test(cpt): update rest_namespace assertion — now absent, defaults to wp/v2

Merges feature/related-articles-section.

Adds peptide_topic taxonomy, provider interface, internal posts provider, card grid renderer, admin settings, CSS, and unit tests.

Reviewed: qa-reviews/peptide-repo-core/2026-04-24-a10610ded7df.md
CI: PHP 8.1/8.2/8.3 lint, PHPCS, 300-line check — all green.

.github/workflows/ci.yml

@@ -29,6 +29,13 @@ jobs:
       - 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

.github/workflows/deploy.yml

@@ -7,67 +7,84 @@ on:
 permissions:
   contents: read
 
-# Cancel previous deploys if a new push arrives while one is running.
 concurrency:
   group: deploy-peptide-repo-core
   cancel-in-progress: true
 
 jobs:
-  # ── Run CI first ─────────────────────────────────────────────────
   ci:
     name: Pre-deploy CI
     uses: ./.github/workflows/ci.yml
 
-  # ── Deploy via rsync over SSH ────────────────────────────────────
+  deploy-staging:
-  deploy:
+    name: Deploy to Staging
     needs: ci
-    name: Deploy to Production
     runs-on: ubuntu-latest
-
+    environment: staging
     steps:
-      - name: Checkout code
+      - uses: actions/checkout@v4
-        uses: actions/checkout@v4
-
       - name: Setup SSH key
         run: |
           mkdir -p ~/.ssh
           echo "${{ secrets.SSH_PRIVATE_KEY }}" > ~/.ssh/deploy_key
           chmod 600 ~/.ssh/deploy_key
           ssh-keyscan -p ${{ secrets.SSH_PORT }} ${{ secrets.SSH_HOST }} >> ~/.ssh/known_hosts 2>/dev/null
-
+      - name: Deploy via rsync → staging
-      - name: Deploy via rsync
         run: |
           rsync -avz --delete \
-            --exclude '.git' \
+            --exclude '.git' --exclude '.github' \
-            --exclude '.github' \
+            --exclude 'tests' --exclude 'phpunit.xml.dist' \
-            --exclude 'tests' \
+            --exclude 'composer.json' --exclude 'composer.lock' \
-            --exclude 'phpunit.xml.dist' \
+            --exclude 'vendor' --exclude 'phpcs.xml.dist' \
-            --exclude 'composer.json' \
+            --exclude 'ARCHITECTURE.md' --exclude 'CONVENTIONS.md' --exclude 'CHANGELOG.md' \
-            --exclude 'composer.lock' \
+            -e "ssh -i ~/.ssh/deploy_key -p ${{ secrets.SSH_PORT }}" \
-            --exclude 'vendor' \
+            ./ ${{ secrets.SSH_USERNAME }}@${{ secrets.SSH_HOST }}:~/domains/peptiderepo.com/public_html/staging/wp-content/plugins/peptide-repo-core/
-            --exclude 'phpcs.xml.dist' \
+      - name: Staging health check
-            --exclude 'ARCHITECTURE.md' \
+        run: |
-            --exclude 'CONVENTIONS.md' \
+          sleep 5
-            --exclude 'CHANGELOG.md' \
+          STATUS=$(curl -s -o /dev/null -w "%{http_code}" https://staging.peptiderepo.com/ || echo "000")
+          echo "Staging responded: HTTP $STATUS"
+      - name: Cleanup
+        if: always()
+        run: rm -f ~/.ssh/deploy_key
+
+  deploy-production:
+    name: Deploy to Production
+    needs: [ci, deploy-staging]
+    runs-on: ubuntu-latest
+    environment: production
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup SSH key
+        run: |
+          mkdir -p ~/.ssh
+          echo "${{ secrets.SSH_PRIVATE_KEY }}" > ~/.ssh/deploy_key
+          chmod 600 ~/.ssh/deploy_key
+          ssh-keyscan -p ${{ secrets.SSH_PORT }} ${{ secrets.SSH_HOST }} >> ~/.ssh/known_hosts 2>/dev/null
+      - name: Deploy via rsync → production
+        run: |
+          rsync -avz --delete \
+            --exclude '.git' --exclude '.github' \
+            --exclude 'tests' --exclude 'phpunit.xml.dist' \
+            --exclude 'composer.json' --exclude 'composer.lock' \
+            --exclude 'vendor' --exclude 'phpcs.xml.dist' \
+            --exclude 'ARCHITECTURE.md' --exclude 'CONVENTIONS.md' --exclude 'CHANGELOG.md' \
             -e "ssh -i ~/.ssh/deploy_key -p ${{ secrets.SSH_PORT }}" \
             ./ ${{ secrets.SSH_USERNAME }}@${{ secrets.SSH_HOST }}:~/domains/peptiderepo.com/public_html/wp-content/plugins/peptide-repo-core/
-
       - name: Purge LiteSpeed Cache
         run: |
           ssh -i ~/.ssh/deploy_key -p ${{ secrets.SSH_PORT }} \
             ${{ secrets.SSH_USERNAME }}@${{ secrets.SSH_HOST }} \
             "cd ~/domains/peptiderepo.com/public_html && find wp-content/litespeed/ -type f -delete 2>/dev/null; touch .lscache_purge 2>/dev/null || true"
-
+      - name: Production health check
-      - name: Health check
         run: |
           sleep 5
           STATUS=$(curl -s -o /dev/null -w "%{http_code}" https://peptiderepo.com)
           if [ "$STATUS" != "200" ] && [ "$STATUS" != "403" ]; then
-            echo "ERROR: Site returned unexpected HTTP $STATUS after deploy"
+            echo "ERROR: Site returned HTTP $STATUS"
             exit 1
           fi
-          echo "Site is responsive (HTTP $STATUS)"
+          echo "Production healthy (HTTP $STATUS)"
-
       - name: Cleanup
         if: always()
         run: rm -f ~/.ssh/deploy_key

ARCHITECTURE.md

@@ -1,6 +1,8 @@
 # Peptide Repo Core — Architecture
 
-Peptide Repo Core is a WordPress plugin that provides the canonical peptide data layer for the peptiderepo.com ecosystem. It defines the `pr_peptide` custom post type, custom tables for dosing rows and legal status cells, typed repository classes, an AI candidate queue for semi-automated data extraction, a shared disclaimer component, and JSON-LD structured data output. Every consumer plugin (PR Theme, PRAutoBlogger, Peptide News, Peptide Search AI, and all Tier 1 tools) reads peptide data through this plugin's versioned PHP API, never directly.
+Peptide Repo Core is a WordPress plugin that provides the canonical peptide data layer for the peptiderepo.com ecosystem. It owns the `peptide` custom post type (consolidated in v0.2.0; previously registered by Peptide Search AI pre-schema-sprint — PSA v4.5.0 drops its registration in favor of this one), the `peptide_category` taxonomy, custom tables for dosing rows and legal status cells, typed repository classes, an AI candidate queue for semi-automated data extraction, a shared disclaimer component, and JSON-LD structured data output. Every consumer plugin (PR Theme, PRAutoBlogger, Peptide News, Peptide Search AI, and all Tier 1 tools) reads peptide data through this plugin's versioned PHP API, never directly.
+
+**Ownership model (v0.2.0+).** PR Core is the sole registrant of the `peptide` CPT and `peptide_category` taxonomy. Registration is guarded by `post_type_exists()` / `taxonomy_exists()` so a second registration from any other plugin (historically PSA, which now defers) no-ops cleanly and deploy order between plugins does not matter. See CONVENTIONS.md for the CPT ownership rule.
 
 ---
 
@@ -25,7 +27,7 @@ Peptide Repo Core is a WordPress plugin that provides the canonical peptide data
                                     │
                                     ▼
                          ┌───────────────────────┐
-                         │  Peptide Repository   │  pr_peptide CPT + meta
+                         │  Peptide Repository   │  peptide CPT + meta
                          └──────────┬────────────┘
                                     │
                     ┌───────────────┼───────────────┐
@@ -44,7 +46,7 @@ Peptide Repo Core is a WordPress plugin that provides the canonical peptide data
 ```
 peptide-repo-core/
 ├── peptide-repo-core.php              # Plugin bootstrap — constants, autoloader, activation hooks
-├── uninstall.php                      # Full teardown: tables, posts, terms, options, capabilities
+├── uninstall.php                      # Selective teardown: plugin-owned posts + tables + options + caps
 ├── ARCHITECTURE.md                    # This file
 ├── CONVENTIONS.md                     # Naming patterns, extension guides
 ├── CHANGELOG.md                       # Semantic versioning changelog
@@ -53,7 +55,7 @@ peptide-repo-core/
 │
 ├── .github/
 │   └── workflows/
-│       └── ci.yml                     # PHP lint (8.1-8.3), PHPCS WordPress, 300-line check
+│       └── ci.yml                     # PHP lint (8.1-8.3), PHPCS WordPress, 300-line check, unit tests
 │
 ├── assets/
 │   └── css/
@@ -61,13 +63,13 @@ peptide-repo-core/
 │
 ├── includes/
 │   ├── class-pr-core.php              # Main orchestrator — boots subsystems, registers public filters
-│   ├── class-pr-core-activator.php    # Activation: migrations, capabilities, rewrite flush
+│   ├── class-pr-core-activator.php    # Activation + version-change flush handler
 │   ├── class-pr-core-deactivator.php  # Deactivation: rewrite flush only (data preserved)
 │   ├── class-pr-core-autoloader.php   # SPL autoloader for PR_Core_ prefixed classes
 │   ├── class-pr-core-seed-data.php    # Dev fixture: 3 peptides, 10 dosing rows, 5 legal cells
 │   │
 │   ├── cpt/
-│   │   └── class-pr-core-peptide-cpt.php  # CPT registration, taxonomies, meta fields, sanitizers
+│   │   └── class-pr-core-peptide-cpt.php  # CPT + peptide_category registration (guarded), meta fields, sanitizers
 │   │
 │   ├── migrations/
 │   │   ├── class-pr-core-migration-runner.php           # Sequential migration engine
@@ -82,7 +84,7 @@ peptide-repo-core/
 │   │   └── class-pr-core-candidate-dto.php   # Typed candidate queue value object
 │   │
 │   ├── repositories/
-│   │   ├── class-pr-core-peptide-repository.php          # CRUD for pr_peptide CPT
+│   │   ├── class-pr-core-peptide-repository.php          # CRUD for peptide CPT
 │   │   ├── class-pr-core-dosing-repository.php           # CRUD for pr_dosing_rows
 │   │   ├── class-pr-core-legal-repository.php            # CRUD for pr_legal_cells
 │   │   └── class-pr-core-candidate-queue-repository.php  # CRUD + approve/reject for queue
@@ -101,8 +103,9 @@ peptide-repo-core/
 │       └── class-pr-core-rest-controller.php  # REST endpoints for peptides, dosing, legal
 │
 └── tests/
-    ├── unit/                          # PHPUnit tests (mocked WP)
+    ├── bootstrap.php                  # Lightweight WP function mocks for no-PHPUnit unit runs
-    └── integration/                   # WordPress integration tests
+    └── unit/
+        └── test-peptide-cpt.php       # CPT + taxonomy guard + args payload assertions
 ```
 
 ---
@@ -180,3 +183,16 @@ Single editorial review point. All consumer plugins render the same versioned di
 
 ### #6: JSON-LD from day one
 Drug schema on single pages increases LLM citation rate. Filter hook allows consumer plugins to extend the schema object.
+
+### #7: PR Core owns the `peptide` CPT and `peptide_category` taxonomy (v0.2.0)
+Prior to v0.2.0, PR Core registered `pr_peptide` while Peptide Search AI registered `peptide` — both claimed the public rewrite slug `peptides`, and WP's rewrite resolver picked PR Core's empty CPT, 404'ing all 89 production peptide detail pages. v0.2.0 consolidates both registrations onto a single `peptide` CPT, owned by PR Core. PSA v4.5.0 drops its CPT/taxonomy registration; its meta boxes (`psa_peptide_data`, `psa_extended_data`), directory shortcode, KB article renderer, and search widget continue operating on the shared `peptide` CPT regardless of who registers it. Registration on both sides is guarded with `post_type_exists()` / `taxonomy_exists()` so deploy order is forgiving.
+
+## §2.9 Uninstall specification
+
+PR Core `uninstall.php` removes plugin-owned data only:
+
+1. **Drops custom tables** — `pr_dosing_rows`, `pr_legal_cells`, `pr_ai_candidate_queue`.
+2. **Deletes `peptide` posts only if they carry the `_pr_core_authored` meta flag.** The 89 canonical peptide posts predate PR Core and were authored via PSA; they are never blanket-deleted on PR Core uninstall.
+3. **Does not delete `peptide_category` terms.** Shared-ownership taxonomy; term metadata the site relies on outlasts this plugin.
+4. **Deletes `pr_core_*` options.**
+5. **Removes `manage_peptide_content` capability from all roles.**

CHANGELOG.md

@@ -3,6 +3,77 @@
 All notable changes to Peptide Repo Core are documented here.
 Format: [Semantic Versioning](https://semver.org/).
 
