Begin Stipple/Vue migration with isolated typed studies UI

.Rprofile

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+source("renv/activate.R")

.bun-version

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+1.3.10

.editorconfig

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+# SPDX-License-Identifier: MPL-2.0
+# Hyperpolymath estate canonical .editorconfig  (standards#343 phase 1)
+# Canon lives in rsr-template-repo; do not add a per-repo name to this header.
+# https://editorconfig.org
+
+root = true
+
+# --- Estate baseline -------------------------------------------------------
+[*]
+charset = utf-8
+end_of_line = lf
+indent_style = space
+indent_size = 2
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+# --- Prose: trailing whitespace is significant -----------------------------
+[*.md]
+trim_trailing_whitespace = false
+
+[*.adoc]
+trim_trailing_whitespace = false
+
+# --- 4-space languages -----------------------------------------------------
+[*.rs]
+indent_size = 4
+
+[*.zig]
+indent_size = 4
+
+[*.jl]
+indent_size = 4
+
+[*.py]
+indent_size = 4
+
+[*.c]
+indent_size = 4
+
+[*.h]
+indent_size = 4
+
+[*.php]
+indent_size = 4
+
+# --- 3-space languages (Ada / GNAT house style) ----------------------------
+[*.ada]
+indent_size = 3
+
+[*.adb]
+indent_size = 3
+
+[*.ads]
+indent_size = 3
+
+[*.gpr]
+indent_size = 3
+
+# --- 2-space languages (explicit; matches the [*] default) -----------------
+[*.hs]
+indent_size = 2
+
+[*.ex]
+indent_size = 2
+
+[*.exs]
+indent_size = 2
+
+[*.ncl]
+indent_size = 2
+
+[*.rkt]
+indent_size = 2
+
+[*.scm]
+indent_size = 2
+
+[*.idr]
+indent_size = 2
+
+[*.ipkg]
+indent_size = 2
+
+[*.k9]
+indent_size = 2
+
+[*.a2ml]
+indent_size = 2
+
+[*.agda]
+indent_size = 2
+
+[*.lean]
+indent_size = 2
+
+[*.ebnf]
+indent_size = 2
+
+# --- Tab-mandatory formats -------------------------------------------------
+[Makefile]
+indent_style = tab
+
+[*.go]
+indent_style = tab
+
+# --- Task runners ----------------------------------------------------------
+[Justfile]
+indent_style = space
+indent_size = 4
+
+[justfile]
+indent_style = space
+indent_size = 4
+
+[*.just]
+indent_style = space
+indent_size = 4
+
+[Mustfile]
+indent_style = space
+indent_size = 4
+
+# --- Platform-mandated line endings ----------------------------------------
+# Windows batch/PowerShell hosts require CRLF; keep in step with .gitattributes.
+[*.bat]
+end_of_line = crlf
+
+[*.cmd]
+end_of_line = crlf
+
+[*.ps1]
+end_of_line = crlf
+
+# --- Legacy / retired toolchains (retained for byte hygiene only) ----------
+# ReScript (LANGUAGE-POLICY 1.2) and Nix (retired 2026-06-01) are no longer
+# adopted for new work. These sections are inert where the files are absent and
+# keep surviving files from drifting. Removal is a per-repo judgement.
+[*.res]
+indent_size = 2
+
+[*.resi]
+indent_size = 2
+
+[*.nix]
+indent_size = 2

.envrc

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+# SPDX-License-Identifier: MPL-2.0
+# SPDX-FileCopyrightText: 2026 Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
+# Activate the MetaManifold-WebUI dev environment on `cd` (direnv).
+# Install direnv: https://direnv.net/
+
+# Precedence: mise (exact CI-pinned binaries) first, Guix shell otherwise.
+if has mise; then
+  use mise
+elif has guix && [ -f guix.scm ]; then
+  use guix
+fi
+
+# Estate launcher discovery.
+export METAMANIFOLD_REPO_DIR="$PWD"
+
+# Real secrets belong in .env (gitignored) — never commit them here.
+dotenv_if_exists

