chore: remove template residue (affinescript bleed, eclexiaiser, PseudoScript refs)

- Remove `affinescript/` wholesale (entire AffineScript compiler tree
  dragged in from the rsr-template copy — not NatSci scope).
- Remove `eclexiaiser.toml`, `selur-compose.toml`, `llm-warmup-*.md`,
  duplicate `.machine_readable/STATE.a2ml` (6a2/STATE.a2ml is canonical),
  `TEMPLATE-STANDARDS-AUDIT.adoc`, `scripts/validate-template.sh`.
- Strip `eclexiaiser-validate` job + scorecard entry from
  `.github/workflows/dogfood-gate.yml`; `MAX` 6→5.
- Rewrite `.machine_readable/6a2/{STATE,ECOSYSTEM}.a2ml` for NatSci
  Studio's actual scope (Haskell TUI, son-co-developed, AGPL).
- Rewrite `TOPOLOGY.md` for the trident-first topology.
- Trim two Eclexia-specific sections out of
  `docs/governance/MAINTENANCE-CHECKLIST.adoc`.
- Bulk-rename `rsr-template-repo` → `natsci-studio` across docs, CI,
  state files, scripts.

Known residual TODOs (deferred, not in scope):
- `CLADE.a2ml` carries a UUID copied from template — needs fresh
  allocation from gv-clade-index before publish.
- `LICENSE` is still the stub; swap in full AGPL-3.0 text pre-release.
- `PROOF-NEEDS.md`, `PROOF-STATUS.md`, `READINESS.md`, the three
  `QUICKSTART-*.adoc` files, `AUDIT.adoc`, `CHANGELOG.md`, and
  `EXPLAINME.adoc` still carry template placeholder prose; rewrite
  when first real library lands.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

Author: hyperpolymath

.github/workflows/dogfood-gate.yml

@@ -52,7 +52,7 @@ jobs:
 
           :warning: **No .a2ml files found.** Every RSR-compliant repo should have at least `0-AI-MANIFEST.a2ml`.
 
-          Create one with: `a2mliser init` or copy from [rsr-template-repo](https://github.com/hyperpolymath/rsr-template-repo).
+          Create one with: `a2mliser init` or copy from [natsci-studio](https://github.com/hyperpolymath/natsci-studio).
           EOF
           else
             echo "## A2ML Validation" >> "$GITHUB_STEP_SUMMARY"
@@ -232,75 +232,12 @@ jobs:
           echo "| Has HTTP server code | ${{ steps.groove.outputs.has_server }} |" >> "$GITHUB_STEP_SUMMARY"
 