+## [0.3.2] — 2026-04-25
+
+### Fixed
+- Remove `rest_namespace` from peptide CPT registration. Custom namespace prevented Gutenberg block editor from loading peptide posts for editing (404 on wp/v2 REST route). All 89 peptide entries are now editable in the block editor. (#5)
+
+## [0.3.1] — 2026-04-24
+
+### Fixed
+- Add missing `PR_Core_Related_Posts_Provider` interface file (`class-pr-core-related-posts-provider.php`).
+  Omitted from v0.3.0 deploy caused a fatal on every page load. Site was down until this fix.
+
+## [0.3.0] — 2026-04-24
+
+### Added
+- **Related Articles feature** — New `peptide_topic` taxonomy links blog posts to peptides by slug. Posts tagged with a peptide's slug appear as a related articles card grid on single peptide pages.
+- `PR_Core_Internal_Posts_Provider` — Fetches related posts via taxonomy matching, with fallback to full-text search. Results cached 1 hour per peptide.
+- `PR_Core_Related_Posts_Section` — Renders the related articles section on peptide single pages via `pr_core_after_peptide_content` action. Respects admin settings for feature toggle and display limit.
+- `PR_Core_Settings` — Admin settings page under Peptides menu. Allows enable/disable of related articles and configuration of display limit (1-6, default 3).
+- Template part `template-parts/related-posts/card.php` — Card layout for individual related articles with featured image (16:9), badge, title, date, and excerpt.
+- CSS file `assets/css/related-posts.css` — Responsive grid (3 cols desktop, 2 tablet, 1 mobile), `prefers-reduced-motion` respected, scoped to `.pr-related-posts`.
+- Unit tests for `PR_Core_Internal_Posts_Provider` — Tests taxonomy matching, fallback search, limit enforcement, and transient caching.
+- `PR_Core_Peptide_CPT::TAX_TOPIC` constant for the new `peptide_topic` taxonomy.
+
+### Changed
+- `PR_Core_Peptide_CPT::register_taxonomies()` now registers both `peptide_category` (peptide → peptide) and `peptide_topic` (post → peptide) taxonomies.
+- `PR_Core_Admin` now instantiates and hooks `PR_Core_Settings` for configuration.
+- `PR_Core::init()` instantiates `PR_Core_Related_Posts_Section` and enqueues `related-posts.css` on single peptide pages.
+- `PR_Core::init()` docblock updated to list `PR_Core_Related_Posts_Section` as a dependency.
+- Version bumped to `0.3.0`.
+
+### Notes
+- The `pr_core_after_peptide_content` action must be called in peptide single-page templates to display the related articles section. This hook fires after the main peptide content.
+- Blog posts can be tagged with `peptide_topic` terms matching any peptide's slug (e.g., 'bpc-157', 'tb-500') to appear as related articles on that peptide's page.
+- Feature is enabled by default but can be toggled in PR Core Settings (Peptides > Settings).
+- Related articles transient caches are invalidated whenever any blog post is saved (via `save_post_post` hook).
+
+## [0.2.1] — 2026-04-22
+
+### Fixed
+- **P1 hotfix: fatal `Undefined constant PR_Core_Peptide_CPT::TAX_FAMILY` on every peptide page.** The v0.2.0 release removed `TAX_FAMILY` from `PR_Core_Peptide_CPT` but left two stale references in `PR_Core_Peptide_Repository` (the `family` filter branch in `find_all()` and the families lookup in `post_to_dto()`). JSON-LD emission on single-peptide templates called `find_by_id()`, which called `post_to_dto()`, which hit the undefined constant and killed page rendering mid-`wp_head()`. QA gate on `874f93b` missed this because the unit tests cover the CPT class in isolation, not the repository's consumption of its constants. Post-mortem + QA checklist update to follow.
+
+### Changed
+- `PR_Core_Peptide_Repository::find_all()` — `family` filter is now silently ignored rather than throwing. Next minor bump will remove it from the REST schema.
+- `PR_Core_Peptide_DTO::$families` is preserved but always populated as `[]`. Keeps REST response shape stable for existing clients; will be dropped with a release note.
+
+## [0.2.0] — 2026-04-22
+
+### Changed (BREAKING)
+- CPT renamed from `pr_peptide` to `peptide`. Consolidates with PSA's existing `peptide` CPT which owns the 89 canonical peptide posts on production.
+- Taxonomy renamed from `pr_peptide_category` to `peptide_category`. Same reason.
+- CPT args harmonized as superset of PSA + prior PR Core registration (supports now includes thumbnail + revisions + custom-fields).
+- Defensive registration: guards with `post_type_exists()` / `taxonomy_exists()` so PSA's parallel registration no-ops cleanly during the PSA v4.5.0 transition.
+
+### Added
+- `PR_Core_Activator::maybe_flush_on_version_change()` — one-shot rewrite flush on in-place version bumps (hooked at `init` priority 999). Eliminates the need for a manual `wp rewrite flush` after updates that change CPT/taxonomy slugs.
+- `_pr_core_authored` post-meta flag contract — peptide posts created via PR Core UI carry this flag; `uninstall.php` uses it to scope teardown to plugin-owned posts only.
+- Lightweight unit-test harness (`tests/bootstrap.php` + `tests/unit/test-peptide-cpt.php`) that exercises CPT/taxonomy guards and args payload shape without a PHPUnit + wp-env dependency. Wired into the existing PHP-lint CI job.
+
+### Removed
+- `pr_peptide_family` taxonomy — never populated, never surfaced in UI.
+- All `pr_peptide*` CPT-slug-derived references (constants, docblock mentions, uninstall string literals).
+- Blanket `DELETE FROM posts WHERE post_type = 'pr_peptide'` on uninstall. Replaced with a join-on-`_pr_core_authored` selective delete so PSA-authored peptide posts are never destroyed by PR Core teardown.
+- Taxonomy-term cleanup on uninstall. `peptide_category` is shared ownership post-v0.2.0; term data the site still needs is preserved.
+
+### Fixed
+- Production peptide detail pages (all 89) were 404'ing due to a rewrite slug collision between PSA's `peptide` CPT and PR Core's `pr_peptide` CPT both claiming `/peptides/%postname%/`. PR Core v0.1.1's empty `pr_peptide` CPT was winning the rewrite resolution. This release consolidates both to a single `peptide` CPT owned by PR Core.
+
+### Notes
+- Scope of the `pr_peptide*` scrub is intentionally narrow: CPT-slug-derived identifiers only. Class names (`PR_Core_Peptide_CPT`), file names (`class-pr-core-peptide-cpt.php`), plugin constants (`PR_CORE_VERSION`), option keys (`pr_core_*`), and the REST namespace (`pr-core/v1`) are the plugin's own namespace, not the CPT slug, and are preserved verbatim.
+- PR Core-defined meta keys (`display_name`, `aliases`, `evidence_strength`, `editorial_review_status`, …) are gated by `manage_peptide_content`. The activator grants this capability to `administrator` and `editor` roles on activation. Prod sites where the activation hook never fired (v0.1.1 was deployed manually) will receive the grant on next `wp plugin activate peptide-repo-core`. Follow-up thread to decide whether a dedicated `peptide_editor` role is more appropriate than extending core `editor`.
+
 ## [0.1.1] — 2026-04-19
 
 ### Fixed

CONVENTIONS.md

@@ -61,3 +61,14 @@ Values: `prescription`, `ruo`, `otc`, `restricted`, `banned`, `unclear`. Validat
 ## Supersede Pattern (Soft Delete)
 
 Dosing rows and legal cells use a `superseded_by_id` column instead of hard deletes. When a correction is needed, the old row gets `superseded_by_id` set to the new row's ID. Queries for "active" data filter on `superseded_by_id IS NULL`. This preserves full audit history.
+
+## CPT Ownership
+
+- **One plugin owns each CPT.** PR Core owns the `peptide` CPT and the `peptide_category` taxonomy (as of v0.2.0). No other plugin in this ecosystem registers these post types or taxonomies directly.
+- **All registrations must guard with existence checks.** CPT registrations call `if ( post_type_exists( $slug ) ) return;` before `register_post_type()`, and taxonomy registrations call `if ( taxonomy_exists( $slug ) ) return;` before `register_taxonomy()`. This makes deploy order between plugins irrelevant — whichever runs first wins, the other no-ops — and prevents rewrite-slug collisions when two plugins temporarily overlap during a transition.
+- **Consumers read, do not register.** Plugins that need to query or display `peptide` posts (PSA, PR Theme, PRAutoBlogger, Peptide News, Tier 1 tools) call `get_posts( [ 'post_type' => 'peptide' ] )` / `WP_Query` without registering the CPT themselves. If a consumer plugin needs its own custom post type for a different domain (e.g., `reconstitution_protocol`), it registers its own slug and does not touch `peptide`.
+- **Meta keys are plugin-namespaced, not CPT-namespaced.** PR Core writes `_pr_core_*` or bare keys registered via `register_post_meta()`. PSA writes `psa_*`. The two namespaces coexist on the same `peptide` post because they don't collide.
+
+## `_pr_core_authored` Flag
+
+Any `peptide` post created via PR Core's own UI (not authored via PSA's meta boxes) must be tagged with post-meta key `_pr_core_authored` = `1`. This is the flag `uninstall.php` uses to scope teardown to plugin-owned posts only. Posts originating from PSA (the 89 canonical peptide monographs on production) do not carry this flag and are never deleted on PR Core uninstall.

assets/css/related-posts.css

@@ -0,0 +1,192 @@
+/**
+ * Related Posts Section Styles
+ * Scoped to .pr-related-posts
+ */
+
+:root {
+	color-scheme: light;
+}
+
+.pr-related-posts {
+	margin-top: 3rem;
+	padding: 2rem 0;
+	border-top: 1px solid var(--wp--preset--color--border, #e5e5e5);
+}
+
+.pr-related-posts h2 {
+	font-size: 1.5rem;
+	font-weight: 600;
+	margin-bottom: 1.5rem;
+	line-height: 1.3;
+}
+
+.pr-related-posts__grid {
+	display: grid;
+	grid-template-columns: repeat(3, 1fr);
+	gap: 1.5rem;
+	margin-bottom: 1rem;
+}
+
+.pr-related-posts__card {
+	display: flex;
+	flex-direction: column;
+	background: white;
+	border: 1px solid var(--wp--preset--color--border, #e5e5e5);
+	border-radius: 0.5rem;
+	overflow: hidden;
+	transition: box-shadow 0.3s ease, transform 0.3s ease;
+}
+
+.pr-related-posts__card:hover {
+	box-shadow: 0 2px 8px rgba(0, 0, 0, 0.1);
+	transform: translateY(-2px);
+}
+
+@media (prefers-reduced-motion: reduce) {
+	.pr-related-posts__card {
+		transition: none;
+	}
+
+	.pr-related-posts__card:hover {
+		transform: none;
+	}
+}
+
+.pr-related-posts__image {
+	position: relative;
+	overflow: hidden;
+	padding-bottom: 56.25%;
+	/* 16:9 aspect ratio */
+	background: var(--wp--preset--color--base, #f5f5f5);
+}
+
+.pr-related-posts__image--fallback {
+	display: flex;
+	align-items: center;
+	justify-content: center;
+	padding-bottom: 0;
+	height: 200px;
+}
+
+.pr-related-posts__image-element {
+	position: absolute;
+	top: 0;
+	left: 0;
+	width: 100%;
+	height: 100%;
+	object-fit: cover;
+	object-position: center;
+}
+
+.pr-related-posts__image--fallback .pr-related-posts__image-element {
+	position: static;
+	width: auto;
+	height: 80px;
+	max-width: 100%;
+}
+
+.pr-related-posts__content {
+	display: flex;
+	flex-direction: column;
+	flex: 1;
+	padding: 1rem;
+}
+
+.pr-related-posts__badge {
+	display: inline-block;
+	font-size: 0.75rem;
+	font-weight: 700;
+	letter-spacing: 0.05em;
+	text-transform: uppercase;
+	color: #666;
+	margin-bottom: 0.5rem;
+}
+
+.pr-related-posts__title {
+	font-size: 1.125rem;
+	font-weight: 600;
+	line-height: 1.4;
+	margin-bottom: 0.5rem;
+}
+
+.pr-related-posts__title a {
+	color: var(--wp--preset--color--heading, #000);
+	text-decoration: none;
+}
+
+.pr-related-posts__title a:hover {
+	text-decoration: underline;
+}
+
+.pr-related-posts__date {
+	font-size: 0.875rem;
+	color: #999;
+	margin-bottom: 0.75rem;
+}
+
+.pr-related-posts__excerpt {
+	font-size: 0.9375rem;
+	line-height: 1.5;
+	color: #666;
+	margin: 0;
+	flex-grow: 1;
+}
+
+.pr-related-posts__view-all {
+	text-align: center;
+	margin-top: 1rem;
+	font-size: 1rem;
+}
+
+.pr-related-posts__view-all a {
+	color: var(--wp--preset--color--primary, #0073aa);
+	text-decoration: none;
+	font-weight: 600;
+}
+
+.pr-related-posts__view-all a:hover {
+	text-decoration: underline;
+}
+
+/* Tablet: 2 columns */
+@media (max-width: 768px) {
+	.pr-related-posts__grid {
+		grid-template-columns: repeat(2, 1fr);
+		gap: 1rem;
+	}
+
+	.pr-related-posts h2 {
+		font-size: 1.25rem;
+	}
+
+	.pr-related-posts {
+		margin-top: 2rem;
+		padding: 1.5rem 0;
+	}
+}
+
+/* Mobile: 1 column */
+@media (max-width: 480px) {
+	.pr-related-posts__grid {
+		grid-template-columns: 1fr;
+		gap: 1rem;
+	}
+
+	.pr-related-posts h2 {
+		font-size: 1.125rem;
+		margin-bottom: 1rem;
+	}
+
+	.pr-related-posts {
+		margin-top: 1.5rem;
+		padding: 1rem 0;
+	}
+
+	.pr-related-posts__content {
+		padding: 0.75rem;
+	}
+
+	.pr-related-posts__title {
+		font-size: 1rem;
+	}
+}

includes/admin/class-pr-core-admin-columns.php

@@ -2,7 +2,7 @@
 declare(strict_types=1);
 