.gitattributes

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+# SPDX-License-Identifier: MPL-2.0
+# Hyperpolymath estate canonical .gitattributes  (standards#343 phase 1)
+# Canon lives in rsr-template-repo; do not add a per-repo name to this header.
+#
+# Only diff drivers that git actually ships are used here. MEASURED on git
+# 2.47.3: diff=go and diff=zig are NOT drivers (git silently falls back to the
+# default heuristic); the Go driver is named `golang`.
+
+* text=auto eol=lf
+
+# --- Source ----------------------------------------------------------------
+*.rs    text eol=lf diff=rust
+*.ex    text eol=lf diff=elixir
+*.exs   text eol=lf diff=elixir
+*.ada   text eol=lf diff=ada
+*.adb   text eol=lf diff=ada
+*.ads   text eol=lf diff=ada
+*.gpr   text eol=lf diff=ada
+*.go    text eol=lf diff=golang
+*.py    text eol=lf diff=python
+*.scm   text eol=lf diff=scheme linguist-language=Scheme
+*.rkt   text eol=lf
+*.jl    text eol=lf
+*.hs    text eol=lf
+*.zig   text eol=lf
+*.chpl  text eol=lf
+*.idr   text eol=lf linguist-language=Idris
+*.ipkg  text eol=lf linguist-language=Idris
+*.agda  text eol=lf linguist-language=Agda
+*.lagda text eol=lf linguist-language=Agda
+*.lean  text eol=lf
+# `.v` is ambiguous (Coq / Verilog / V). This estate's `.v` files are Coq
+# proofs; 49 repos currently mislabel them `linguist-language=V`.
+*.v     text eol=lf linguist-language=Coq
+*.ncl   text eol=lf
+*.k9    text eol=lf linguist-language=Nickel
+*.a2ml  text eol=lf linguist-language=TOML
+*.ebnf  text eol=lf
+*.ts    text eol=lf
+*.js    text eol=lf
+*.sh    text eol=lf diff=bash
+*.bash  text eol=lf diff=bash
+
+# --- Windows hosts require CRLF --------------------------------------------
+*.bat   text eol=crlf
+*.cmd   text eol=crlf
+*.ps1   text eol=crlf
+
+# --- Docs ------------------------------------------------------------------
+*.md    text eol=lf diff=markdown
+*.adoc  text eol=lf
+*.txt   text eol=lf
+*.tex   text eol=lf diff=tex
+*.bib   text eol=lf diff=bibtex
+
+# --- Data / config ---------------------------------------------------------
+*.json  text eol=lf
+*.jsonl text eol=lf
+*.yaml  text eol=lf
+*.yml   text eol=lf
+*.toml  text eol=lf
+*.svg   text eol=lf
+*.csv   text eol=lf
+*.html  text eol=lf diff=html
+*.css   text eol=lf diff=css
+
+# --- Repo control files ----------------------------------------------------
+.gitignore     text eol=lf
+.gitattributes text eol=lf
+.editorconfig  text eol=lf
+.tool-versions text eol=lf
+Justfile       text eol=lf
+justfile       text eol=lf
+*.just         text eol=lf
+Mustfile       text eol=lf
+Makefile       text eol=lf
+Containerfile  text eol=lf
+
+# --- Binary ----------------------------------------------------------------
+*.png   binary
+*.jpg   binary
+*.jpeg  binary
+*.gif   binary
+*.webp  binary
+*.ico   binary
+*.pdf   binary
+*.woff  binary
+*.woff2 binary
+*.ttf   binary
+*.otf   binary
+*.eot   binary
+*.zip   binary
+*.tar   binary
+*.gz    binary
+*.xz    binary
+*.bz2   binary
+*.so    binary
+*.dylib binary
+*.dll   binary
+*.exe   binary
+*.wasm  binary
+*.rlib  binary
+*.beam  binary
+
+# --- Sequencing data -------------------------------------------------------
+# History carried 269 MiB of these. They are binary, they must never be
+# line-ending-normalised (a CRLF rewrite corrupts a gzip member), and they are
+# not source. The recurrence guard with teeth is scripts/check-blob-hygiene.sh,
+# run by .githooks/pre-commit and by CI; these lines are hygiene, not the gate.
+*.fastq    binary -diff linguist-generated=true
+*.fastq.gz binary -diff linguist-generated=true
+*.fq       binary -diff linguist-generated=true
+*.fq.gz    binary -diff linguist-generated=true
+*.fasta    binary -diff linguist-generated=true
+*.fa       binary -diff linguist-generated=true
+*.sam      binary -diff linguist-generated=true
+*.bam      binary -diff linguist-generated=true
+
+# --- Generated lockfiles: no diff noise, not counted as source -------------
+Cargo.lock        text eol=lf -diff linguist-generated=true
+mix.lock          text eol=lf -diff linguist-generated=true
+bun.lock          text eol=lf -diff linguist-generated=true
+bun.lockb         binary -diff linguist-generated=true
+pnpm-lock.yaml    text eol=lf -diff linguist-generated=true
+package-lock.json text eol=lf -diff linguist-generated=true
+
+# --- Legacy / retired toolchains (byte hygiene only) -----------------------
+# ReScript is retired (LANGUAGE-POLICY 1.2); Nix was retired 2026-06-01. These
+# lines keep surviving files normalised and keep retired tech out of the
+# GitHub primary-language badge. Removal is a per-repo judgement, never a sweep.
+*.res      text eol=lf
+*.resi     text eol=lf
+**/*.res   linguist-detectable=false
+*.nix      text eol=lf
+flake.lock text eol=lf -diff linguist-generated=true