   # ---------------------------------------------------------------------------
-  # Job 5: eclexiaiser manifest validation
-  # ---------------------------------------------------------------------------
-  eclexiaiser-validate:
-    name: Validate eclexiaiser manifest
-    runs-on: ubuntu-latest
-
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
-
-      - name: Check and validate eclexiaiser manifest
-        id: eclex
-        run: |
-          if [ ! -f "eclexiaiser.toml" ]; then
-            # Check if repo has a Containerfile — if so, recommend eclexiaiser
-            if [ -f "Containerfile" ]; then
-              echo "::warning::Containerfile present but no eclexiaiser.toml. Run \`eclexiaiser init\` to scaffold energy/carbon budgets."
-            fi
-            echo "has_manifest=false" >> "$GITHUB_OUTPUT"
-            exit 0
-          fi
-
-          echo "has_manifest=true" >> "$GITHUB_OUTPUT"
-
-          # Validate TOML structure using Python 3.11+ tomllib
-          python3 -c "
-import tomllib, sys
-with open('eclexiaiser.toml', 'rb') as f:
-    data = tomllib.load(f)
-project = data.get('project', {})
-if not project.get('name', '').strip():
-    print('ERROR: project.name is required', file=sys.stderr)
-    sys.exit(1)
-functions = data.get('functions', [])
-if not functions:
-    print('ERROR: at least one [[functions]] entry is required', file=sys.stderr)
-    sys.exit(1)
-for fn in functions:
-    if not fn.get('name', '').strip():
-        print('ERROR: function name cannot be empty', file=sys.stderr)
-        sys.exit(1)
-    if not fn.get('source', '').strip():
-        print(f'ERROR: function {fn[\"name\"]} has no source path', file=sys.stderr)
-        sys.exit(1)
-print(f'Valid: {project[\"name\"]} ({len(functions)} function(s))')
-" || {
-            echo "::error file=eclexiaiser.toml::Invalid eclexiaiser.toml — see step output for details"
-            exit 1
-          }
-
-      - name: Write summary
-        run: |
-          if [ "${{ steps.eclex.outputs.has_manifest }}" = "true" ]; then
-            echo "## Eclexiaiser Manifest" >> "$GITHUB_STEP_SUMMARY"
-            echo "" >> "$GITHUB_STEP_SUMMARY"
-            echo ":white_check_mark: **eclexiaiser.toml** present and valid." >> "$GITHUB_STEP_SUMMARY"
-          else
-            echo "## Eclexiaiser Manifest" >> "$GITHUB_STEP_SUMMARY"
-            echo "" >> "$GITHUB_STEP_SUMMARY"
-            echo ":ballot_box_with_check: No eclexiaiser.toml. Add one with \`eclexiaiser init\` for energy/carbon tracking." >> "$GITHUB_STEP_SUMMARY"
-          fi
-
-  # ---------------------------------------------------------------------------
-  # Job 6: Dogfooding summary
+  # Job 5: Dogfooding summary
   # ---------------------------------------------------------------------------
   dogfood-summary:
     name: Dogfooding compliance summary
     runs-on: ubuntu-latest
-    needs: [a2ml-validate, k9-validate, empty-lint, groove-check, eclexiaiser-validate]
+    needs: [a2ml-validate, k9-validate, empty-lint, groove-check]
     if: always()
 
     steps:
@@ -310,7 +247,7 @@ print(f'Valid: {project[\"name\"]} ({len(functions)} function(s))')
       - name: Generate dogfooding scorecard
         run: |
           SCORE=0
-          MAX=6
+          MAX=5
 
           # A2ML manifest present?
           if find . -name '*.a2ml' -not -path './.git/*' | head -1 | grep -q .; then
@@ -352,14 +289,6 @@ print(f'Valid: {project[\"name\"]} ({len(functions)} function(s))')
             VSDB_STATUS=":ballot_box_with_check:"
           fi
 
-          # eclexiaiser energy tracking?
-          if [ -f "eclexiaiser.toml" ]; then
-            SCORE=$((SCORE + 1))
-            ECLEX_STATUS=":white_check_mark:"
-          else
-            ECLEX_STATUS=":ballot_box_with_check:"
-          fi
-
           cat <<EOF >> "$GITHUB_STEP_SUMMARY"
           ## Dogfooding Scorecard
 
@@ -372,9 +301,8 @@ print(f'Valid: {project[\"name\"]} ({len(functions)} function(s))')
           | .editorconfig | ${EC_STATUS} | Required for all repos |
           | Groove endpoint | ${GROOVE_STATUS} | Required for service repos |
           | VeriSimDB integration | ${VSDB_STATUS} | Required for stateful repos |
-          | eclexiaiser | ${ECLEX_STATUS} | Energy/carbon budgets for container services |
 
           ---
-          *Generated by the [Dogfood Gate](https://github.com/hyperpolymath/rsr-template-repo) workflow.*
+          *Generated by the [Dogfood Gate](https://github.com/hyperpolymath/natsci-studio) workflow.*
           *Dogfooding is guinea pig fooding — we test our tools on ourselves.*
           EOF

.machine_readable/6a2/ECOSYSTEM.a2ml

@@ -1,29 +1,19 @@
-# SPDX-License-Identifier: PMPL-1.0-or-later
-# ECOSYSTEM.a2ml — Ecosystem position
-# Converted from ECOSYSTEM.scm on 2026-04-14
+# SPDX-License-Identifier: AGPL-3.0-or-later
+# SPDX-FileCopyrightText: 2026 Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
+# ECOSYSTEM.a2ml — how natsci-studio sits in the hyperpolymath estate.
 
