feat(cpt): consolidate peptide CPT with PSA; drop pr_peptide (v0.2.0) (#1)

Consolidates the `peptide` CPT under PR Core ownership, dropping the `pr_peptide` slug-collision that was 404ing all 89 peptide detail pages.

- POST_TYPE: pr_peptide -> peptide
- TAX_CATEGORY: pr_peptide_category -> peptide_category
- TAX_FAMILY + pr_peptide_family taxonomy removed
- Defensive post_type_exists/taxonomy_exists guards on both registrations
- Args harmonized as superset of PSA + prior PR Core (adds thumbnail support)
- Activation hook + init:999 version-change flush handler
- Uninstall scoped to _pr_core_authored flag (PSA-authored posts survive)
- Plugin version 0.1.1 -> 0.2.0, CHANGELOG in same commit
- ARCHITECTURE.md + CONVENTIONS.md updated with CPT ownership rule

QA gate verdict: PASS (qa-reviews/peptide-repo-core/2026-04-22-874f93b.md)
Sibling release: peptiderepo/peptide-search-ai#15 (PSA v4.5.0)

Known follow-up: manage_peptide_content capability is not granted to any role as of v0.2.0. No current UI/theme reads or writes PR Core-defined meta keys, so no regression. Follow-up thread to decide role assignment.

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-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/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.
- * Dependencies: PR_Core_Migration_Runner.
+ *       Also detects version changes on subsequent init cycles and re-flushes
+ *       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

@@ -30,6 +30,12 @@ class PR_Core {
 		$cpt = new PR_Core_Peptide_CPT();
 		$cpt->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();

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

@@ -2,25 +2,29 @@
 declare(strict_types=1);
 
 /**
- * Registers the pr_peptide custom post type and associated taxonomies.
+ * Registers the peptide custom post type and associated taxonomy.
  *
  * What: Defines the peptide CPT with REST support, archive, and monograph meta fields.
  * 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. */
-	public const POST_TYPE = 'pr_peptide';
+	/** @var string Post type slug (owned by PR Core since v0.2.0; PSA previously registered this). */
+	public const POST_TYPE = 'peptide';
 
 	/** @var string Taxonomy: category (e.g., GLP-1 agonist). */
-	public const TAX_CATEGORY = 'pr_peptide_category';
-
-	/** @var string Taxonomy: family grouping. */
-	public const TAX_FAMILY = 'pr_peptide_family';
+	public const TAX_CATEGORY = 'peptide_category';
 
 	/** @var string Capability required for editing peptide data. */
 	public const CAPABILITY = 'manage_peptide_content';
@@ -129,13 +133,22 @@ 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 +163,77 @@ 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,
-			'rewrite'            => [ 'slug' => 'peptides', 'with_front' => false ],
+			'publicly_queryable' => true,
+			'show_ui'            => true,
+			'show_in_menu'       => true,
+			'show_in_nav_menus'  => true,
 			'show_in_rest'       => true,
 			'rest_base'          => 'peptides',
 			'rest_namespace'     => 'pr-core/v1',
-			'supports'           => [ 'title', 'editor', 'excerpt', 'revisions', 'custom-fields' ],
+			'menu_position'      => 25,
 			'menu_icon'          => 'dashicons-database',
 			'capability_type'    => 'post',
 			'map_meta_cap'       => true,
-			'show_in_menu'       => true,
-			'menu_position'      => 25,
+			'hierarchical'       => false,
+			'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 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.
+	 *
+	 * Side effects: registers taxonomy with WordPress.
 	 *
 	 * @return void
 	 */
 	public static function register_taxonomies(): void {
+		if ( taxonomy_exists( self::TAX_CATEGORY ) ) {
+			return;
+		}
+
 		register_taxonomy( self::TAX_CATEGORY, self::POST_TYPE, [
-			'labels'            => [
+			'labels'             => [
 				'name'          => __( 'Peptide Categories', 'peptide-repo-core' ),
 				'singular_name' => __( 'Peptide Category', 'peptide-repo-core' ),
 			],
-			'hierarchical'      => true,
-			'show_in_rest'      => true,
-			'show_admin_column' => true,
-			'rewrite'           => [ 'slug' => 'peptide-category' ],
-		] );
-
-		register_taxonomy( self::TAX_FAMILY, self::POST_TYPE, [
-			'labels'            => [
-				'name'          => __( 'Peptide Families', 'peptide-repo-core' ),
-				'singular_name' => __( 'Peptide Family', 'peptide-repo-core' ),
-			],
-			'hierarchical'      => false,
-			'show_in_rest'      => true,
-			'show_admin_column' => true,
-			'rewrite'           => [ 'slug' => 'peptide-family' ],
+			'public'             => true,
+			'publicly_queryable' => true,
+			'show_in_rest'       => true,
+			'show_ui'            => true,
+			'show_admin_column'  => true,
+			'hierarchical'       => true,
+			'rewrite'            => [ 'slug' => 'peptide-category', 'with_front' => false ],
 		] );
 	}
 
 	/**
-	 * Register post-meta fields with the REST API.
-	 *
-	 * Side effects: registers meta with WordPress.
+	 * Register post-meta fields. Auth gated on manage_peptide_content.
 	 *
 	 * @return void
 	 */

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/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.
  *