 /**
- * Custom admin list-table columns for the pr_peptide CPT.
+ * Custom admin list-table columns for the peptide CPT.
  *
  * What: Adds evidence strength, editorial status, and dosing count columns.
  * Who calls it: PR_Core_Admin via manage_posts_columns and custom_column hooks.

includes/admin/class-pr-core-admin.php

@@ -4,13 +4,16 @@ declare(strict_types=1);
 /**
  * Admin initialization and hook registration.
  *
- * What: Registers admin menu pages, meta boxes, and custom columns for peptides.
+ * What: Registers admin menu pages, meta boxes, custom columns, and settings
+ *       for peptides and related features.
  * Who calls it: PR_Core::init() when is_admin().
- * Dependencies: PR_Core_Peptide_Metaboxes, PR_Core_Candidate_Queue_Page, PR_Core_Admin_Columns.
+ * Dependencies: PR_Core_Peptide_Metaboxes, PR_Core_Candidate_Queue_Page,
+ *               PR_Core_Admin_Columns, PR_Core_Settings.
  *
  * @see admin/class-pr-core-peptide-metaboxes.php    — Dosing + legal meta boxes.
  * @see admin/class-pr-core-candidate-queue-page.php — Candidate review screen.
  * @see admin/class-pr-core-admin-columns.php        — Custom list-table columns.
+ * @see admin/class-pr-core-settings.php             — Plugin settings page.
  */
 class PR_Core_Admin {
 
@@ -30,6 +33,9 @@ class PR_Core_Admin {
 		add_filter( 'manage_' . PR_Core_Peptide_CPT::POST_TYPE . '_posts_columns', [ $columns, 'add_columns' ] );
 		add_action( 'manage_' . PR_Core_Peptide_CPT::POST_TYPE . '_posts_custom_column', [ $columns, 'render_column' ], 10, 2 );
 
+		$settings = new PR_Core_Settings();
+		$settings->register_hooks();
+
 		add_action( 'admin_menu', [ $this, 'add_admin_pages' ] );
 		add_action( 'admin_enqueue_scripts', [ $this, 'enqueue_admin_styles' ] );
 	}

includes/admin/class-pr-core-peptide-metaboxes.php

@@ -4,7 +4,7 @@ declare(strict_types=1);
 /**
  * Meta boxes for the peptide edit screen: scientific identifiers, dosing, and legal.
  *
- * What: Renders and saves three meta boxes on the pr_peptide edit screen.
+ * What: Renders and saves three meta boxes on the peptide edit screen.
  * Who calls it: PR_Core_Admin via add_meta_boxes and save_post hooks.
  * Dependencies: PR_Core_Dosing_Repository, PR_Core_Legal_Repository.
  *

includes/admin/class-pr-core-settings.php

@@ -0,0 +1,176 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Settings page for PR Core plugin features.
+ *
+ * What: Registers admin menu, renders settings form, and handles option saves
+ *       for features like Related Articles.
+ * Who calls it: PR_Core_Admin::register_hooks().
+ * Dependencies: None (reads/writes wp_options).
+ */
+class PR_Core_Settings {
+
+	/** @var string Option key: enable/disable related articles. */
+	private const ENABLED_OPTION = 'pr_core_related_posts_enabled';
+
+	/** @var string Option key: related articles limit (1-6). */
+	private const LIMIT_OPTION = 'pr_core_related_posts_limit';
+
+	/**
+	 * Register admin page and settings hooks.
+	 *
+	 * @return void
+	 */
+	public function register_hooks(): void {
+		add_action( 'admin_menu', [ $this, 'add_settings_page' ] );
+		add_action( 'admin_init', [ $this, 'register_settings' ] );
+	}
+
+	/**
+	 * Add submenu page under Peptides.
+	 *
+	 * @return void
+	 */
+	public function add_settings_page(): void {
+		add_submenu_page(
+			'edit.php?post_type=' . PR_Core_Peptide_CPT::POST_TYPE,
+			__( 'PR Core Settings', 'peptide-repo-core' ),
+			__( 'Settings', 'peptide-repo-core' ),
+			'manage_options',
+			'pr-core-settings',
+			[ $this, 'render_page' ]
+		);
+	}
+
+	/**
+	 * Register settings fields.
+	 *
+	 * @return void
+	 */
+	public function register_settings(): void {
+		register_setting(
+			'pr_core_settings',
+			self::ENABLED_OPTION,
+			[
+				'type'              => 'boolean',
+				'default'           => true,
+				'sanitize_callback' => 'rest_sanitize_boolean',
+			]
+		);
+
+		register_setting(
+			'pr_core_settings',
+			self::LIMIT_OPTION,
+			[
+				'type'              => 'integer',
+				'default'           => 3,
+				'sanitize_callback' => [ $this, 'sanitize_limit' ],
+			]
+		);
+
+		add_settings_section(
+			'pr_core_related_articles',
+			__( 'Related Articles', 'peptide-repo-core' ),
+			[ $this, 'render_section' ],
+			'pr_core_settings'
+		);
+
+		add_settings_field(
+			self::ENABLED_OPTION,
+			__( 'Enable Related Articles', 'peptide-repo-core' ),
+			[ $this, 'render_enabled_field' ],
+			'pr_core_settings',
+			'pr_core_related_articles'
+		);
+
+		add_settings_field(
+			self::LIMIT_OPTION,
+			__( 'Number of Articles to Display', 'peptide-repo-core' ),
+			[ $this, 'render_limit_field' ],
+			'pr_core_settings',
+			'pr_core_related_articles'
+		);
+	}
+
+	/**
+	 * Render the settings page.
+	 *
+	 * @return void
+	 */
+	public function render_page(): void {
+		?>
+		<div class="wrap">
+			<h1><?php esc_html_e( 'Peptide Repo Core Settings', 'peptide-repo-core' ); ?></h1>
+			<form method="post" action="options.php">
+				<?php
+				settings_fields( 'pr_core_settings' );
+				do_settings_sections( 'pr_core_settings' );
+				submit_button();
+				?>
+			</form>
+		</div>
+		<?php
+	}
+
+	/**
+	 * Render section description.
+	 *
+	 * @return void
+	 */
+	public function render_section(): void {
+		echo '<p>' . esc_html__( 'Configure the Related Articles section that appears on peptide single pages.', 'peptide-repo-core' ) . '</p>';
+	}
+
+	/**
+	 * Render enabled toggle field.
+	 *
+	 * @return void
+	 */
+	public function render_enabled_field(): void {
+		$checked = (bool) get_option( self::ENABLED_OPTION, true );
+		?>
+		<input
+			type="checkbox"
+			name="<?php echo esc_attr( self::ENABLED_OPTION ); ?>"
+			value="1"
+			<?php checked( $checked, true ); ?>
+		/>
+		<label>
+			<?php esc_html_e( 'Display related articles on peptide pages', 'peptide-repo-core' ); ?>
+		</label>
+		<?php
+	}
+
+	/**
+	 * Render limit field.
+	 *
+	 * @return void
+	 */
+	public function render_limit_field(): void {
+		$limit = (int) get_option( self::LIMIT_OPTION, 3 );
+		?>
+		<input
+			type="number"
+			name="<?php echo esc_attr( self::LIMIT_OPTION ); ?>"
+			value="<?php echo esc_attr( (string) $limit ); ?>"
+			min="1"
+			max="6"
+		/>
+		<p class="description">
+			<?php esc_html_e( 'Number of articles to display (1-6). Default: 3.', 'peptide-repo-core' ); ?>
+		</p>
+		<?php
+	}
+
+	/**
+	 * Sanitize limit to 1-6 range.
+	 *
+	 * @param mixed $value Raw input.
+	 * @return int Sanitized value.
+	 */
+	public function sanitize_limit( $value ): int {
+		$limit = (int) $value;
+		return min( 6, max( 1, $limit ) );
+	}
+}

includes/class-pr-core-activator.php

@@ -5,17 +5,26 @@ declare(strict_types=1);
  * Plugin activation handler.
  *
  * What: Runs migrations, adds capabilities, flushes rewrite rules.
- * Who calls it: register_activation_hook() in peptide-repo-core.php.
+ *       Also detects version changes on subsequent init cycles and re-flushes
- * Dependencies: PR_Core_Migration_Runner.
+ *       rewrite rules once so in-place plugin updates (without a deactivate +
+ *       reactivate cycle) still pick up CPT/taxonomy slug changes.
+ * Who calls it: register_activation_hook() in peptide-repo-core.php; and
+ *               PR_Core::init() registers maybe_flush_on_version_change on init:999.
+ * Dependencies: PR_Core_Migration_Runner, PR_Core_Peptide_CPT.
  *
  * @see peptide-repo-core.php — Registers this class on activation.
+ * @see includes/class-pr-core.php — Wires the init:999 version-change handler.
  */
 class PR_Core_Activator {
 
+	/** @var string Option key storing the last activated/seen plugin version. */
+	private const VERSION_OPTION = 'pr_core_version';
+
 	/**
 	 * Run on plugin activation.
 	 *
-	 * Side effects: database table creation, capability grants, rewrite flush.
+	 * Side effects: database table creation, capability grants, rewrite flush,
+	 *               pr_core_version option write.
 	 *
 	 * @return void
 	 */
@@ -32,7 +41,39 @@ class PR_Core_Activator {
 		self::add_capabilities();
 
 		// Flush rewrite rules for the new CPT.
-		flush_rewrite_rules();
+		flush_rewrite_rules( false );
+
+		// Record the activated version so the init:999 drift handler can
+		// detect future in-place updates and re-flush without a manual
+		// deactivate/reactivate cycle.
+		update_option( self::VERSION_OPTION, PR_CORE_VERSION, false );
+	}
+
+	/**
+	 * Detect in-place plugin version changes and flush rewrite rules once.
+	 *
+	 * Wired to init:999 so all CPTs + taxonomies (ours and anyone else's)
+	 * are registered before the flush. When the option is absent (first
+	 * install that bypassed the activation hook — e.g., manual SCP deploy)
+	 * or is older than the current constant, we flush once and update.
+	 *
+	 * Side effects: may call flush_rewrite_rules( false ); updates option.
+	 *
+	 * @return void
+	 */
+	public static function maybe_flush_on_version_change(): void {
+		if ( ! defined( 'PR_CORE_VERSION' ) ) {
+			return;
+		}
+
+		$recorded = get_option( self::VERSION_OPTION, '' );
+
+		if ( PR_CORE_VERSION === $recorded ) {
+			return;
+		}
+
+		flush_rewrite_rules( false );
+		update_option( self::VERSION_OPTION, PR_CORE_VERSION, false );
 	}
 
 	/**

includes/class-pr-core.php

@@ -6,11 +6,12 @@ declare(strict_types=1);
  *
  * What: Registers all hooks, runs migrations, boots subsystems.
  * Who calls it: peptide-repo-core.php on plugins_loaded.
- * Dependencies: PR_Core_Migration_Runner, PR_Core_Peptide_CPT, PR_Core_Admin,
+ * Dependencies: PR_Core_Migration_Runner, PR_Core_Peptide_CPT, PR_Core_Topic_Taxonomy,
- *               PR_Core_Disclaimer, PR_Core_Jsonld, PR_Core_Rest_Controller.
+ *              PR_Core_Admin, PR_Core_Disclaimer, PR_Core_Jsonld,
+ *              PR_Core_Rest_Controller, PR_Core_Related_Posts_Section.
  *
  * @see peptide-repo-core.php — Bootstrap that instantiates this class.
- * @see ARCHITECTURE.md       — Full data flow diagram.
+ * @see ARCHITECTURE.md    — Full data flow diagram.
  */
 class PR_Core {
 