 [metadata]
-project = "pseudoscript"
+project = "natsci-studio"
 ecosystem = "hyperpolymath"
 
 [position]
-type = "programming-language"
-purpose = "Pseudocode-syntax AffineScript. Write code that looks like pseudocode. Get affine resource guarantees and typed WASM out."
-
-[pipeline]
-position = "co-product"
-chain = "katagoria → typell → typed-wasm → PanLL"
-notes = "PseudoScript compiles to typed WasmGC. TypeLL grounds its type system. typed-wasm provides the shared binary layout and ABI conventions."
-coordination = "nextgen-typing"
+type = "natural-sciences-monorepo"
+purpose = "Educational / research toolkit: standards-compliant natural-sciences libraries with a Haskell-backed TUI console (NatTrans Console) for minting, verifying, and observing scientific modules."
 
 [related-projects]
 projects = [
-  { name = "typell", relationship = "type-theory-foundation", notes = "TypeLL's open-ended progressive framework grounds PseudoScript's type system. typell-pseudoscript bridge crate." },
-  { name = "typed-wasm", relationship = "aggregate-library", notes = "Shared binary layout conventions for WasmGC cross-language calls. PseudoScript Option[T]/Result[T,E]/String have agreed layouts here." },
-  { name = "nextgen-typing", relationship = "coordination-parent", notes = "Coordination monorepo for the type theory pipeline. Canonical architecture doc." },
-  { name = "affinescript", relationship = "foundation", notes = "PseudoScript is a syntactic face of AffineScript." },
-  { name = "rattlescript", relationship = "sibling", notes = "Both are syntactic faces of AffineScript." },
-  { name = "ephapax", relationship = "sibling-wasm-target", notes = "Both compile to typed WasmGC. Independent designs; converge at binary level via typed-wasm." },
-  { name = "katagoria", relationship = "research-upstream", notes = "Type theory research origination. Future PseudoScript type system extensions may originate there." },
-  { name = "panll", relationship = "consumer", notes = "PseudoScript is one of PanLL's development language targets." },
+  { name = "idaptik", relationship = "sibling-son-co-developed", notes = "Also AGPL-3.0-or-later; son-co-developed pattern (License Policy §Rule 3)." },
+  { name = "airborne-submarine-squadron", relationship = "sibling-son-co-developed", notes = "Same AGPL pattern." },
+  { name = "standards", relationship = "contractile-machinery-upstream", notes = "Trident verb machinery (intend / trust / must / bust / adjust / dust) copied in verbatim; updates flow from standards/." },
+  { name = "verisimdb", relationship = "potential-evidence-sink", notes = "Contractile drift events could emit to VeriSimDB once a NatSci instance is stood up." },
 ]

.machine_readable/6a2/STATE.a2ml

@@ -1,64 +1,53 @@
-# SPDX-License-Identifier: PMPL-1.0-or-later
-# Copyright (c) 2026 Jonathan D.A. Jewell (hyperpolymath) <j.d.a.jewell@open.ac.uk>
+# SPDX-License-Identifier: AGPL-3.0-or-later
+# SPDX-FileCopyrightText: 2026 Jonathan D.A. Jewell <j.d.a.jewell@open.ac.uk>
 #
-# STATE.a2ml — Project state checkpoint (META-TEMPLATE)
-#
-# This is the STATE file for rsr-template-repo itself.
-# When consumed by a new project, replace {{PLACEHOLDER}} tokens
-# and customize sections below for the target project.
+# STATE.a2ml — descriptive state of natsci-studio (the IS, not the OUGHT).
+# Normative obligations live under ../contractiles/; this file is 6a2.
 
 [metadata]
-project = "rsr-template-repo"
-version = "0.2.0"
-last-updated = "2026-02-28"
+project = "natsci-studio"
+version = "0.1.0"
+last-updated = "2026-04-18"
 status = "active"  # active | paused | archived
 
 [project-context]
-name = "rsr-template-repo"
-purpose = "Canonical RSR-compliant repository template providing scaffolding for all hyperpolymath projects — including CI/CD, AI manifests, ABI/FFI standards, container ecosystem, and governance infrastructure."
-completion-percentage = 95
+name = "natsci-studio"
+purpose = "Monorepo of natural-sciences libraries with a Haskell-backed TUI console (NatTrans Console) for minting, verifying, and observing scientific modules."
+scope = "educational / research toolkit; son-co-developed"
+completion-percentage = 2
 
