With full history the fork and upstream share the root commit (7884553) and diverged at the second commit, developing in parallel (fork 221, upstream 89). The earlier "unrelated histories" note was a depth-1 shallow-clone artifact; the 159-conflict one-shot merge is real, but the fix is a rebase, not unrelated-history surgery. - scripts/reanchor.sh + just reanchor{,-plan,-manual}: replay the fork's commits one-by-one onto upstream (git auto-applies the clean ones), turning the 159-file wall into per-commit decisions. Measured: 206 granular commits, 0 residual conflicts, 3 logged decisions (all "respect upstream's deletion of pipelinesteps.txt"). Runs in an isolated worktree; never touches the current branch. - docs: correct the premise in README/conflict-map; add the re-anchor layer and a HANDOFF brief to land it. - CONTRIBUTING: point at reanchor-plan/reanchor and the handoff. The re-anchored branch also shares a real base with upstream, so future upstream changes merge cleanly too. Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>
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Summary
Makes merging this fork's work into upstream (
JoshuaJewell/MetaManifold-WebUI) tractable, and keeps both sides runnable with zero extra effort. The two commits are tooling, config, and docs only — no application/analysis logic changes.The fork and upstream share only the root commit and then developed in parallel, so a one-shot
git mergesurfaces 159 conflicting files at once. This PR removes that wall three ways:.gitattributes,just merge-drivers).base, the default) to partially transitional to everything (full), with per-component toggles and automatic conflict triage (config/integration.toml,scripts/integrate.sh,just integrate …).scripts/reanchor.sh,just reanchor).It also makes the environment turnkey:
mise.tomlstays the single source of truth andjust bootstrap/setup-full/heal/doctornow cover the whole toolchain and the R lane (renv-restore), so a fresh clone always runs.Base check
hyperpolymath/MetaManifold-WebUI:main(engineering/tooling work lands on this fork perCONTRIBUTING.md)Changes
.gitattributes— lockfiles / build output markedmerge: unset,linguist-generated(never hand-merge a generated file).config/integration.toml+scripts/integrate.sh+just integrate …— profiles (base/transitional/full), per-componentaugment/suspend, conflicttriage(auto / component / human),verify.scripts/reanchor.sh+just reanchor{,-plan,-manual}— granular re-anchor onto upstream (isolated worktree; never touches the current branch).Justfile—doctor(full toolchain report),heal(repair),merge-drivers(opt-in lockfile auto-resolve),renv-restore;bootstrap/setup-fullnow cover the R lane and merge drivers.docs/integration/—README.md(guide),conflict-map-2026-09-25.md(measured),HANDOFF-granular-reanchor.md(brief to land it)..gitignore(trackdocs/integration/),CONTRIBUTING.md(pointer).Engineering checklist
Required
bun run check— N/A: nofrontend/changes (frontend untouched).scripts/check-spdx.sh/scripts/check-format.shpass (check-lint.shN/A: no TS changes).feat(integration):,feat(reanchor):).MPL-2.0code/scripts,CC-BY-SA-4.0docs)..env, or sequencing data.As applicable
CHANGELOG.md— tooling/docs PR; changelog entry optional.docs/reproducibility.md— environment unchanged (mise.tomluntouched; only additive Justfile lanes).Testing
reanchor.shvalidated end-to-end (plan+run): 206 granular commits, 0 residual conflicts, 3 logged decisions (all "respect upstream's deletion ofpipelinesteps.txt"); runs in an isolated worktree, auto-cleans, branch untouched.integrate.shvalidated:status/profiles/plan/triage/enable/disable/verify.mainwith no file overlap againstmain's newer commits.