@@ -30,6 +31,16 @@ class PR_Core {
 		$cpt = new PR_Core_Peptide_CPT();
 		$cpt->register_hooks();
 
+		// Register peptide_topic taxonomy (fires on init).
+		$topic_tax = new PR_Core_Topic_Taxonomy();
+		$topic_tax->register_hooks();
+
+		// One-shot rewrite flush on in-place version bumps. Runs at the very
+		// end of init (priority 999) so all CPTs/taxonomies — ours and
+		// anyone else's — are registered first. Handles updates deployed
+		// without a deactivate/reactivate cycle (e.g., SCP/rsync pushes).
+		add_action( 'init', [ PR_Core_Activator::class, 'maybe_flush_on_version_change' ], 999 );
+
 		// Admin UI (fires on admin_init, admin_menu).
 		if ( is_admin() ) {
 			$admin = new PR_Core_Admin();
@@ -43,6 +54,15 @@ class PR_Core {
 		$jsonld = new PR_Core_Jsonld();
 		$jsonld->register_hooks();
 
+		// Related Articles section (frontend).
+		$related_posts = new PR_Core_Related_Posts_Section(
+			new PR_Core_Internal_Posts_Provider()
+		);
+		$related_posts->register_hooks();
+
+		// Enqueue related-posts CSS on single peptide pages.
+		add_action( 'wp_enqueue_scripts', [ $this, 'enqueue_frontend_styles' ] );
+
 		// REST API.
 		$rest = new PR_Core_Rest_Controller();
 		$rest->register_hooks();
@@ -51,6 +71,24 @@ class PR_Core {
 		$this->register_public_filters();
 	}
 
+	/**
+	 * Enqueue frontend CSS on single peptide pages.
+	 *
+	 * @return void
+	 */
+	public function enqueue_frontend_styles(): void {
+		if ( ! is_singular( PR_Core_Peptide_CPT::POST_TYPE ) ) {
+			return;
+		}
+
+		wp_enqueue_style(
+			'pr-core-related-posts',
+			PR_CORE_PLUGIN_URL . 'assets/css/related-posts.css',
+			[],
+			PR_CORE_VERSION
+		);
+	}
+
 	/**
 	 * Register the public filter hooks that consumer plugins rely on.
 	 *
@@ -95,7 +133,7 @@ class PR_Core {
 	/**
 	 * Return disclaimer text for a given surface identifier.
 	 *
-	 * @param string $text    Existing text (empty string default).
+	 * @param string $text     Existing text (empty string default).
 	 * @param string $surface Surface identifier (dosing, legal, reconstitution, ai-answer).
 	 * @return string Disclaimer HTML.
 	 */
@@ -106,18 +144,18 @@ class PR_Core {
 	/**
 	 * Map evidence_strength enum value to human-readable label.
 	 *
-	 * @param string $label    Existing label (empty string default).
+	 * @param string $label     Existing label (empty string default).
 	 * @param string $strength Enum value.
 	 * @return string Localized label.
 	 */
 	public function filter_evidence_label( string $label, string $strength ): string {
 		$map = [
-			'preclinical'   => __( 'Preclinical', 'peptide-repo-core' ),
+			'preclinical'    => __( 'Preclinical', 'peptide-repo-core' ),
-			'case-series'   => __( 'Case Series', 'peptide-repo-core' ),
+			'case-series'    => __( 'Case Series', 'peptide-repo-core' ),
-			'observational' => __( 'Observational', 'peptide-repo-core' ),
+			'observational'  => __( 'Observational', 'peptide-repo-core' ),
-			'rct-small'     => __( 'Small RCT', 'peptide-repo-core' ),
+			'rct-small'      => __( 'Small RCT', 'peptide-repo-core' ),
-			'rct-large'     => __( 'Large RCT', 'peptide-repo-core' ),
+			'rct-large'      => __( 'Large RCT', 'peptide-repo-core' ),
-			'meta-analysis' => __( 'Meta-Analysis', 'peptide-repo-core' ),
+			'meta-analysis'  => __( 'Meta-Analysis', 'peptide-repo-core' ),
 		];
 
 		return $map[ $strength ] ?? $strength;

includes/core/class-pr-core-internal-posts-provider.php

@@ -0,0 +1,102 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Fetches posts related to a peptide via taxonomy and fallback text search.
+ *
+ * What: Implements PR_Core_Related_Posts_Provider by querying posts tagged
+ *       with the peptide's slug as a peptide_topic term. Falls back to
+ *       full-text search if no taxonomy matches found.
+ * Who calls it: PR_Core_Related_Posts_Section instantiates and calls this.
+ * Dependencies: PR_Core_Related_Posts_Provider interface, WP_Query,
+ *               peptide_topic taxonomy.
+ *
+ * @see includes/interfaces/interface-related-posts-provider.php
+ * @see includes/core/class-related-posts-section.php
+ */
+class PR_Core_Internal_Posts_Provider implements PR_Core_Related_Posts_Provider {
+
+	/**
+	 * Get posts related to a peptide.
+	 *
+	 * 1. Queries posts tagged with the peptide slug as a peptide_topic term.
+	 * 2. If 0 posts found, falls back to full-text search on post_title.
+	 * 3. Caches result as a transient (1 hour TTL).
+	 * 4. Never exceeds $limit posts.
+	 *
+	 * Side effects: Sets/updates transient cache for this peptide.
+	 *
+	 * @param int $peptide_id The peptide post ID.
+	 * @param int $limit      Maximum number of posts to return.
+	 * @return array<int, \WP_Post> Array of WP_Post objects (may be empty).
+	 */
+	public function get_posts( int $peptide_id, int $limit ): array {
+		$peptide = get_post( $peptide_id );
+		if ( ! $peptide || 'peptide' !== $peptide->post_type ) {
+			return [];
+		}
+
+		$cache_key = 'pr_core_related_' . $peptide_id;
+		$cached    = get_transient( $cache_key );
+		if ( is_array( $cached ) ) {
+			return array_slice( $cached, 0, $limit );
+		}
+
+		// Primary: query posts tagged with peptide's slug as peptide_topic.
+		$posts = $this->query_by_taxonomy( $peptide->post_name, $limit );
+
+		// Fallback: if empty, search by peptide title.
+		if ( empty( $posts ) ) {
+			$posts = $this->query_by_search( $peptide->post_title, $limit );
+		}
+
+		// Cache for 1 hour.
+		set_transient( $cache_key, $posts, HOUR_IN_SECONDS );
+
+		return $posts;
+	}
+
+	/**
+	 * Query posts tagged with a specific peptide_topic term.
+	 *
+	 * @param string $peptide_slug The peptide's post_name (slug).
+	 * @param int    $limit        Maximum posts to return.
+	 * @return array<int, \WP_Post>
+	 */
+	private function query_by_taxonomy( string $peptide_slug, int $limit ): array {
+		$query = new WP_Query( [
+			'post_type'      => 'post',
+			'posts_per_page' => $limit,
+			'orderby'        => 'date',
+			'order'          => 'DESC',
+			'tax_query'      => [
+				[
+					'taxonomy' => 'peptide_topic',
+					'field'    => 'slug',
+					'terms'    => $peptide_slug,
+				],
+			],
+		] );
+
+		return $query->posts ?: [];
+	}
+
+	/**
+	 * Fallback: query posts by full-text search on post_title.
+	 *
+	 * @param string $search_term The peptide's display title.
+	 * @param int    $limit       Maximum posts to return.
+	 * @return array<int, \WP_Post>
+	 */
+	private function query_by_search( string $search_term, int $limit ): array {
+		$query = new WP_Query( [
+			'post_type'      => 'post',
+			'posts_per_page' => $limit,
+			'orderby'        => 'date',
+			'order'          => 'DESC',
+			's'              => $search_term,
+		] );
+
+		return $query->posts ?: [];
+	}
+}

includes/core/class-pr-core-related-posts-provider.php

@@ -0,0 +1,24 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Contract for any provider that retrieves posts related to a peptide.
+ *
+ * What: Interface defining the get_posts() contract for related-post providers.
+ * Who calls it: PR_Core_Related_Posts_Section accepts any implementation.
+ * Dependencies: None.
+ *
+ * @see includes/core/class-pr-core-internal-posts-provider.php — default implementation.
+ * @see includes/core/class-pr-core-related-posts-section.php   — consumer.
+ */
+interface PR_Core_Related_Posts_Provider {
+
+	/**
+	 * Get posts related to a peptide.
+	 *
+	 * @param int $peptide_id The peptide post ID.
+	 * @param int $limit      Maximum number of posts to return.
+	 * @return array<int, \WP_Post> Array of WP_Post objects (may be empty).
+	 */
+	public function get_posts( int $peptide_id, int $limit ): array;
+}

includes/core/class-pr-core-related-posts-section.php

@@ -0,0 +1,126 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Renders the related articles section on peptide single pages.
+ *
+ * What: Hooks into pr_core_after_peptide_content and renders a card grid
+ *       of related posts fetched via PR_Core_Related_Posts_Provider.
+ * Who calls it: PR_Core::init() instantiates and registers hooks.
+ * Dependencies: PR_Core_Related_Posts_Provider interface, template-parts/related-posts/card.php.
+ *
+ * Settings read:
+ * - pr_core_related_posts_enabled (bool, default true)
+ * - pr_core_related_posts_limit (int, default 3, range 1-6)
+ */
+class PR_Core_Related_Posts_Section {
+
+	/** @var PR_Core_Related_Posts_Provider */
+	private $provider;
+
+	/**
+	 * Constructor.
+	 *
+	 * @param PR_Core_Related_Posts_Provider $provider Provider instance.
+	 */
+	public function __construct( PR_Core_Related_Posts_Provider $provider ) {
+		$this->provider = $provider;
+	}
+
+	/**
+	 * Register the action hook.
+	 *
+	 * @return void
+	 */
+	public function register_hooks(): void {
+		add_action( 'pr_core_after_peptide_content', [ $this, 'render' ] );
+		add_action( 'save_post_post', [ $this, 'invalidate_caches' ] );
+	}
+
+	/**
+	 * Render the related posts section.
+	 *
+	 * Called via do_action( 'pr_core_after_peptide_content', $peptide_id ) in templates.
+	 * If feature disabled or no posts found, renders nothing.
+	 *
+	 * @param int $peptide_id The peptide post ID.
+	 * @return void
+	 */
+	public function render( int $peptide_id ): void {
+		$enabled = (bool) get_option( 'pr_core_related_posts_enabled', true );
+		if ( ! $enabled ) {
+			return;
+		}
+
+		$limit = (int) get_option( 'pr_core_related_posts_limit', 3 );
+		$limit = min( 6, max( 1, $limit ) );
+
+		$posts = $this->provider->get_posts( $peptide_id, $limit + 5 );
+		if ( empty( $posts ) ) {
+			return;
+		}
+
+		$peptide = get_post( $peptide_id );
+		?>
+		<section class="pr-related-posts" aria-label="<?php esc_attr_e( 'Related Articles', 'peptide-repo-core' ); ?>">
+			<h2><?php esc_html_e( 'Related Articles', 'peptide-repo-core' ); ?></h2>
+			<div class="pr-related-posts__grid">
+				<?php
+				$count = 0;
+				foreach ( $posts as $post ) {
+					if ( $count >= $limit ) {
+						break;
+					}
+					setup_postdata( $post );
+					get_template_part( 'template-parts/related-posts/card', null, [ 'post' => $post ] );
+					++$count;
+				}
+				wp_reset_postdata();
+				?>
+			</div>
+			<?php
+			if ( count( $posts ) > $limit && $peptide ) {
+				$term = get_term_by( 'slug', $peptide->post_name, 'peptide_topic' );
+				if ( $term ) {
+					$archive_url = get_term_link( $term );
+					if ( ! is_wp_error( $archive_url ) ) {
+						?>
+						<p class="pr-related-posts__view-all">
+							<a href="<?php echo esc_url( $archive_url ); ?>">
+								<?php
+								echo wp_kses_post(
+									sprintf(
+										__( 'View all %s articles &rarr;', 'peptide-repo-core' ),
+										esc_html( $peptide->post_title )
+									)
+								);
+								?>
+							</a>
+						</p>
+						<?php
+					}
+				}
+			}
+			?>
+		</section>
+		<?php
+	}
+
+	/**
+	 * Invalidate related posts transient caches when a post is saved.
+	 *
+	 * Hooks into save_post_post to clear any cached related-post queries
+	 * since the post corpus has changed.
+	 *
+	 * @return void
+	 */
+	public function invalidate_caches(): void {
+		global $wpdb;
+		$cache_keys = $wpdb->get_col(
+			"SELECT option_name FROM {$wpdb->options} WHERE option_name LIKE 'pr_core_related_%'"
+		);
+		foreach ( $cache_keys as $key ) {
+			delete_transient( str_replace( '_transient_', '', $key ) );
+		}
+	}
+}

includes/cpt/class-pr-core-peptide-cpt.php

@@ -2,25 +2,30 @@
 declare(strict_types=1);
 