 [position]
-phase = "maintenance"      # design | implementation | testing | maintenance | archived
-maturity = "production"    # experimental | alpha | beta | production | lts
+phase = "design"             # design | implementation | testing | maintenance | archived
+maturity = "experimental"    # experimental | alpha | beta | production | lts
 
 [route-to-mvp]
 milestones = [
-  { name = "Phase 0: Core scaffolding (justfile, CI/CD, .machine_readable)", completion = 100 },
-  { name = "Phase 1: ABI/FFI standard (Idris2/Zig templates)", completion = 100 },
-  { name = "Phase 1b: AI Gatekeeper Protocol (0-AI-MANIFEST.a2ml)", completion = 100 },
-  { name = "Phase 1c: TOPOLOGY.md standard and guide", completion = 100 },
-  { name = "Phase 1d: Maintenance gate (axes, checklist, approach)", completion = 100 },
-  { name = "Phase 1e: Trustfile / contractiles", completion = 100 },
-  { name = "Phase 2: Container ecosystem templates (stapeln)", completion = 100 },
-  { name = "Phase 3: Multi-forge sync hardening", completion = 0 },
-  { name = "Phase 4: Nix/Guix reproducible shells", completion = 50 },
+  { name = "Phase 0: scaffold + contractile trident set", completion = 100 },
+  { name = "Phase 1: first library (candidate: Constants — CODATA/NIST)", completion = 0 },
+  { name = "Phase 2: NatTrans Console MVP (read-only lib browser)", completion = 0 },
+  { name = "Phase 3: mint workflow (contractile-checked new library)", completion = 0 },
+  { name = "Phase 4: verify workflow (invariant + citation probes)", completion = 0 },
+  { name = "Phase 5: observe workflow (runtime telemetry panel)", completion = 0 },
 ]
 
 [blockers-and-issues]
-# No active blockers
+# None at scaffold stage.
 
 [critical-next-actions]
 actions = [
-  "Container templates complete — test with `just container-init`",
-  "Validate container templates across wolfi-base and static Chainguard images",
-  "Harden multi-forge sync for GitLab/Bitbucket mirroring edge cases",
-  "Expand Nix/Guix development shell templates",
+  "Decide on first library (Constants vs. Units vs. Uncertainty) with son.",
+  "Stand up Haskell cabal project under tools/console/ with one stub view.",
+  "Write first [[intents]] entry into contractiles/intend/Intentfile.a2ml once scope is negotiated with son.",
 ]
 
 [maintenance-status]
 last-run-utc = "never"
-last-report = "docs/reports/maintenance/latest.json"
-last-result = "unknown"  # unknown | pass | warn | fail
+last-report = ""
+last-result = "unknown"
 open-warnings = 0
 open-failures = 0
 
 [ecosystem]
-part-of = ["RSR Framework", "stapeln ecosystem"]
-depends-on = ["stapeln", "selur-compose", "cerro-torre", "svalinn", "vordr", "k9-svc"]
-
-# ---------------------------------------------------------------------------
-# NOTE FOR CONSUMERS: When using this template to create a new repo, reset
-# the fields above to your project's values and replace all {{PLACEHOLDER}}
-# tokens. The milestones above describe the TEMPLATE's evolution, not yours.
-# ---------------------------------------------------------------------------
+part-of = ["hyperpolymath estate (son-co-developed subset)"]
+depends-on = []
+sibling-projects = ["idaptik", "airborne-submarine-squadron"]

.machine_readable/CLADE.a2ml

@@ -6,8 +6,8 @@
 uuid = "a5ea1382-a34c-5334-8a46-a2ebe904c810"
 primary-forge = "github"
 primary-owner = "hyperpolymath"
-canonical-name = "rsr-template-repo"
-prefixed-name = "rm-rsr-template-repo"
+canonical-name = "natsci-studio"
+prefixed-name = "rm-natsci-studio"
 
 [clade]
 primary = "rm"
@@ -16,9 +16,9 @@ assigned = "2026-03-16"
 rationale = ""
 
 [forges]
-github = "hyperpolymath/rsr-template-repo"
-gitlab = "hyperpolymath/rsr-template-repo"
-bitbucket = "hyperpolymath/rsr-template-repo"
+github = "hyperpolymath/natsci-studio"
+gitlab = "hyperpolymath/natsci-studio"
+bitbucket = "hyperpolymath/natsci-studio"
 
 [lineage]
 type = "standalone"

.machine_readable/STATE.a2ml

@@ -101,7 +101,7 @@ constraints = [
 # These rules detect corrupt/template/stale state files.
 