.githooks/commit-msg

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+#!/usr/bin/env bash
+# SPDX-License-Identifier: MPL-2.0
+# SPDX-FileCopyrightText: 2026 Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
+#
+# commit-msg hook — enforces the estate conventional-commit subject.
+# Enable once per clone:  git config core.hooksPath .githooks
+# (The corresponding template is .gitmessage; CI re-checks on push.)
+msg_file=$1
+subject=$(head -1 "$msg_file")
+
+# Types per .gitmessage "Allowed Types" list.
+if ! printf '%s' "$subject" | grep -qE '^(feat|fix|docs|style|refactor|perf|test|build|ci|chore|revert)(\([a-zA-Z0-9_/-]+\))?!?: .{1,72}$'; then
+  cat >&2 <<EOF
+commit-msg: REJECTED subject:
+  $subject
+Required form:
+  <type>(<optional scope>): <subject>   (type in: feat fix docs style
+  refactor perf test build ci chore revert; subject 1..72 chars)
+EOF
+  exit 1
+fi
+exit 0

.githooks/pre-commit

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+#!/usr/bin/env bash
+# SPDX-License-Identifier: MPL-2.0
+# SPDX-FileCopyrightText: 2026 Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
+#
+# pre-commit hook -- refuses a commit that would reintroduce the sequencing
+# blobs stripped from history. Enable once per clone with `just hooks`
+# (or `git config core.hooksPath .githooks`).
+#
+# The rule itself lives in scripts/check-blob-hygiene.sh and is shared verbatim
+# with the CI blob-hygiene step, so the local gate and the remote gate cannot
+# disagree about what is allowed.
+exec "$(git rev-parse --show-toplevel)/scripts/check-blob-hygiene.sh" --staged

.github/CODEOWNERS

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+# SPDX-License-Identifier: MPL-2.0
+# Ownership for the hyperpolymath fork. Application/domain questions are
+# routed to upstream (JoshuaJewell/MetaManifold-WebUI).
+
+*                 @hyperpolymath
+
+# Engineering estate (types, tests, CI, tooling) — fork owner
+frontend/src/types/   @hyperpolymath
+frontend/tests/       @hyperpolymath
+frontend/bench/       @hyperpolymath
+.github/              @hyperpolymath
+scripts/              @hyperpolymath