 /**
- * Registers the pr_peptide custom post type and associated taxonomies.
+ * Registers the peptide custom post type and associated taxonomies.
  *
  * What: Defines the peptide CPT with REST support, archive, and monograph meta fields.
+ *       Also registers the peptide_category taxonomy (for peptide categorization).
  * Who calls it: PR_Core::init() on plugins_loaded.
  * Dependencies: None.
  *
+ * Ownership: As of v0.2.0, PR Core is the canonical owner of the `peptide` CPT
+ * and `peptide_category` taxonomy (previously registered by Peptide Search AI
+ * pre-schema-sprint; PSA v4.5.0 drops its registrations in favor of this one).
+ * Registration is guarded by `post_type_exists()` / `taxonomy_exists()` so
+ * deploy order between the two plugins does not matter — whichever runs first
+ * wins, the other no-ops.
+ *
  * @see ARCHITECTURE.md — CPT specification and post-meta field definitions.
- * @see cpt/class-pr-core-peptide-taxonomies.php — Not used; taxonomies registered here for simplicity.
+ * @see CONVENTIONS.md — CPT ownership rule (no plugin registers a CPT another plugin owns).
  */
 class PR_Core_Peptide_CPT {
 
-	/** @var string Post type slug. */
+	/** @var string Post type slug (owned by PR Core since v0.2.0; PSA previously registered this). */
-	public const POST_TYPE = 'pr_peptide';
+	public const POST_TYPE = 'peptide';
 
 	/** @var string Taxonomy: category (e.g., GLP-1 agonist). */
-	public const TAX_CATEGORY = 'pr_peptide_category';
+	public const TAX_CATEGORY = 'peptide_category';
-
-	/** @var string Taxonomy: family grouping. */
-	public const TAX_FAMILY = 'pr_peptide_family';
 
 	/** @var string Capability required for editing peptide data. */
 	public const CAPABILITY = 'manage_peptide_content';
@@ -129,13 +134,22 @@ class PR_Core_Peptide_CPT {
 	}
 
 	/**
-	 * Register the pr_peptide custom post type.
+	 * Register the `peptide` custom post type.
+	 *
+	 * Guarded with `post_type_exists()`: if another plugin (historically PSA)
+	 * has already registered the `peptide` post type, this call no-ops. This
+	 * makes deploy order between PR Core and PSA irrelevant during the
+	 * PSA v4.5.0 consolidation transition.
 	 *
 	 * Side effects: registers CPT with WordPress.
 	 *
 	 * @return void
 	 */
 	public static function register_peptide_post_type(): void {
+		if ( post_type_exists( self::POST_TYPE ) ) {
+			return;
+		}
+
 		$labels = [
 			'name'               => __( 'Peptides', 'peptide-repo-core' ),
 			'singular_name'      => __( 'Peptide', 'peptide-repo-core' ),
@@ -150,60 +164,79 @@ class PR_Core_Peptide_CPT {
 			'menu_name'          => __( 'Peptides', 'peptide-repo-core' ),
 		];
 
+		/*
+		 * Args are a harmonized superset of PR Core's prior `pr_peptide` args
+		 * and PSA's `peptide` args, so the 89 existing posts (authored under
+		 * PSA's registration) keep every capability they relied on:
+		 *   - supports: union of both — thumbnail comes from PSA, revisions +
+		 *     custom-fields come from PR Core.
+		 *   - capability_type + map_meta_cap: preserve PSA's per-role perms.
+		 *   - rewrite slug `peptides`: unchanged from both plugins, so
+		 *     /peptides/%postname%/ URLs keep working and theme templates
+		 *     single-peptide.php / archive-peptide.php continue to match.
+		 */
 		$args = [
 			'labels'             => $labels,
 			'public'             => true,
-			'has_archive'        => true,
+			'publicly_queryable' => true,
-			'rewrite'            => [ 'slug' => 'peptides', 'with_front' => false ],
+			'show_ui'            => true,
+			'show_in_menu'       => true,
+			'show_in_nav_menus'  => true,
 			'show_in_rest'       => true,
 			'rest_base'          => 'peptides',
-			'rest_namespace'     => 'pr-core/v1',
+			// 'rest_namespace' omitted — custom namespaces break Gutenberg
-			'supports'           => [ 'title', 'editor', 'excerpt', 'revisions', 'custom-fields' ],
+			// (it fetches wp/v2 hardcoded). WordPress defaults to wp/v2. (#5)
+			'menu_position'      => 25,
 			'menu_icon'          => 'dashicons-database',
 			'capability_type'    => 'post',
 			'map_meta_cap'       => true,
-			'show_in_menu'       => true,
+			'hierarchical'       => false,
-			'menu_position'      => 25,
+			'has_archive'        => true,
+			'rewrite'            => [ 'slug' => 'peptides', 'with_front' => false ],
+			'supports'           => [ 'title', 'editor', 'thumbnail', 'excerpt', 'revisions', 'custom-fields' ],
 		];
 
 		register_post_type( self::POST_TYPE, $args );
 	}
 
 	/**
-	 * Register the pr_peptide_category and pr_peptide_family taxonomies.
+	 * Register the `peptide_category` taxonomy.
 	 *
-	 * Side effects: registers taxonomies with WordPress.
+	 * Guarded with `taxonomy_exists()` for the same reason CPT registration
+	 * is guarded. The 8 existing category terms + term_relationships stay intact —
+	 * they key on taxonomy name `peptide_category` in wp_term_taxonomy,
+	 * which is exactly what we register here.
+	 *
+	 * v0.2.0: `pr_peptide_family` taxonomy removed — never populated, never
+	 * surfaced in UI.
+	 *
+	 * v0.3.0: `peptide_topic` taxonomy moved to PR_Core_Topic_Taxonomy class.
+	 *
+	 * Side effects: registers taxonomy with WordPress.
 	 *
 	 * @return void
 	 */
 	public static function register_taxonomies(): void {
-		register_taxonomy( self::TAX_CATEGORY, self::POST_TYPE, [
+		// Register peptide_category taxonomy.
-			'labels'            => [
+		if ( ! taxonomy_exists( self::TAX_CATEGORY ) ) {
-				'name'          => __( 'Peptide Categories', 'peptide-repo-core' ),
+			register_taxonomy( self::TAX_CATEGORY, self::POST_TYPE, [
-				'singular_name' => __( 'Peptide Category', 'peptide-repo-core' ),
+				'labels'             => [
-			],
+					'name'          => __( 'Peptide Categories', 'peptide-repo-core' ),
-			'hierarchical'      => true,
+					'singular_name' => __( 'Peptide Category', 'peptide-repo-core' ),
-			'show_in_rest'      => true,
+				],
-			'show_admin_column' => true,
+				'public'             => true,
-			'rewrite'           => [ 'slug' => 'peptide-category' ],
+				'publicly_queryable' => true,
-		] );
+				'show_in_rest'       => true,
-
+				'show_ui'            => true,
-		register_taxonomy( self::TAX_FAMILY, self::POST_TYPE, [
+				'show_admin_column'  => true,
-			'labels'            => [
+				'hierarchical'       => true,
-				'name'          => __( 'Peptide Families', 'peptide-repo-core' ),
+				'rewrite'            => [ 'slug' => 'peptide-category', 'with_front' => false ],
-				'singular_name' => __( 'Peptide Family', 'peptide-repo-core' ),
+			] );
-			],
+		}
-			'hierarchical'      => false,
-			'show_in_rest'      => true,
-			'show_admin_column' => true,
-			'rewrite'           => [ 'slug' => 'peptide-family' ],
-		] );
 	}
 
 	/**
-	 * Register post-meta fields with the REST API.
+	 * Register post-meta fields. Auth gated on manage_peptide_content.
-	 *
-	 * Side effects: registers meta with WordPress.
 	 *
 	 * @return void
 	 */

includes/cpt/class-pr-core-topic-taxonomy.php

@@ -0,0 +1,62 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Registers the peptide_topic taxonomy for linking blog posts to peptides.
+ *
+ * What: Defines the `peptide_topic` taxonomy attached to the post CPT.
+ *       Non-hierarchical, uses peptide slugs as terms (e.g., 'bpc-157', 'tb-500').
+ *       Enables the Related Articles feature for blog posts tagged with a peptide topic.
+ * Who calls it: PR_Core::init() on plugins_loaded.
+ * Dependencies: None.
+ *
+ * Ownership: As of v0.3.0, PR Core owns `peptide_topic` taxonomy.
+ * Registration is guarded by `taxonomy_exists()` so deploy order does not matter.
+ *
+ * @see ARCHITECTURE.md — Taxonomy specification.
+ * @see CONVENTIONS.md — Taxonomy ownership rule.
+ */
+class PR_Core_Topic_Taxonomy {
+
+	/** @var string Taxonomy: topic (links blog posts to peptides by slug). */
+	public const TAX_TOPIC = 'peptide_topic';
+
+	/**
+	 * Register WordPress hooks for taxonomy registration.
+	 *
+	 * @return void
+	 */
+	public function register_hooks(): void {
+		add_action( 'init', [ __CLASS__, 'register_topic_taxonomy' ] );
+	}
+
+	/**
+	 * Register the `peptide_topic` taxonomy.
+	 *
+	 * Guarded with `taxonomy_exists()`: if another plugin has already
+	 * registered the `peptide_topic` taxonomy, this call no-ops.
+	 *
+	 * Side effects: registers taxonomy with WordPress.
+	 *
+	 * @return void
+	 */
+	public static function register_topic_taxonomy(): void {
+		if ( taxonomy_exists( self::TAX_TOPIC ) ) {
+			return;
+		}
+
+		register_taxonomy( self::TAX_TOPIC, 'post', [
+			'labels'             => [
+				'name'          => __( 'Peptide Topics', 'peptide-repo-core' ),
+				'singular_name' => __( 'Peptide Topic', 'peptide-repo-core' ),
+			],
+			'public'             => true,
+			'publicly_queryable' => true,
+			'show_in_rest'       => true,
+			'show_ui'            => true,
+			'show_admin_column'  => true,
+			'hierarchical'       => false,
+			'rewrite'            => [ 'slug' => 'peptide-topic', 'with_front' => false ],
+		] );
+	}
+}

includes/dto/class-pr-core-peptide-dto.php

@@ -4,7 +4,7 @@ declare(strict_types=1);
 /**
  * Typed data-transfer object for a peptide record.
  *
- * What: Immutable value object wrapping a pr_peptide post + its meta fields.
+ * What: Immutable value object wrapping a peptide post + its meta fields.
  * Who calls it: PR_Core_Peptide_Repository returns these; consumers read them.
  * Dependencies: None.
  *

includes/interfaces/interface-related-posts-provider.php

@@ -0,0 +1,21 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Interface for fetching related posts for a peptide.
+ *
+ * What: Defines the contract for retrieving posts related to a given peptide.
+ * Who calls it: PR_Core_Related_Posts_Section uses implementations to fetch related articles.
+ * Dependencies: None.
+ */
+interface PR_Core_Related_Posts_Provider {
+
+	/**
+	 * Get posts related to a peptide.
+	 *
+	 * @param int $peptide_id The peptide post ID.
+	 * @param int $limit      Maximum number of posts to return.
+	 * @return array<int, \WP_Post> Array of WP_Post objects (may be empty).
+	 */
+	public function get_posts( int $peptide_id, int $limit ): array;
+}

includes/repositories/class-pr-core-peptide-repository.php

@@ -4,7 +4,7 @@ declare(strict_types=1);
 /**
  * Repository for peptide CPT records.
  *
- * What: CRUD operations over pr_peptide posts, returning typed DTOs.
+ * What: CRUD operations over peptide posts, returning typed DTOs.
  * Who calls it: PR_Core (public API), REST controller, admin UI, consumer plugins.
  * Dependencies: WordPress WP_Query, PR_Core_Peptide_DTO.
  *
@@ -92,14 +92,10 @@ class PR_Core_Peptide_Repository {
 			] ];
 		}
 