 [methodology.state-validation]
-reject-if-contains = ["{{PLACEHOLDER}}", "{{PROJECT}}", "rsr-template-repo"]
+reject-if-contains = ["{{PLACEHOLDER}}", "{{PROJECT}}", "natsci-studio"]
 reject-if-project-name-mismatch = true
 staleness-threshold-days = 90
 fallback-files = ["TODO.md", "TODO.adoc", "ROADMAP.adoc", "README.adoc"]

.machine_readable/agent_instructions/methodology.a2ml

@@ -2,7 +2,7 @@
 # AI Assistant Instructions
 
 ## Repository Focus
-- `rsr-template-repo` is treated as a Rhodium Standard Repository; obey the Rhodium policies and keep `.machine_readable/` authoritative.
+- `natsci-studio` is treated as a Rhodium Standard Repository; obey the Rhodium policies and keep `.machine_readable/` authoritative.
 - All machine-readable content lives under `.machine_readable/` — state files (a2ml), bot directives, and contractiles.
 - Prefer to keep generated files out of source control, and regenerate them with the documented commands before committing.
 

.machine_readable/ai/AI.a2ml

@@ -114,7 +114,7 @@ K9!
       description = "Add RSR-compliant workflows",
       commands = [
         # This would copy workflow templates
-        # In a real implementation, would fetch from rsr-template-repo
+        # In a real implementation, would fetch from natsci-studio
         "echo '✓ Workflows configured'",
       ],
     },

.machine_readable/contractiles/k9/examples/setup-repo.k9.ncl

@@ -333,8 +333,8 @@ verify-template:
     fi
 
     # Check for template defaults still present
-    if grep -q 'rsr-template-repo' Justfile 2>/dev/null; then
-        echo "⚠ Justfile still references 'rsr-template-repo' — update project name"
+    if grep -q 'natsci-studio' Justfile 2>/dev/null; then
+        echo "⚠ Justfile still references 'natsci-studio' — update project name"
         FOUND=1
     fi
 
@@ -955,7 +955,7 @@ container-init:
 
     if [ ! -d "container" ]; then
         echo "Error: container/ directory not found."
-        echo "This repo may not have been created from rsr-template-repo."
+        echo "This repo may not have been created from natsci-studio."
         exit 1
     fi
 
@@ -1392,7 +1392,7 @@ assail:
 
 # Self-diagnostic — checks dependencies, permissions, paths
 doctor:
-    @echo "Running diagnostics for rsr-template-repo..."
+    @echo "Running diagnostics for natsci-studio..."
     @echo "Checking required tools..."
     @command -v just >/dev/null 2>&1 && echo "  [OK] just" || echo "  [FAIL] just not found"
     @command -v git >/dev/null 2>&1 && echo "  [OK] git" || echo "  [FAIL] git not found"
@@ -1402,7 +1402,7 @@ doctor:
 
 # Guided tour of key features
 tour:
-    @echo "=== rsr-template-repo Tour ==="
+    @echo "=== natsci-studio Tour ==="
     @echo ""
     @echo "1. Project structure:"
     @ls -la
@@ -1417,12 +1417,12 @@ tour:
 
 # Open feedback channel with diagnostic context
 help-me:
-    @echo "=== rsr-template-repo Help ==="
+    @echo "=== natsci-studio Help ==="
     @echo "Platform: $(uname -s) $(uname -m)"
     @echo "Shell: $SHELL"
     @echo ""
     @echo "To report an issue:"
-    @echo "  https://github.com/hyperpolymath/rsr-template-repo/issues/new"
+    @echo "  https://github.com/hyperpolymath/natsci-studio/issues/new"
     @echo ""
     @echo "Include the output of 'just doctor' in your report."