ci: adopt estate CI standard + convert 7 hand-rolled tests to PHPUnit (v0.7.0)

- Replace hand-rolled ci.yml jobs with thin caller to reusable estate workflow
  (peptiderepo/peptide-e2e/.github/workflows/ci.yml@main); tests: stubs; has_js: false.
  workflow_call + permissions: contents: write added per estate standard so deploy.yml
  can gate on it and phpcbf auto-commit step has required token scope.

- Convert 7 hand-rolled test-*.php scripts to PHPUnit TestCase classes:
    PeptideCptTest        <- test-peptide-cpt.php
    VerificationScannerTest <- test-verification-scanner.php
    VerificationSettingsTest <- test-verification-settings.php
    Migration0004Test     <- test-migration-0004.php
    JsonldTest            <- test-jsonld.php
    JsonldWebpageTest     <- test-jsonld-webpage.php
    JsonldPeptidePieceTest <- test-jsonld-peptide-piece.php

  All assertions preserved; old scripts remain in tests/unit/ but CI no longer
  runs them (PHPUnit discovery matches *Test.php only).

- Rewrite tests/bootstrap.php: full WP stub library for PHPUnit (WP_Post, WP_Error,
  all option/cron/CPT/taxonomy/permalink stubs); registers PR_Core_Autoloader.
- Add phpunit.xml.dist (bootstrap, unit suite, includes/ coverage).
- Add phpunit/phpunit ^9.6 + yoast/phpunit-polyfills ^2.0 to require-dev.
- Add composer test script (vendor/bin/phpunit --configuration phpunit.xml.dist).
- deploy.yml: add permissions: contents: write.
- Version bump 0.6.2 -> 0.7.0.

Agent-Session: claude-adopt-ci-20260616

.github/workflows/ci.yml

@@ -1,78 +1,27 @@
+##
+# Thin CI caller — peptide-repo-core
+#
+# Delegates all lint/test/file-size jobs to the estate reusable workflow.
+# Per estate standard: workflow_call is required so deploy.yml can gate on it.
+# See: peptiderepo/peptide-e2e/.github/workflows/ci.yml@main for job definitions.
+##
 name: CI
 
 on:
+  pull_request: {}
   push:
-    branches: [ main ]
-  pull_request:
-    branches: [ main ]
-  workflow_call:
+    branches: [main]
+  workflow_call: {}
 
+# Required: calling workflow must declare contents: write so the reusable
+# phpcs job can commit phpcbf auto-fixes back to the PR branch.
 permissions:
-  contents: read
+  contents: write
 
 jobs:
-  # ── PHP Syntax Check ─────────────────────────────────────────────
-  lint-php:
-    name: PHP Lint (${{ matrix.php }})
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        php: [ '8.1', '8.2', '8.3' ]
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Set up PHP ${{ matrix.php }}
-        uses: shivammathur/setup-php@v2
-        with:
-          php-version: ${{ matrix.php }}
-
-      - name: Syntax check all PHP files
-        run: find . -name "*.php" -not -path "./vendor/*" | xargs -n 1 php -l
-
-      - name: Unit tests (lightweight, no PHPUnit)
-        run: |
-          for test in tests/unit/test-*.php; do
-            echo "=== Running $test ==="
-            php "$test"
-          done
-
-  # ── WordPress Coding Standards (PHP CodeSniffer) ──────────────────
-  lint-phpcs:
-    name: WordPress Coding Standards
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Set up PHP
-        uses: shivammathur/setup-php@v2
-        with:
-          php-version: '8.1'
-
-      - name: Install Composer dependencies
-        run: composer install --no-interaction --prefer-dist --no-progress
-
-      - name: Run PHPCS
-        run: composer run lint
-        continue-on-error: true
-
-  # ── 300-line file check ──────────────────────────────────────────
-  file-size:
-    name: 300-line file check
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - name: Check no PHP file exceeds 300 lines
-        run: |
-          violations=0
-          while IFS= read -r file; do
-            lines=$(wc -l < "$file")
-            if [ "$lines" -gt 300 ]; then
-              echo "VIOLATION: $file ($lines lines)"
-              violations=$((violations + 1))
-            fi
-          done < <(find . -name "*.php" -not -path "./vendor/*" -not -path "./tests/*")
-          if [ "$violations" -gt 0 ]; then
-            echo "$violations file(s) exceed 300 lines"
-            exit 1
-          fi
-          echo "All PHP files are 300 lines or fewer."
+  ci:
+    uses: peptiderepo/peptide-e2e/.github/workflows/ci.yml@main
+    with:
+      tests: stubs
+      has_js: false
+    secrets: inherit

.github/workflows/deploy.yml

@@ -4,8 +4,10 @@ on:
   push:
     branches: [ main ]
 
+# contents: write required so the ci.yml caller can pass write permission
+# through to the phpcbf auto-commit step in the reusable workflow.
 permissions:
-  contents: read
+  contents: write
 
 concurrency:
   group: deploy-peptide-repo-core