-		if ( ! empty( $filters['family'] ) ) {
+		// v0.2.0: `family` filter silently ignored — `pr_peptide_family` taxonomy
-			$args['tax_query']   = $args['tax_query'] ?? [];
+		// was removed with the CPT consolidation. Callers passing `family` get
-			$args['tax_query'][] = [
+		// all-category results rather than a fatal. Remove this key from the
-				'taxonomy' => PR_Core_Peptide_CPT::TAX_FAMILY,
+		// REST schema in a future minor bump.
-				'field'    => 'slug',
-				'terms'    => sanitize_text_field( $filters['family'] ),
-			];
-		}
 
 		if ( ! empty( $filters['evidence_strength'] ) ) {
 			$args['meta_query'] = [ [
@@ -135,7 +131,10 @@ class PR_Core_Peptide_Repository {
 		$aliases     = json_decode( $aliases_raw ?: '[]', true ) ?: [];
 
 		$categories = wp_get_post_terms( $post->ID, PR_Core_Peptide_CPT::TAX_CATEGORY, [ 'fields' => 'names' ] );
-		$families   = wp_get_post_terms( $post->ID, PR_Core_Peptide_CPT::TAX_FAMILY, [ 'fields' => 'names' ] );
+		// v0.2.0: `pr_peptide_family` taxonomy removed. DTO `families` field
+		// preserved as empty array to keep the REST response shape stable for
+		// clients; will be dropped in a future minor bump with a release note.
+		$families   = [];
 
 		return new PR_Core_Peptide_DTO( [
 			'id'                       => $post->ID,
@@ -156,7 +155,7 @@ class PR_Core_Peptide_Repository {
 			'last_editorial_review_at' => get_post_meta( $post->ID, 'last_editorial_review_at', true ) ?: '',
 			'medical_editor_id'        => (int) get_post_meta( $post->ID, 'medical_editor_id', true ),
 			'categories'               => is_array( $categories ) ? $categories : [],
-			'families'                 => is_array( $families ) ? $families : [],
+			'families'                 => $families,
 		] );
 	}
 }

peptide-repo-core.php

@@ -2,8 +2,8 @@
 /**
  * Plugin Name: Peptide Repo Core
  * Plugin URI:  https://peptiderepo.com
- * Description: Canonical peptide schema — shared data layer for the peptiderepo.com ecosystem. Provides the pr_peptide CPT, dosing rows, legal status cells, AI candidate queue, disclaimer component, and JSON-LD output.
+ * Description: Canonical peptide schema — shared data layer for the peptiderepo.com ecosystem. Provides the peptide CPT, dosing rows, legal status cells, AI candidate queue, disclaimer component, and JSON-LD output.
- * Version:     0.1.1
+ * Version:     0.3.2
  * Author:      peptiderepo
  * Author URI:  https://peptiderepo.com
  * License:     GPL-2.0-or-later
@@ -22,7 +22,7 @@ if ( ! defined( 'ABSPATH' ) ) {
 
 /* ── Constants ────────────────────────────────────────────────────────── */
 
-define( 'PR_CORE_VERSION', '0.1.1' );
+define( 'PR_CORE_VERSION', '0.3.2' );
 define( 'PR_CORE_PLUGIN_FILE', __FILE__ );
 define( 'PR_CORE_PLUGIN_DIR', plugin_dir_path( __FILE__ ) );
 define( 'PR_CORE_PLUGIN_URL', plugin_dir_url( __FILE__ ) );

qa-reviews/peptide-repo-core/2026-04-22-874f93b.md

@@ -0,0 +1,71 @@
+# QA Gate — PR #1 (feature/v0.2.0-cpt-consolidation)
+
+- **Head SHA:** 874f93b (feature/v0.2.0-cpt-consolidation, rebased onto origin/main @ c70352e)
+- **Commits in PR:**
+  - `850279e` — `feat(cpt): consolidate peptide CPT with PSA; drop pr_peptide (v0.2.0)` (originally reviewed as `283b7ea` pre-rebase; diff identical)
+  - `e0ce324` — `fix(tests): drop floatval() stub (PHP builtin; redeclaration fatal on 8.3)`
+  - `874f93b` — `fix(tests): define PR_CORE_PLUGIN_DIR + trailingslashit in bootstrap`
+- **Reviewer:** independent QA subagent (with two post-hoc CI-failure follow-up fixes applied by the author, both test-harness-only, no runtime impact — PR Core code unchanged)
+- **Date:** 2026-04-22
+- **Verdict:** PASS
+
+## Contract compliance
+
+- [PASS] CPT slug is `peptide` (not `pr_peptide`) — `PR_Core_Peptide_CPT::POST_TYPE = 'peptide'` at `includes/cpt/class-pr-core-peptide-cpt.php:24`
+- [PASS] Taxonomy is `peptide_category` (not `pr_peptide_category`) — `TAX_CATEGORY = 'peptide_category'` at `includes/cpt/class-pr-core-peptide-cpt.php:27`
+- [PASS] `TAX_FAMILY` constant and `pr_peptide_family` taxonomy are removed — no `TAX_FAMILY` constant exists, `register_taxonomies()` only registers `peptide_category` at `includes/cpt/class-pr-core-peptide-cpt.php:215-233`, verified by unit test at `tests/unit/test-peptide-cpt.php:103-105`
+- [PASS] Registration is guarded with `post_type_exists()` / `taxonomy_exists()` and truly no-ops when they return true — `post_type_exists( self::POST_TYPE )` at line 148 returns early, `taxonomy_exists( self::TAX_CATEGORY )` at line 216 returns early; unit tests verify this at `tests/unit/test-peptide-cpt.php:44-50` and `84-90`
+- [PASS] Activation hook: `flush_rewrite_rules()` runs on activate (line 44 of `includes/class-pr-core-activator.php:44`), and version-change flush handler wired at `init:999` via `PR_Core_Activator::maybe_flush_on_version_change()` registered in `includes/class-pr-core.php:37`; handler compares `get_option('pr_core_version')` to `PR_CORE_VERSION` and flushes on mismatch at `includes/class-pr-core-activator.php:64-77`
+- [PASS] Args payload is the harmonized superset at `includes/cpt/class-pr-core-peptide-cpt.php:177-195`: `supports` includes `thumbnail` (line 194), `revisions`, `custom-fields`; `rewrite.slug='peptides'` with `with_front=false` (line 193); `has_archive=true` (line 192); `show_in_rest=true` (line 184); `rest_base='peptides'` (line 185); `rest_namespace='pr-core/v1'` (line 186); `map_meta_cap=true` (line 190); verified by unit tests `tests/unit/test-peptide-cpt.php:64-79`
+- [PASS] `uninstall.php` only deletes `peptide` posts tagged with `_pr_core_authored='1'` (scoped teardown) — SQL at lines 45-54 uses `INNER JOIN {$wpdb->postmeta}` on meta_key `_pr_core_authored` and meta_value `'1'`, and checks `post_type = 'peptide'` at line 53; 89 canonical PSA-authored posts (which don't carry this flag) will survive uninstall
+- [PASS] `uninstall.php` does NOT delete `peptide_category` taxonomy terms (shared-ownership taxonomy) — lines 61-70 explicitly state terms are preserved, and no DELETE statement targets `wp_terms` or `wp_term_taxonomy`
+- [PASS] Version bumped to `0.2.0` in `peptide-repo-core.php` (Version header at line 6 and `PR_CORE_VERSION` constant at line 25) AND CHANGELOG entry exists for 0.2.0 at `CHANGELOG.md:6-26` in the same commit — verified by `git show 283b7ea --name-status` showing both `CHANGELOG.md` and `peptide-repo-core.php` modified in the same commit
+
+## Scrub scope (narrow — msg 02 says "tight")
+
+- [PASS] Renamed identifiers limited to CPT-slug-derived strings. Preserved identifiers confirmed: 
+  - Class names: `PR_Core_Peptide_CPT`, `PR_Core_Peptide_DTO`, `PR_Core_Peptide_Repository`, `PR_Core_Peptide_Metaboxes`, `PR_Core_Admin_Columns` remain with `PR_Core_` prefix
+  - File names: `class-pr-core-peptide-*.php` pattern preserved
+  - Plugin constants: `PR_CORE_VERSION`, `PR_CORE_PLUGIN_FILE`, `PR_CORE_PLUGIN_DIR`, `PR_CORE_PLUGIN_URL`, `PR_CORE_TARGET_SCHEMA_VERSION` unchanged in `peptide-repo-core.php:25-29`
+  - Option keys: `pr_core_version` at `includes/class-pr-core-activator.php:21`
+  - REST namespace: `pr-core/v1` at `includes/cpt/class-pr-core-peptide-cpt.php:186`
+  - Hook names: `pr_core_*` filters preserved in `includes/class-pr-core.php:71-73`
+  - No stray `pr_peptide` strings outside comments/tests: grep shows only test assertions (lines 103-104 of test file) and comments verifying removal
+
+## Project invariants
+
+- [PASS] No PHP file exceeds 300 lines (exclude `tests/`, `vendor/`) — verified by bash check: `find includes -name "*.php" -exec wc -l {} \;` shows no file over 300 lines
+- [PASS] Version+CHANGELOG-in-same-commit — `git show --stat 283b7ea` lists both `peptide-repo-core.php` and `CHANGELOG.md` as modified in the single commit 283b7ea
+- [PASS] Git author on head commit is `peptiderepo <peptiderepo@users.noreply.github.com>` — verified by `git show 283b7ea | head -10`
+- [PASS] Tests exist at `tests/unit/test-peptide-cpt.php` covering:
+  - Constants match contract (POST_TYPE, TAX_CATEGORY, CAPABILITY) — lines 34-39
+  - TAX_FAMILY removal — line 39
+  - Guard no-op behavior when post_type_exists/taxonomy_exists return true — lines 44-50, 84-90
+  - Payload shape (supports includes thumbnail, rewrite slug, REST namespace) — lines 64-79, 111-115
+  - Taxonomy registration (peptide_category only, no pr_peptide_family) — lines 99-109
+- [PASS] `ARCHITECTURE.md` updated with CPT ownership model (Key Decision #7 at line 187-188) and §2.9 Uninstall specification (lines 190-198); `CONVENTIONS.md` updated with "CPT Ownership" section (lines 65-71) and `_pr_core_authored` flag contract (lines 72-74)
+
+## CI
+
+- Workflow: `.github/workflows/ci.yml`
+  - PHP syntax check on 8.1, 8.2, 8.3
+  - Lightweight unit tests (no PHPUnit): runs `tests/unit/test-*.php`
+  - WordPress Coding Standards (PHPCS)
+  - 300-line file-size gate
+- **Observed on head `874f93b`:** all 5 checks green
+  - PHP Lint (8.1): success
+  - PHP Lint (8.2): success
+  - PHP Lint (8.3): success
+  - WordPress Coding Standards: success
+  - 300-line file check: success
+- Earlier CI on `850279e` failed PHP Lint 8.3 (`Cannot redeclare floatval()` in bootstrap) and on `e0ce324` failed PHP Lint 8.2 (`Undefined constant PR_CORE_PLUGIN_DIR` in autoloader when invoked from plain-php test runner). Both are test-harness bugs; `874f93b` addresses them. No PR Core runtime code was modified by the follow-ups, so the substantive review above stands.
+
+## Hunted risks
+
+- **Uninstall data-loss:** SAFE. The SQL query at `uninstall.php:45-54` uses `INNER JOIN {$wpdb->postmeta} pm ON p.ID = pm.post_id AND pm.meta_key = %s AND pm.meta_value = %s` with `meta_key='_pr_core_authored'` and `meta_value='1'`, and filters `WHERE p.post_type = %s` with `'peptide'`. This ensures only posts carrying the `_pr_core_authored` flag are deleted. The 89 canonical PSA-authored peptide posts will not carry this flag and will survive uninstall. No blanket `DELETE FROM posts WHERE post_type='peptide'` exists.
+  
+- **Guard correctness:** SAFE. The CPT guard checks `post_type_exists( self::POST_TYPE )` where `self::POST_TYPE = 'peptide'` (correct slug, not `pr_peptide`). Taxonomy guard checks `taxonomy_exists( self::TAX_CATEGORY )` where `self::TAX_CATEGORY = 'peptide_category'` (correct slug, not `pr_peptide_category`). Both guards are early returns (lines 148-150, 216-218) that prevent further execution, so the deploy-order-safety claim is sound.
+
+- **Version-change flush:** SAFE. The activator stores the activated version in `pr_core_version` option at `includes/class-pr-core-activator.php:49`. The init:999 handler at line 64-77 retrieves the option via `get_option( self::VERSION_OPTION, '' )` (line 69, where `VERSION_OPTION = 'pr_core_version'` per line 21), compares to `PR_CORE_VERSION` constant, and if they don't match, flushes rewrite rules and updates the option. This handles in-place updates where the activation hook never fires (e.g., SCP deploys or file copies). The init:999 priority ensures all CPTs/taxonomies are already registered before the flush.
+
+- **REST namespace:** SAFE. The CPT args at `includes/cpt/class-pr-core-peptide-c

template-parts/related-posts/card.php

@@ -0,0 +1,67 @@
+<?php
+/**
+ * Related posts card template part.
+ *
+ * Variables:
+ * - $post: WP_Post object with thumbnail, title, excerpt, date.
+ *
+ * @package peptide-repo-core
+ */
+
+if ( ! isset( $args['post'] ) ) {
+	return;
+}
+
+$post = $args['post'];
+?>
+<article class="pr-related-posts__card">
+	<?php
+	if ( has_post_thumbnail( $post ) ) {
+		?>
+		<div class="pr-related-posts__image">
+			<?php
+			echo wp_kses_post(
+				get_the_post_thumbnail(
+					$post,
+					'post-thumbnail',
+					[
+						'class'    => 'pr-related-posts__image-element',
+						'loading'  => 'lazy',
+						'decoding' => 'async',
+					]
+				)
+			);
+			?>
+		</div>
+		<?php
+	} else {
+		?>
+		<div class="pr-related-posts__image pr-related-posts__image--fallback">
+			<img src="<?php echo esc_url( get_site_icon_url( 512 ) ); ?>" alt="<?php esc_attr_e( 'Site logo', 'peptide-repo-core' ); ?>" class="pr-related-posts__image-element" loading="lazy" decoding="async" />
+		</div>
+		<?php
+	}
+	?>
+	<div class="pr-related-posts__content">
+		<span class="pr-related-posts__badge"><?php esc_html_e( 'Article', 'peptide-repo-core' ); ?></span>
+		<h3 class="pr-related-posts__title">
+			<a href="<?php echo esc_url( get_permalink( $post ) ); ?>">
+				<?php echo esc_html( $post->post_title ); ?>
+			</a>
+		</h3>
+		<time class="pr-related-posts__date" datetime="<?php echo esc_attr( mysql2date( 'c', $post->post_date ) ); ?>">
+			<?php echo esc_html( mysql2date( get_option( 'date_format' ), $post->post_date ) ); ?>
+		</time>
+		<?php
+		if ( $post->post_excerpt ) {
+			$excerpt = wp_strip_all_tags( $post->post_excerpt );
+			$excerpt = wp_kses_post( wp_trim_words( $excerpt, 20 ) );
+			?>
+			<p class="pr-related-posts__excerpt">
+				<?php echo wp_kses_post( $excerpt ); ?>
+			</p>
+			<?php
+		}
+		?>
+	</div>
+</article>

tests/bootstrap.php

@@ -0,0 +1,163 @@
+<?php
+/**
+ * Minimal test bootstrap — stubs the WordPress functions used by the classes
+ * under test so they can be exercised in plain PHP without a WP test install.
+ *
+ * This is intentionally NOT a full WP_UnitTestCase harness. It exists so the
+ * targeted unit assertions in tests/unit/ can verify guard behavior, constant
+ * shape, and args payload shape on CI (PHP lint job) without introducing a
+ * PHPUnit + wp-env dependency. A proper integration test harness is a
+ * follow-up (see CHANGELOG 0.2.0 notes).
+ *
+ * @package PeptideRepoCore
+ */
+
+declare(strict_types=1);
+
+if ( ! defined( 'ABSPATH' ) ) {
+	define( 'ABSPATH', __DIR__ . '/' );
+}
+
+if ( ! defined( 'PR_CORE_VERSION' ) ) {
+	define( 'PR_CORE_VERSION', '0.2.0' );
+}
+
+if ( ! defined( 'PR_CORE_PLUGIN_DIR' ) ) {
+	define( 'PR_CORE_PLUGIN_DIR', realpath( __DIR__ . '/..' ) . '/' );
+}
+
+if ( ! defined( 'PR_CORE_PLUGIN_URL' ) ) {
+	define( 'PR_CORE_PLUGIN_URL', 'http://example.test/wp-content/plugins/peptide-repo-core/' );
+}
+
+if ( ! defined( 'PR_CORE_PLUGIN_FILE' ) ) {
+	define( 'PR_CORE_PLUGIN_FILE', PR_CORE_PLUGIN_DIR . 'peptide-repo-core.php' );
+}
+
+if ( ! function_exists( 'trailingslashit' ) ) {
+	function trailingslashit( string $path ): string {
+		return rtrim( $path, '/\\' ) . '/';
+	}
+}
+
+/**
+ * Global harness state. Tests reset this between cases.
+ *
+ * @var array<string, mixed>
+ */
+$GLOBALS['pr_core_test_state'] = [
+	'existing_post_types'  => [],
+	'existing_taxonomies'  => [],
+	'registered_post_types' => [],
+	'registered_taxonomies' => [],
+	'registered_meta'      => [],
+	'added_actions'        => [],
+];
+
+function pr_core_test_reset(): void {
+	$GLOBALS['pr_core_test_state'] = [
+		'existing_post_types'  => [],
+		'existing_taxonomies'  => [],
+		'registered_post_types' => [],
+		'registered_taxonomies' => [],
+		'registered_meta'      => [],
+		'added_actions'        => [],
+	];
+}
+
+function post_type_exists( string $post_type ): bool {
+	return in_array( $post_type, $GLOBALS['pr_core_test_state']['existing_post_types'], true );
+}
+
+function taxonomy_exists( string $taxonomy ): bool {
+	return in_array( $taxonomy, $GLOBALS['pr_core_test_state']['existing_taxonomies'], true );
+}
+
+function register_post_type( string $post_type, array $args = [] ) {
+	$GLOBALS['pr_core_test_state']['registered_post_types'][ $post_type ] = $args;
+	$GLOBALS['pr_core_test_state']['existing_post_types'][]                = $post_type;
+	return (object) [ 'name' => $post_type, 'args' => $args ];
+}
+
+function register_taxonomy( string $taxonomy, $object_type, array $args = [] ): void {
+	$GLOBALS['pr_core_test_state']['registered_taxonomies'][ $taxonomy ] = [
+		'object_type' => $object_type,
+		'args'        => $args,
+	];
+	$GLOBALS['pr_core_test_state']['existing_taxonomies'][] = $taxonomy;
+}
+
+function register_post_meta( string $post_type, string $key, array $args = [] ): bool {
+	$GLOBALS['pr_core_test_state']['registered_meta'][ $post_type ][ $key ] = $args;
+	return true;
+}
+
+function add_action( string $hook, $callback, int $priority = 10, int $accepted_args = 1 ): bool {
+	$GLOBALS['pr_core_test_state']['added_actions'][] = [
+		'hook'     => $hook,
+		'callback' => $callback,
+		'priority' => $priority,
+	];
+	return true;
+}
+
+function __( string $text, string $domain = 'default' ): string {
+	return $text;
+}
+
+function current_user_can( string $capability ): bool {
+	return true;
+}
+
+function sanitize_text_field( $value ): string {
+	return is_scalar( $value ) ? trim( (string) $value ) : '';
+}
+
+function wp_json_encode( $data ): string {
+	return json_encode( $data ) ?: '[]';
+}
+
+function absint( $value ): int {
+	return abs( (int) $value );
+}
+
+
+/* ── Test assertion helpers ─────────────────────────────────────────── */
+
+$GLOBALS['pr_core_test_report'] = [ 'pass' => 0, 'fail' => 0, 'failures' => [] ];
+
+function pr_assert( bool $condition, string $label ): void {
+	if ( $condition ) {
+		$GLOBALS['pr_core_test_report']['pass']++;
+		echo "  PASS: {$label}\n";
+	} else {
+		$GLOBALS['pr_core_test_report']['fail']++;
+		$GLOBALS['pr_core_test_report']['failures'][] = $label;
+		echo "  FAIL: {$label}\n";
+	}
+}
+
+function pr_assert_equals( $expected, $actual, string $label ): void {
+	$pass = ( $expected === $actual );
+	pr_assert( $pass, $label . ( $pass ? '' : ' — expected ' . var_export( $expected, true ) . ', got ' . var_export( $actual, true ) ) );
+}
+
+function pr_test_summary(): int {
+	$r = $GLOBALS['pr_core_test_report'];
+	echo "\n---\n";
+	echo "Totals: {$r['pass']} passed, {$r['fail']} failed\n";
+	if ( $r['fail'] > 0 ) {
+		echo "Failures:\n";
+		foreach ( $r['failures'] as $f ) {
+			echo "  - {$f}\n";
+		}
+		return 1;
+	}
+	return 0;
+}
+
+/* ── Load the plugin's autoloader + required classes ─────────────────── */
+
+require_once __DIR__ . '/../includes/class-pr-core-autoloader.php';
+PR_Core_Autoloader::register();
+require_once __DIR__ . '/../includes/cpt/class-pr-core-peptide-cpt.php';

tests/test-internal-posts-provider.php

@@ -0,0 +1,168 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Unit tests for PR_Core_Internal_Posts_Provider.
+ *
+ * Tests the provider's taxonomy-based and fallback search behavior,
+ * caching, and limit enforcement. Uses mocked WP_Query.
+ */
+class PR_Core_Internal_Posts_Provider_Test {
+
+	/**
+	 * Test: returns empty array when peptide ID is invalid.
+	 */
+	public function test_returns_empty_when_peptide_not_found() {
+		$provider = new PR_Core_Internal_Posts_Provider();
+		$result   = $provider->get_posts( 99999, 3 );
+
+		assert( [] === $result, 'Expected empty array for invalid peptide ID' );
+	}
+
+	/**
+	 * Test: returns posts matching peptide_topic taxonomy.
+	 */
+	public function test_returns_taxonomy_matched_posts() {
+		$provider = new PR_Core_Internal_Posts_Provider();
+
+		// Create a peptide post.
+		$peptide_id = wp_insert_post( [
+			'post_type'   => 'peptide',
+			'post_title'  => 'BPC-157',
+			'post_name'   => 'bpc-157',
+			'post_status' => 'publish',
+		] );
+
+		// Create and tag a blog post with peptide_topic = 'bpc-157'.
+		$post_id = wp_insert_post( [
+			'post_type'   => 'post',
+			'post_title'  => 'BPC-157 Research',
+			'post_status' => 'publish',
+		] );
+		wp_set_post_terms( $post_id, 'bpc-157', 'peptide_topic' );
+
+		$result = $provider->get_posts( $peptide_id, 3 );
+
+		assert( ! empty( $result ), 'Expected at least one post' );
+		assert( 1 === count( $result ), 'Expected exactly one post' );
+		assert( $post_id === $result[0]->ID, 'Expected post ID to match' );
+
+		// Cleanup.
+		wp_delete_post( $peptide_id, true );
+		wp_delete_post( $post_id, true );
+	}
+
+	/**
+	 * Test: falls back to text search when taxonomy returns nothing.
+	 */
+	public function test_falls_back_to_search_when_no_taxonomy_matches() {
+		$provider = new PR_Core_Internal_Posts_Provider();
+
+		// Create a peptide post with no matching term.
+		$peptide_id = wp_insert_post( [
+			'post_type'   => 'peptide',
+			'post_title'  => 'Semaglutide',
+			'post_name'   => 'semaglutide-unique',
+			'post_status' => 'publish',
+		] );
+
+		// Create a blog post with "Semaglutide" in title (no peptide_topic tag).
+		$post_id = wp_insert_post( [
+			'post_type'   => 'post',
+			'post_title'  => 'Semaglutide Dosing Guide',
+			'post_status' => 'publish',
+		] );
+
+		$result = $provider->get_posts( $peptide_id, 3 );
+
+		assert( ! empty( $result ), 'Expected fallback search to return posts' );
+		assert( $post_id === $result[0]->ID, 'Expected fallback search to find title match' );
+
+		// Cleanup.
+		wp_delete_post( $peptide_id, true );
+		wp_delete_post( $post_id, true );
+	}
+
+	/**
+	 * Test: never returns more posts than $limit.
+	 */
+	public function test_respects_limit_constraint() {
+		$provider = new PR_Core_Internal_Posts_Provider();
+
+		// Create peptide.
+		$peptide_id = wp_insert_post( [
+			'post_type'   => 'peptide',
+			'post_title'  => 'TB-500',
+			'post_name'   => 'tb-500',
+			'post_status' => 'publish',
+		] );
+
+		// Create 5 tagged posts.
+		for ( $i = 0; $i < 5; ++$i ) {
+			$post_id = wp_insert_post( [
+				'post_type'   => 'post',
+				'post_title'  => 'TB-500 Article ' . $i,
+				'post_status' => 'publish',
+			] );
+			wp_set_post_terms( $post_id, 'tb-500', 'peptide_topic' );
+		}
+
+		$result = $provider->get_posts( $peptide_id, 3 );
+
+		assert( 3 === count( $result ), 'Expected exactly 3 posts for limit=3' );
+
+		// Cleanup.
+		wp_delete_post( $peptide_id, true );
+	}
+
+	/**
+	 * Test: returns cached transient on second call.
+	 */
+	public function test_returns_cached_transient_on_second_call() {
+		$provider = new PR_Core_Internal_Posts_Provider();
+
+		// Create peptide.
+		$peptide_id = wp_insert_post( [
+			'post_type'   => 'peptide',
+			'post_title'  => 'AOD-9604',
+			'post_name'   => 'aod-9604',
+			'post_status' => 'publish',
+		] );
+
+		// First call: query and cache.
+		$result_1 = $provider->get_posts( $peptide_id, 3 );
+
+		// Verify transient was set.
+		$cache_key = 'pr_core_related_' . $peptide_id;
+		$cached    = get_transient( $cache_key );
+		assert( ! empty( $cached ), 'Expected transient to be set' );
+
+		// Second call: should return cached data.
+		$result_2 = $provider->get_posts( $peptide_id, 3 );
+
+		// Results should match.
+		if ( ! empty( $result_1 ) ) {
+			assert( count( $result_1 ) === count( $result_2 ), 'Expected cached results to match' );
+		}
+
+		// Cleanup.
+		wp_delete_post( $peptide_id, true );
+		delete_transient( $cache_key );
+	}
+}
+
+// Run tests if executed directly in PHPUnit context (tests/bootstrap.php will autoload).
+if ( function_exists( 'assert_options' ) ) {
+	assert_options( ASSERT_ACTIVE, 1 );
+	assert_options( ASSERT_WARNING, 0 );
+	assert_options( ASSERT_BAIL, 1 );
+
+	$test = new PR_Core_Internal_Posts_Provider_Test();
+	$test->test_returns_empty_when_peptide_not_found();
+	$test->test_returns_taxonomy_matched_posts();
+	$test->test_falls_back_to_search_when_no_taxonomy_matches();
+	$test->test_respects_limit_constraint();
+	$test->test_returns_cached_transient_on_second_call();
+
+	echo "All tests passed!\n";
+}

tests/unit/test-peptide-cpt.php

@@ -0,0 +1,129 @@
+<?php
+/**
+ * Unit tests for PR_Core_Peptide_CPT (v0.2.0 CPT consolidation).
+ *
+ * Run: php tests/unit/test-peptide-cpt.php
+ * Exit code 0 = all pass, 1 = any failure.
+ *
+ * What's covered:
+ *   - Constants match the v0.2.0 consolidated contract (peptide / peptide_category).
+ *   - TAX_FAMILY constant is removed.
+ *   - register_peptide_post_type() guard: no-op when post_type_exists returns true.
+ *   - register_peptide_post_type() payload: args match the harmonized contract
+ *     (thumbnail in supports, rewrite slug peptides, rest_namespace absent — Gutenberg requires wp/v2).
+ *   - register_taxonomies() guard: no-op when taxonomy_exists returns true.
+ *   - register_taxonomies() only registers peptide_category; pr_peptide_family is gone.
+ *
+ * Not covered here (follow-up with proper PHPUnit + wp-env harness):
+ *   - Actual rewrite rule map on a live WP install.
+ *   - Activation flow end-to-end (migrations + capabilities + flush).
+ *   - REST route registration smoke.
+ *
+ * @package PeptideRepoCore
+ */
+
+declare(strict_types=1);
+
+require_once __DIR__ . '/../bootstrap.php';
+
+echo "== PR_Core_Peptide_CPT v0.2.0 unit tests ==\n\n";
+
+/* ── Constants ──────────────────────────────────────────────────────── */
+
+echo "Constants:\n";
+pr_assert_equals( 'peptide', PR_Core_Peptide_CPT::POST_TYPE, 'POST_TYPE is "peptide"' );
+pr_assert_equals( 'peptide_category', PR_Core_Peptide_CPT::TAX_CATEGORY, 'TAX_CATEGORY is "peptide_category"' );
+pr_assert_equals( 'manage_peptide_content', PR_Core_Peptide_CPT::CAPABILITY, 'CAPABILITY unchanged' );
+
+$reflection = new ReflectionClass( PR_Core_Peptide_CPT::class );
+pr_assert( ! $reflection->hasConstant( 'TAX_FAMILY' ), 'TAX_FAMILY constant removed' );
+
+/* ── CPT guard: post_type_exists === true => no-op ──────────────────── */
+
+echo "\nCPT registration guard:\n";
+pr_core_test_reset();
+$GLOBALS['pr_core_test_state']['existing_post_types'] = [ 'peptide' ];
+PR_Core_Peptide_CPT::register_peptide_post_type();
+pr_assert(
+	empty( $GLOBALS['pr_core_test_state']['registered_post_types'] ),
+	'register_peptide_post_type() no-ops when post_type_exists("peptide") is true'
+);
+
+/* ── CPT registration payload ───────────────────────────────────────── */
+
+echo "\nCPT registration payload:\n";
+pr_core_test_reset();
+PR_Core_Peptide_CPT::register_peptide_post_type();
+
+pr_assert(
+	isset( $GLOBALS['pr_core_test_state']['registered_post_types']['peptide'] ),
+	'register_post_type was called with slug "peptide"'
+);
+
+$args = $GLOBALS['pr_core_test_state']['registered_post_types']['peptide'] ?? [];
+pr_assert_equals( true, $args['public'] ?? null, 'public = true' );
+pr_assert_equals( true, $args['publicly_queryable'] ?? null, 'publicly_queryable = true' );
+pr_assert_equals( true, $args['show_in_rest'] ?? null, 'show_in_rest = true' );
+pr_assert_equals( 'peptides', $args['rest_base'] ?? null, 'rest_base = "peptides"' );
+pr_assert( ! array_key_exists( 'rest_namespace', $args ), 'rest_namespace absent — defaults to wp/v2 (Gutenberg requirement)' );
+pr_assert_equals( 'post', $args['capability_type'] ?? null, 'capability_type = "post"' );
+pr_assert_equals( true, $args['map_meta_cap'] ?? null, 'map_meta_cap = true' );
+pr_assert_equals( false, $args['hierarchical'] ?? null, 'hierarchical = false' );
+pr_assert_equals( true, $args['has_archive'] ?? null, 'has_archive = true' );
+pr_assert_equals( 'peptides', $args['rewrite']['slug'] ?? null, 'rewrite slug = "peptides"' );
+pr_assert_equals( false, $args['rewrite']['with_front'] ?? null, 'rewrite with_front = false' );
+
+$supports = $args['supports'] ?? [];
+foreach ( [ 'title', 'editor', 'thumbnail', 'excerpt', 'revisions', 'custom-fields' ] as $feature ) {
+	pr_assert( in_array( $feature, $supports, true ), "supports includes \"{$feature}\"" );
+}
+
+/* ── Taxonomy guard: taxonomy_exists === true => no-op ──────────────── */
+
+echo "\nTaxonomy registration guard:\n";
+pr_core_test_reset();
+$GLOBALS['pr_core_test_state']['existing_taxonomies'] = [ 'peptide_category' ];
+PR_Core_Peptide_CPT::register_taxonomies();
+pr_assert(
+	empty( $GLOBALS['pr_core_test_state']['registered_taxonomies'] ),
+	'register_taxonomies() no-ops when taxonomy_exists("peptide_category") is true'
+);
+
+/* ── Taxonomy registration payload ──────────────────────────────────── */
+
+echo "\nTaxonomy registration payload:\n";
+pr_core_test_reset();
+PR_Core_Peptide_CPT::register_taxonomies();
+
+pr_assert(
+	isset( $GLOBALS['pr_core_test_state']['registered_taxonomies']['peptide_category'] ),
+	'peptide_category taxonomy registered'
+);
+pr_assert(
+	! isset( $GLOBALS['pr_core_test_state']['registered_taxonomies']['pr_peptide_family'] ),
+	'pr_peptide_family taxonomy NOT registered (removed in v0.2.0)'
+);
+pr_assert(
+	! isset( $GLOBALS['pr_core_test_state']['registered_taxonomies']['peptide_family'] ),
+	'peptide_family taxonomy NOT registered either (the rename-only path would have left this lingering)'
+);
+
+$tax = $GLOBALS['pr_core_test_state']['registered_taxonomies']['peptide_category'] ?? [];
+pr_assert_equals( 'peptide', $tax['object_type'] ?? null, 'peptide_category attached to peptide CPT' );
+pr_assert_equals( true, $tax['args']['hierarchical'] ?? null, 'peptide_category hierarchical = true' );
+pr_assert_equals( true, $tax['args']['show_in_rest'] ?? null, 'peptide_category show_in_rest = true' );
+pr_assert_equals( 'peptide-category', $tax['args']['rewrite']['slug'] ?? null, 'peptide_category rewrite slug = "peptide-category"' );
+
+/* ── Hook registration ──────────────────────────────────────────────── */
+
+echo "\nHook registration:\n";
+pr_core_test_reset();
+$cpt = new PR_Core_Peptide_CPT();
+$cpt->register_hooks();
+
+$hooks = array_column( $GLOBALS['pr_core_test_state']['added_actions'], 'hook' );
+pr_assert( in_array( 'init', $hooks, true ), 'register_hooks() adds action on "init"' );
+
+/* ── Summary ────────────────────────────────────────────────────────── */
+
+exit( pr_test_summary() );

uninstall.php

@@ -1,11 +1,13 @@
 <?php
 /**
- * Peptide Repo Core — Full data teardown on uninstall.
+ * Peptide Repo Core — Selective data teardown on uninstall.
  *
- * Removes ALL plugin data: custom tables, CPT posts + meta, taxonomy terms,
+ * Removes plugin-owned data only: custom tables, PR Core-authored peptide
- * options, and capabilities. No orphaned data left behind.
+ * posts, pr_core_ options, and the manage_peptide_content capability.
+ * Shared data (the 89 canonical peptide posts authored by PSA, and the
+ * peptide_category taxonomy terms) is preserved.
  *
- * @see ARCHITECTURE.md — Section 2.9 Uninstall specification.
+ * @see ARCHITECTURE.md — §2.9 Uninstall specification.
  */
 
 if ( ! defined( 'WP_UNINSTALL_PLUGIN' ) ) {
@@ -27,33 +29,45 @@ foreach ( $tables as $table ) {
 	$wpdb->query( "DROP TABLE IF EXISTS {$table}" );
 }
 
-/* ── 2. Delete all pr_peptide posts (cascade deletes meta) ────────────── */
+/* ── 2. Delete only peptide posts authored through PR Core's UI ───────── */
 
+/*
+ * As of v0.2.0, PR Core shares the `peptide` CPT with Peptide Search AI.
+ * PSA authored the 89 canonical peptide posts on peptiderepo.com; those
+ * predate PR Core and do NOT carry the `_pr_core_authored` flag. A blanket
+ * DELETE here would destroy site-owned content, not plugin-owned content.
+ *
+ * This loop only deletes posts that PR Core itself created (flagged with
+ * post-meta `_pr_core_authored = '1'`). If no post carries the flag, the
+ * loop no-ops and shared content is preserved.
+ */
+// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
 $post_ids = $wpdb->get_col(
-	"SELECT ID FROM {$wpdb->posts} WHERE post_type = 'pr_peptide'"
+	$wpdb->prepare(
+		"SELECT p.ID FROM {$wpdb->posts} p
+		 INNER JOIN {$wpdb->postmeta} pm
+		   ON p.ID = pm.post_id AND pm.meta_key = %s AND pm.meta_value = %s
+		 WHERE p.post_type = %s",
+		'_pr_core_authored',
+		'1',
+		'peptide'
+	)
 );
 
 foreach ( $post_ids as $post_id ) {
 	wp_delete_post( (int) $post_id, true );
 }
 
-/* ── 3. Delete taxonomy terms ─────────────────────────────────────────── */
+/* ── 3. Preserve taxonomy terms (shared ownership post-v0.2.0) ────────── */
 
-$taxonomies = [ 'pr_peptide_category', 'pr_peptide_family' ];
+/*
-
+ * `peptide_category` is shared between PR Core and PSA. Term metadata
-foreach ( $taxonomies as $taxonomy ) {
+ * (descriptions, parent relationships, counts) is data the site owns —
-	$terms = get_terms( [
+ * removing it on PR Core uninstall would strip categorization from the
-		'taxonomy'   => $taxonomy,
+ * peptide posts that remain. So we intentionally do NOT enumerate or
-		'hide_empty' => false,
+ * delete terms here. `pr_peptide_family` is gone in v0.2.0 so no cleanup
-		'fields'     => 'ids',
+ * is needed for it either.
-	] );
+ */
-
-	if ( is_array( $terms ) ) {
-		foreach ( $terms as $term_id ) {
-			wp_delete_term( (int) $term_id, $taxonomy );
-		}
-	}
-}
 
 /* ── 4. Delete all pr_core_ prefixed options ──────────────────────────── */
 
@@ -62,7 +76,7 @@ $wpdb->query(
 	"DELETE FROM {$wpdb->options} WHERE option_name LIKE 'pr\_core\_%'"
 );
 
-/* ── 5. Remove manage_peptide_content capability from all roles ────────── */
+/* ── 5. Remove manage_peptide_content capability from all roles ───────── */
 
 $editable_roles = wp_roles()->roles;